@article {pmid42786310,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Li, J and Guo, X and Xu, H and Wang, Y and Tang, H and Han, JJ},
title = {Multi-modality profiling identifies Neisseria flavescens as a central geroprotective oral commensal in humans.},
journal = {Nature aging},
volume = {6},
number = {10},
pages = {2202-2217},
pmid = {42786310},
issn = {2662-8465},
support = {32330017//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82361148130//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025YFA1805300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2024YFF0729200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2025YFC3409300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; L2604004//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; GZC20230084//China Postdoctoral Science Foundation/ ; },
mesh = {*Neisseria/physiology ; Humans ; *Aging/physiology ; Animals ; Mice ; Caenorhabditis elegans/physiology ; *Mouth/microbiology ; Multiomics ; Metagenome ; *Senotherapeutics ; Gastrointestinal Microbiome ; Biosynthetic Pathways ; Liver/metabolism ; Probiotics/administration & dosage ; Akkermansia/physiology ; Bifidobacterium/physiology ; Lactobacillaceae/physiology ; Random Allocation ; Male ; Mice, Inbred C57BL ; Tongue/microbiology ; },
abstract = {Aging is accompanied by progressive physiological decline, yet the microbiome determinants that modulate aging remain unclear. Here, we identify Neisseria flavescens (Nf) as an oral commensal associated with decelerated aging in humans. Using AURORA, a generative multi-modality framework, we developed multi-modality aging clocks, performed in silico screening for age-gap-reducing interventions and predicted Nf as a top hit. In silico perturbations linked increased Nf abundance to favorable physiological signatures, beneficial gut taxa and biosynthesis of beneficial metabolites. We isolated two Nf strains and validated their production of beneficial metabolites. Functional assays demonstrated that live Nf extended lifespan and healthspan in Caenorhabditis elegans. In aged mice, heat-killed Nf supplementation restored the serum metabolome, liver transcriptome and gut microbiome toward younger states. By establishing an AI-driven intervention discovery engine and identifying Nf as a geroprotective microorganism, these findings highlight the oral microbiome as an underestimated axis of systemic aging and a candidate for geroprotective interventions.},
}

*Neisseria/physiology
Humans
*Aging/physiology
Animals
Mice
Caenorhabditis elegans/physiology
*Mouth/microbiology
Multiomics
Metagenome
*Senotherapeutics
Gastrointestinal Microbiome
Biosynthetic Pathways
Liver/metabolism
Probiotics/administration & dosage
Akkermansia/physiology
Bifidobacterium/physiology
Lactobacillaceae/physiology
Random Allocation
Male
Mice, Inbred C57BL
Tongue/microbiology

@article {pmid42925771,
year = {2026},
author = {Pradeep, A and Mathew, AI and Koyyappurath, S and Vemula, PK and Bhat, SG and Narayanan, S},
title = {An exploratory study of gut microbiota and humoral immune responses following bacterial ghost administration in rats.},
journal = {Vaccine},
volume = {95},
number = {},
pages = {129284},
doi = {10.1016/j.vaccine.2026.129284},
pmid = {42925771},
issn = {1873-2518},
abstract = {The rise of multidrug-resistant pathogens necessitates innovative immunotherapeutic approaches. Bacterial ghosts (BGs) are non-viable empty cell envelopes retaining antigenic determinants, offer a safe and potent immunomodulatory alternative to live bacterial vaccines. This exploratory study examined the selected tolerability parameters, humoral immune responses, and gut microbiota profiles potential of Staphylococcus aureus-derived ghost cells (GCs) in Sprague Dawley rats. Animals received three doses at one-week intervals via oral and intramuscular (IM) administration at low (10[6] units/mL) and high (10[9] units/mL) doses over a 21-day period. Hemocompatibility, serum biochemistry, and histopathology of key organs provided preliminary insights into the tolerability of the formulation under the experimental conditions. Serum immunoglobulin profiling revealed increases in GC-specific IgG and IgA levels with oral administration, while IM delivery showed less systemic variations in antibody production. qRT-PCR analyses indicated a minimal but detectable pro-inflammatory cytokine expression, notably TNF-α, especially in high-dose IM groups. Gut microbiome analysis via 16S rRNA sequencing identified differences in microbial diversity indices and the relative abundance of selected bacterial taxa across experimental groups. Histological assessments of gut tissue indicated mild, non-pathological mucosal changes only at high oral doses. Overall, the findings provide preliminary observations on humoral immune responses, selected tolerability parameters, and gut microbiota profiles following GC administration. These preliminary findings encourage further investigation of BGs as engineerable platforms with potential applications in immunomodulation, mucosal vaccine development, and microbiome-targeted interventions.},
}

@article {pmid42926052,
year = {2026},
author = {Wang, W and Chu, W and Lan, S and He, Y and Chen, Y and Zhou, H and Wang, L and Yu, Y and Wang, Z and Tan, Z and Zhang, Y and Li, X},
title = {Stage-dependent nutrient assimilation, protein accumulation and microbial instability during fed-batch cultivation of Chlorella mutant strain in Chinese Baijiu brewing wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136122},
doi = {10.1016/j.biortech.2026.136122},
pmid = {42926052},
issn = {1873-2976},
abstract = {Chinese Baijiu brewing wastewater (CBBW) is a high-strength organic wastewater rich in recoverable nutrients, but its direct conversion into microalgal protein remains limited by unstable loading and microbial succession. This study established a photobioreactor using real CBBW and the heavy-ion-mutagenized Chlorella mutant SLJ-Q1 under fed-batch culture. During the early phase (Days 0-10), SLJ-Q1 achieved a specific growth rate of 0.069/d, with total nitrogen (TN) and chemical oxygen demand (COD) removal rates of 12.6 and 332.8 mg/(L·d). This phase featured enhanced bacterial network complexity and genetic potential for carbon-nitrogen co-metabolism and amino acid biosynthesis, promoting nutrient conversion into protein-rich biomass. The harvested biomass reached 1.85 g/L, containing 65.5% crude protein with an essential amino acid index (EAAI) of 0.94-0.99 and heavy metals below feed safety limits. However, the bacterial count (5.93 × 10[7] CFU/g) exceeded GB 13078-2017, indicating that post-harvest hygienic treatment is required. Prolonged feeding caused oxygen-limiting conditions, Clostridium enrichment, enhanced genetic potential for anaerobic nitrogen metabolism, nutrient accumulation, and photobioreactor (PBR) destabilization. These findings suggested the feasibility of producing microalgal protein from CBBW and highlight feed loading control, dissolved oxygen balance, and post-harvest hygienic treatment as key considerations for sustainable scale-up.},
}

@article {pmid42926093,
year = {2026},
author = {Li, X and Liu, H and Wu, J and Xi, C},
title = {Source Apportionment and Resistome Signatures of Community and Hospital Effluents in Urban Sewer Networks.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129378},
doi = {10.1016/j.envpol.2026.129378},
pmid = {42926093},
issn = {1873-6424},
abstract = {Antibiotic resistance surveillance has traditionally focused on clinical settings, potentially overlooking broader microbial reservoirs in the community. Wastewater-based epidemiology (WBE) provides a powerful tool for capturing these population-level signals. This study aimed to identify source-specific resistome characteristics and estimate the relative compositional contributions of hospital and residential wastewater to the downstream wastewater treatment plant (WWTP). By integrating droplet digital polymerase chain reaction (ddPCR) with metagenomic sequencing, spatiotemporal dynamics across an urban sewer network were characterized. Bacterial 16S rRNA gene concentrations did not differ significantly between hospital and residential wastewater. Under the specified flow scenarios, hospital wastewater represented a small fraction of the estimated total influent volume. Bayesian source tracking further indicated that residential sources collectively accounted for nearly 80% of the inferred source contribution to the influent antibiotic resistance genes (ARGs) profile and 70.9% of the influent microbial community composition, whereas hospital wastewater accounted for only 5.5% of the inferred resistome contribution. These findings show that hospital wastewater contained clinically important resistance genes (e.g., blaKPC-2), whereas the sampled residential references accounted for the largest combined inferred contribution to the influent microbiome and resistome. Together, these results highlight the importance of incorporating community surveillance through wastewater-based approaches within the One Health framework.},
}

@article {pmid42926479,
year = {2026},
author = {Norton, GJ and Dudek, AM and Gerner, RR and Guo, C and Castillo, V and Argueta, FA and Beebout, CJ and Kamyabi, G and Drushell, J and Walker, GT and Hsu, CY and Bessho, S and Nuccio, SP and Chu, H and Zengler, K and Nolan, EM and Raffatellu, M},
title = {Targeting catecholate siderophore systems enables precision depletion of gut enterobacteria during colitis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.02.756324},
pmid = {42926479},
issn = {2692-8205},
abstract = {Adherent-invasive Escherichia coli (AIEC) is frequently isolated from the dysbiotic gut microbiome in inflammatory bowel disease and is implicated in disease progression, highlighting its potential as a therapeutic target. Here we show that iron acquisition is essential for AIEC colonization of the inflamed gut. Mechanistically, four catecholate siderophore receptors act redundantly to support AIEC growth under iron-limited conditions and during colitis. Immunization of colitis-prone Il10 [-/-] mice against catecholate siderophores reduced intestinal AIEC colonization, particularly its association with the mucosa, while largely preserving overall gut microbiome composition. Longitudinal metagenomic profiling identified immunization-associated shifts in Akkermansiaceae and Lactobacillaceae , and experiments in gnotobiotic Il10 [-/-] mice demonstrated that Limosilactobacillus reuteri , a member of the Lactobacillaceae , limited AIEC colonization, whereas Akkermansiaceae exacerbated disease. Our findings establish catecholate siderophore-mediated iron acquisition as a therapeutic target in AIEC and provide proof-of-principle that virulence-targeted immunization can selectively antagonize a disease-associated bacterium while preserving the gut microbiota.},
}

@article {pmid42926633,
year = {2026},
author = {Oliver, A and Podell, S and Allen, EE},
title = {Conserved synteny reveals a saccharolytic lifestyle across Kiritimatiellia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.06.756941},
pmid = {42926633},
issn = {2692-8205},
abstract = {Kiritimatiellia are a class of Verrucomicrobiota whose few cultured representatives are known for hosting large repertoires of carbohydrate-active enzymes and sulfatases. Many families of this class are restricted to metagenome-assembled genomes not yet discussed in literature, leaving their genome organization undescribed. Here, we survey 898 Kiritimatiellia genomes using similarity-colocalization networks (SCoNes), a data structure that captures conserved synteny among homologous genes across genomes. Using this approach, we investigate four metabolic adaptations to a glycan-rich environment: complex polysaccharide degradation, nitrogen cycling, hydrogenase activity, and natural product biosynthesis. Rather than unrelated functions, these capacities envelop a single anaerobic and saccharolytic strategy where sulfated glycan hydrolysis fuels fermentation, hydrogenases balance redox, and excess carbon supports nitrogen fixation.},
}

@article {pmid42926716,
year = {2026},
author = {Jiang, AK and Arp, G and Kato, M and Brunner, T and Grant, MR and Clarke, AM and Sidebottom, AM and McMillin, M and Lehmann, CJ and Odenwald, MA and Wolfe, KS and Patel, BK and Odenike, O and Li, Y and Light, SH and Hall, B and Jiang, X},
title = {SpiE is a distinct gut microbial 4-cholesten-3-one 5β-reductase that acts with SpiR to convert cholesterol to coprostanol.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.06.757028},
pmid = {42926716},
issn = {2692-8205},
abstract = {Gut microbes convert cholesterol into coprostanol, a poorly absorbed sterol that is largely excreted in feces and is linked to lower serum cholesterol levels. However, the enzymes responsible for this process remain poorly characterized. The second step of the pathway, cholestenone reduction into coprostanone, has long been established, yet the enzyme(s) responsible were unknown. Here, we use comparative genomics to identify SpiE, a cholestenone (4-cholesten-3-one) reductase that is part of the steroid processing (spi) pathway with SpiR. We confirm that SpiE binds to and reduces both cholestenone and progesterone into 5β-reduced forms. SpiR and SpiE together convert cholesterol into coprostanol, indicating that both enzymes are sufficient for coprostanol formation. SpiE belongs to the short-chain dehydrogenase (SDR) family and represents an evolutionarily distinct lineage of SDR ene-reductases. Metagenomic analyses reveal that spiE relative abundance is strongly correlated with stool coprostanol (Spearman's ρ=0.81, p =5.99e-65). In longitudinal patient cohorts, antibiotic treatment coincided with loss of SpiE and coprostanol production. Post antibiotics, the emergence of distinct SpiE-encoding genera rescued coprostanol production in some individuals. Our findings provide the biochemical basis of the cholesterol to coprostanol pathway and lay the groundwork for future studies linking it to host physiology.},
}

@article {pmid42926794,
year = {2026},
author = {Faure, R and Nakshi, AH and Abrar, MH and Chikhi, R and Lemane, T and Taheri, M and Won, S and Wu, H and Koslicki, D and Medvedev, P},
title = {Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.07.757297},
pmid = {42926794},
issn = {2692-8205},
abstract = {Recent efforts have demonstrated that systematic analysis of the millions of metagenomes in the Sequence Read Archive (SRA) enables groundbreaking biological discoveries. However, SRA-scale comparison of whole metagenomes has remained elusive. Here, we introduce the most comprehensive resource to date for experiment-to-experiment analysis of all SRA metagenomes, comprising FracMinHash sketches (470GB), hypergen sketches (19GB), and an all-pairs Jaccard similarity matrix (90GB), which we release online at https://github.com/RolandFaure/SRA-metagenome-sketches-databases . These resources enable a wide range of analyses, which we demonstrate with several applications. First, we use the FracMinHash sketches to uncover temporal trends, finding that the amount of newly discovered microbial sequence continues to grow, rather than saturate or shrink. Second, we use the hypergen sketches, which enable nearest-neighbor search, to identify co-assembly candidates and thereby improve assembly quality. Third, we use the similarity matrix to analyze all SRA metagenomes, identifying duplicated submissions and over 50K candidates for metadata correction. Together, our resources unlock systematic analysis of metagenomic data at unprecedented scale.},
}

@article {pmid42926836,
year = {2026},
author = {Guo, J and Tran, HTT and Cai, Q and Hoang, MV and Tran, TV and Shu, XO and Nguyen, SM},
title = {Rural-urban differences in gut microbiome among Vietnamese women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.04.26364707},
pmid = {42926836},
abstract = {Gut microbiome plays an important role in human health. Urbanization has been suggested to alter the gut microbiome. We comprehensively evaluated differences in gut microbiome profiles of 76 urban and 81 rural female residents of Vietnam using shotgun metagenomic data. We evaluated rural-urban differences in gut microbial diversity, individual microbial taxa, and metabolic pathways. Rural residents had higher alpha and beta diversities in age-adjusted models (p<0.05). Additionally, significant rural-urban differences were observed for 35 microbial taxa in age-adjusted models (FDR<0.1). Rural residents had higher relative abundance of classes, orders, and families of FGB2982 and FGB38642 and strain SGB15332 of the species Faecalibacterium prausnitzii , whereas urban residents had higher relative abundances of species Bacteroides thetaiotaomicron, Coprobacter fastidiosus, Bilophila wadsworthia, Enterobacter cloacae, Enterobacter hormaechei, Klebsiella aerogenes , Dielma fastidiosa, and Holdemania massiliensis. Notably, these associations were attenuated after further adjustment for socioeconomic characteristics, lifestyle, dietary factors, and comorbidity (FDR>0.1). In the fully adjusted model, significant rural-urban differences were observed in the abundance of 17 microbial taxa, including Ruminococcus sp AF13 28 and Prevotella pectinovora, as well as in three metabolic pathways (FDR<0.1). This study suggests that urbanization-related factors may contribute to differences in the gut microbiome between urban and rural Vietnamese women.},
}

@article {pmid42926938,
year = {2026},
author = {Vatanen, T and Kreuze, K and Björkgren, L and Turkington, C and Nezam-Abadi, N and Seymour, S and Shkoporov, A and Hill, C and Friman, V and Knip, M},
title = {Maternal transmission and limited virulent phage replication shape early infant gut virome maturation.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-11232673/v1},
pmid = {42926938},
issn = {2693-5015},
abstract = {Early life gut microbiome dynamics are increasingly recognized as important determinants of microbiome maturation, yet the ecological dynamics of its associated bacteriophages remain poorly resolved. Here, we performed bulk and virus like particle (VLP)-enriched metagenomic sequencing and fecal metabolomic profiling of longitudinal fecal samples from 32 mother-infant dyads, incorporating an exogenous phage spike in to enable absolute quantification of viral loads. Our results show that early infant gut phageome is defined by a profound lack of virulent phage genome copies while temperate phages remain relatively stable, challenging previous assumptions. We further identified extensive maternal sharedness of mainly virulent phages predicted to infect Bacteroidaceae, which could explain recovery of virulent phage absolute abundances. Virulent phage concentrations were further associated with several fecal metabolites including primary bile acids. These findings revise the current model of infant phageome assembly highlighting the underappreciated role of virulent phages.},
}

@article {pmid42927839,
year = {2026},
author = {Li, X and Cai, Y and Yin, F and Chen, WS and Huang, S and Li, A and Zhou, T and Fernandes, TV and Dong, H},
title = {Staged waste-based lactic acid broth redistributes multi-gas emission windows during swine manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136127},
doi = {10.1016/j.biortech.2026.136127},
pmid = {42927839},
issn = {1873-2976},
abstract = {Composting recycles livestock manure, but temporally distinct ammonia, nitrous oxide and methane emissions can obscure trade-offs between nitrogen conservation and climate mitigation. We evaluated staged supplementation with waste-based lactic acid fermentation broth (LA) during 42-d forced-aeration rotary-drum composting of swine manure and maize straw, using three parallel reactors per treatment and equal-mass water addition (WA) as the control. LA showed a short initial heating/decomposition lag followed by thermophilic and carbon-transformation catch-up. Reactor-mean ammonia release during temperature-defined days 2-6 was 49.9% lower; the sampled peak shifted from day 3 to day 5 and was 17.3% lower. Later compensation limited the day-42 mean difference to 7.8%, indicating early-window attenuation and redistribution. Observed cumulative means of nitrous oxide and methane were 41.5% and 37.3% lower, respectively, producing a 38.5% lower direct non-CO2 greenhouse-gas mean. Lower early pH was consistent with a lower estimated free-ammonia fraction and temporary maintenance of an ammoniacal pool. Higher early nosZ/(nirK + nirS) and nosZ/nirK ratios indicated greater annotated terminal nitrous-oxide-reduction potential relative to nitrite-reduction potential. After day 21, methane approached zero despite a higher sampled methane peak under LA, as late carbon dioxide release weakened and mcrA, mcrB and mcrG abundances remained low. These DNA profiles represent functional potential rather than gene activity. Both germination index (GI) means exceeded the 70% criterion by day 7; late temperature, carbon dioxide, total organic carbon (TOC) and humic-like dissolved organic matter (DOM) supported progressive stabilization. Strong early ammonia attenuation is promising for recurrent-feed thermophilic semi-continuous systems with captured exhaust, based on batch results.},
}

@article {pmid42927840,
year = {2026},
author = {Yi, MM and Lv, PL and He, SY and Li, Q and Chen, R},
title = {How acetate alleviates ammonium inhibition and enhances methane-fed single-cell protein production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136124},
doi = {10.1016/j.biortech.2026.136124},
pmid = {42927840},
issn = {1873-2976},
abstract = {Anaerobic digestion produces methane-rich biogas and ammonium-rich digestate, but their joint conversion into single-cell protein (SCP) requires coordinated carbon and nitrogen utilisation. Here, a methane-fed mixed consortium was operated in a membrane biofilm reactor to determine how acetate regulates carbon-nitrogen coordination under ammonium stress. Ammonium addition impaired nitrogen conversion and protein enrichment without eliminating methylotrophs. Acetate restored these functions, increasing protein content to 61.25 % and the apparent N-based SCP yield from 0.34 to 1.46 g SCP/g N. Nitrogen balances showed greater incorporation of inorganic nitrogen into cellular organic nitrogen with acetate, consistent with the increased metagenomic potential for the glyoxylate shunt and ammonium assimilation. Excess acetate, however, promoted soluble microbial products and extracellular polymeric substances, lowering the apparent carbon-based SCP yield. These findings suggest that acetate improves nitrogen incorporation and protein production in a methane-fed mixed consortium while methane utilisation remains active. Controlled acetate retention in anaerobic digestate may therefore support the joint recovery of waste-derived carbon and nitrogen as microbial protein.},
}

@article {pmid42928761,
year = {2026},
author = {Liu, J and Wang, X and Xie, P and Dong, L and Bai, P and Liu, Y and Chen, G and Hao, D},
title = {Tropheryma whipplei Pneumonia with Myelofibrosis: A Rare Actinomycetia Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {636054},
pmid = {42928761},
issn = {1178-6973},
abstract = {Tropheryma whipplei (T. whipplei) is an uncommon pathogen that infects multiple sites, predominantly the gastrointestinal tract. However, pulmonary involvement is uncommon, and its clinical manifestations and imaging features lack specificity, making it prone to misdiagnosis. However, with the development of metagenomic next-generation sequencing (mNGS), clinicians have a potent tool at their disposal for detecting T. whipplei infections. We report a case of an elderly woman with a history Myelofibrosis who presented with a dry cough, fever, fatigue and difficulty breathing. Routine microbiological tests were negative; mNGS of bronchoalveolar lavage fluid (BALF) suggested T. whipplei infection. Following a definitive diagnosis, the patient was treated with a regimen of meropenem in combination with trimethoprim-sulfamethoxazole (TMP-SMX) for 16 days followed by 2 weeks of TMP-SMX maintenance, after which the patient improved and was discharged uneventfully.},
}

@article {pmid42928806,
year = {2026},
author = {Chaumeil, PA and Hugenholtz, P and Parks, DH},
title = {gTranslate: rapid and accurate translation table prediction for prokaryotic genomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21825},
pmid = {42928806},
issn = {2167-8359},
mesh = {*Computational Biology/methods ; *Genome, Bacterial ; *Protein Biosynthesis ; *Software ; Machine Learning ; },
abstract = {BACKGROUND: Bioinformatic tools often require the prediction of protein-coding genes to make inferences about prokaryotic genomes. Typically, the genetic code used for translating genes to proteins must be specified by the user based on the taxonomic classification of a genome assembly or, for some widely used tools, established using a heuristic rule based on gene coding densities. Manual specification is at best inconvenient, but more challenging is that many bioinformatic tools are applied before taxonomic classifications have been established making specifying the translation table impractical.

METHODS: Here we provide a computationally efficient tool, gTranslate, that uses an ensemble of five machine learning methods to accurately predict translation tables for prokaryotic genomes. The feature vector used by gTranslate takes advantage of differences in gene coding densities when predicting genes under different translation tables along with features that consider the number and ratio of UGA stop codon reassignments to tryptophan or glycine. gTranslate is freely available at https://github.com/cmc-aau/gTranslate and archived on Zenodo.

RESULTS: We demonstrate that gTranslate correctly predicts the translation table of prokaryotic genomes >99.99% of the time (i.e., <1 error per 10,000 genomes) and outperforms a more computationally expensive prediction method and a coding density heuristic used by popular bioinformatic tools. Using gTranslate, we identify a basal lineage of Ca. Stammera capleta that uses the standard bacterial genetic code instead of the UGA stop codon to tryptophan reassignment common to other members of this species. We also identify the first instances of UGA-to-tryptophan reassignment in the Patescibacteriota making this the first bacterial phylum with members capable of using translation tables 4, 11, and 25.},
}

*Computational Biology/methods
*Genome, Bacterial
*Protein Biosynthesis
*Software
Machine Learning

@article {pmid42929531,
year = {2026},
author = {Zhang, J and Fang, L and Ma, C and Hu, Z and Chen, C and Zhu, T and Ying, J and Zhu, W and Huang, G and Ni, J and Zhang, C and Yu, G},
title = {Gut Clostridium aminophilum as a protective microbe in never-smoker lung cancer: insights from metagenomics and machine learning.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0099426},
doi = {10.1128/spectrum.00994-26},
pmid = {42929531},
issn = {2165-0497},
abstract = {Lung cancer in never-smoking patients (LCINS) has gradually gained attention in recent years, and emerging evidence points to a potential role of the gut microbiota in LCINS by modulating host immunity and metabolism. In this study, metagenomics was performed on stool samples from 24 LCINS patients and 18 healthy individuals. LCINS patients exhibited reduced microbial richness in α-diversity compared with healthy controls, and differences in principal component distribution were observed. Pathway enrichment analyses revealed that LPS biosynthesis capacity was significantly increased, whereas the fatty acid biosynthesis pathway was significantly decreased in LCINS. A total of 317 differentially abundant species were identified, including 29 assigned to the module most strongly associated with LCINS based on weighted gene co-expression network (WGCNA). Then, 36 machine learning-based diagnostic models were constructed based on these 29 species, with the glmBoost + Ridge model showing the best performance for LCINS discrimination (AUC = 0.855). SHAP (SHapley Additive exPlanations) identified Clostridium aminophilum as a protective factor and the top contributor to model performance (SHAP value = 0.068), with a single-species AUC of 0.743. In vitro, the culture supernatant of Clostridium aminophilum markedly suppressed A549 cell proliferation and migration. In vivo, oral administration of Clostridium aminophilum (5 × 10[6] CFU) for 21 days significantly suppressed tumor growth in subcutaneous A549-derived xenograft models. These findings suggest a significant association between LCINS and the gut microbiota, characterized by a marked depletion of Clostridium aminophilum. Notably, metabolites derived from Clostridium aminophilum were shown to inhibit lung cancer progression.IMPORTANCELung cancer remains the leading cause of cancer incidence and mortality worldwide, and the proportion of lung cancer in patients who have never smoked (LCINS) has been steadily increasing. However, the potential role of the gut microbiota in this disease has not been fully explored. In this study, we characterized the gut microbial spectrum of LCINS patients using metagenomic sequencing and developed a lung cancer predictive model with translational potential. Importantly, we identified a beneficial bacterium, Clostridium aminophilum, which may be developed as a probiotic to support conventional lung cancer treatments. These findings offer promising avenues for early diagnosis, adjunctive therapy, and personalized management of gut microbiota in LCINS patients.},
}

@article {pmid42930067,
year = {2026},
author = {Liakopoulou, G and Koutsiaris, AG},
title = {Artificial Intelligence in Virus Detection: From Metagenomic Discovery to Clinical Decision Support and Population Surveillance.},
journal = {Biotech (Basel (Switzerland))},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biotech15040090},
pmid = {42930067},
issn = {2673-6284},
abstract = {Artificial intelligence (AI) is increasingly central to modern virus detection, particularly as metagenomic next-generation sequencing (mNGS) expands diagnostic and surveillance capabilities beyond targeted assays. This paper reviews how AI supports virus detection across three interconnected levels. The metagenomic layer forms the technical core of the review, while the clinical and population sections examine how sequence-level AI outputs are translated into patient-level and public-health decision support. At the metagenomic level, AI addresses key bottlenecks caused by fragmented assemblies and weak homology signals. Foundation-model approaches such as ViraLM leverage pretrained genome representations to improve viral contig discrimination under short-contig conditions, whereas LucaProt integrates sequence- and structure-informed learning to detect highly divergent RNA viruses via RdRP (RNA-dependent RNA polymerase)-focused discovery. At the clinical level, targeted molecular tests remain effective when the suspected pathogen is known, while mNGS provides a complementary, hypothesis-free approach that can broaden etiological investigation in complex infections when laboratories apply appropriate quality control and clinicians interpret results in context. At the population level, early warning systems combine heterogeneous data sources (epidemiological, open-source, digital, environmental, and wastewater signals) with AI methods to enhance outbreak detection and forecasting. Across all levels, robust contamination control, transparent reporting, external validation, and standardized interpretation criteria determine real-world value. Overall, hybrid pipelines that integrate molecular evidence, clinical metadata, and population-scale surveillance within governed, reproducible workflows are likely to provide the greatest impact.},
}

@article {pmid42925753,
year = {2026},
author = {Zhang, Q and Yang, Y and Hou, L and Ng, HY},
title = {Sequential quorum-sensing regulation mitigates the trade-off between methane production and biofouling in anaerobic membrane bioreactors.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127167},
doi = {10.1016/j.watres.2026.127167},
pmid = {42925753},
issn = {1879-2448},
abstract = {Anaerobic membrane bioreactors (AnMBRs) enable simultaneous wastewater treatment and methane recovery, but their long-term operation is constrained by the conflict between enhanced microbial activity and membrane biofouling. Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) regulates anaerobic metabolism, extracellular polymeric substance (EPS) production, and biofilm formation, making microbial signaling a potential means of balancing methane production and membrane fouling control. Here, we developed a sequential QS modulation strategy that couples metabolic activation with signal attenuation in AnMBRs. C10-HSL, a medium-chain AHL, was first introduced to activate LuxR-type QS signaling and strengthen methanogenic electron transfer, while a naringenin-β-cyclodextrin inclusion complex (NAR-β-CD) was subsequently applied to attenuate biofilm-associated QS responses with improved system stability. C10-HSL stimulation increased sludge electron-transfer activity by 19.95 % and cumulative methane production by 18.42 %, confirming the effectiveness of QS activation in intensifying anaerobic conversion. Subsequent NAR-β-CD addition reduced EPS accumulation and alleviated membrane fouling while maintaining methane recovery. Metagenomic profiling revealed distinct regulatory outcomes: C10-HSL enriched genes associated with secretion systems, redox mediator biosynthesis, and biofilm formation, whereas NAR-β-CD altered QS-associated signaling, transport, and metabolic functions, accompanied by reduced EPS production. These findings establish sequential QS modulation as a microbial signaling-oriented strategy to balance methanogenic intensification from biofouling development, offering a new route toward stable energy recovery in AnMBRs.},
}

@article {pmid42925759,
year = {2026},
author = {Yue, H and Guan, X and Shen, Y},
title = {Sewer-relevant aging of microplastics drives plastic-class-dependent N2O emissions from denitrifying sludge.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127194},
doi = {10.1016/j.watres.2026.127194},
pmid = {42925759},
issn = {1879-2448},
abstract = {Microplastics (MPs) accumulate in sewer systems and wastewater treatment plants (WWTPs), where they undergo aging processes distinct from photo-oxidation in surface waters. How such sewer-relevant aging impacts denitrification-associated nitrous oxide (N2O) emissions remains unknown. Here, we simulated sewer-relevant aging (sulfidation and mechanical abrasion) for non-biodegradable, compostable and biodegradable MPs (NMPs, CMPs, BMPs) and evaluated their effects on N2O emissions relative to pristine MPs, while linking MP-derived dissolved organic carbon (DOC) characteristics to microbial physiological and community responses. Aging increased DOC release from CMPs and BMPs by 30.0% and 115.8%, respectively, and generated plastic-dependent molecular signatures enriched in aromatic and sulfur-containing compounds. Rather than bioavailable carbon sources, aged MP-derived DOC could barely be consumed as the electron donor yet acted as a potent physiological disruptor. Correspondingly, aged CMPs and BMPs increased N2O emissions to 2.5- and 8.0-fold those of their pristine counterparts, with a stimulation order of BMPs > CMPs > NMPs under carbon-sufficient conditions (C/N = 4:1). Stronger N2O stimulation was associated with more severe membrane damage and greater impairment of electron supply. Metagenomic analysis further revealed enrichment of Paracoccus under stronger N2O stimulation, together with shifts in denitrification-related genomic potential. As a genus capable of degrading diverse plastic additives while harboring a complete denitrification pathway, Paracoccus could favor N2O accumulation under electron-limited conditions, where N2O reduction is disadvantaged relative to upstream denitrification steps. These findings showed that sewer-relevant aging reshaped MP effects on denitrification-associated N2O emissions in a plastic-dependent manner and challenged the presumed environmental benignity of compostable and biodegradable plastics, underscoring the need to incorporate MPs aging into risk assessment for WWTPs.},
}

@article {pmid42923188,
year = {2026},
author = {Wang, X and Li, J and Cheng, Y and Liu, Y and Li, H and Tan, H and Hu, Y and Zhao, M and Liu, J},
title = {Microbiota-assisted screening for colorectal neoplasia: advanced adenoma as the key translational endpoint-a narrative review.},
journal = {American journal of translational research},
volume = {18},
number = {9},
pages = {8227-8253},
pmid = {42923188},
issn = {1943-8141},
abstract = {Microbial differences between established colorectal cancer (CRC) and cancer-free controls are reproducible, but screening translation depends on detecting advanced adenoma and early CRC in asymptomatic populations. We examined the gut microbiota as an adjunct to fecal immunochemical testing (FIT), stool deoxyribonucleic acid (DNA) testing, and colonoscopy, with advanced adenoma as the prevention-relevant endpoint. This narrative review used a structured, purposive search of PubMed, Embase, Web of Science, Scopus, and the Cochrane Library through April 10, 2026, prioritizing human neoplasia cohorts, stage-specific biomarkers, multi-omics studies, FIT comparators, and reporting standards. Across studies, microbial signals were strongest for established CRC and weaker and less consistently reported for advanced adenoma. Quantitative evidence supports selected adjunctive approaches, including fecal Fusobacterium nucleatum and multitaxon panels combined with FIT, but external validation remains sparse. The 2025 pooled analysis of 3,741 metagenomes demonstrated reproducible CRC-related features across 18 cohorts but did not report advanced-adenoma-specific accuracy. Clinical utility cannot be inferred from sensitivity, specificity, or the area under the receiver operating characteristic curve alone: prevalence-dependent positive predictive value (PPV), negative predictive value (NPV), calibration, a prespecified action threshold, decision-curve net benefit, and colonoscopy burden are decisive. Translation therefore requires a locked assay and model tested prospectively before bowel preparation in a representative screening cohort, with advanced adenoma reported separately and performance compared directly with FIT or stool DNA testing. Microbiota-based markers currently merit evaluation as adjuncts, not replacements, within established screening pathways.},
}

@article {pmid42923191,
year = {2026},
author = {Li, Z and Wang, Y and Lai, L and Huang, Y and Li, L},
title = {A novel multiplex assay for species-level identification of non-tuberculous mycobacteria in culture-positive respiratory specimens based on capillary electrophoresis: development and clinical validation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1966137},
pmid = {42923191},
issn = {1664-302X},
abstract = {Nontuberculous mycobacterial pulmonary disease (NTM-PD) is rising globally, driven predominantly by Mycobacterium avium complex (MAC), yet treatment is highly species-dependent. We developed a Multiplex assay targeting four clinically important non-tuberculous mycobacteria (NTM) species-M. avium, M. intracellulare, M. abscessus, and M. fortuitum-and compared it with metagenomic next-generation sequencing (mNGS), using colony-based multigene Sanger sequencing as the reference method. Among 101 specimens, 63 (62.4%) yielded polymicrobial results, of which mixed-species detection of M. avium-M. intracellulare accounted for 46 (73.0%). The Multiplex assay and mNGS showed no statistically significant difference in overall accuracy in this cohort (82.2% vs. 81.2%; raw agreement 83.2%, P = 1.000). The Multiplex assay achieved 100.0% sensitivity for all four species, with specificity of 87.8% and 87.5% for M. avium and M. intracellulare, respectively, and >98% for M. abscessus and M. fortuitum; mNGS showed the converse pattern, with lower MAC sensitivity (88.5%, 92.2%) but higher MAC specificity (93.9%, 95.8%). Requiring only a single PCR reaction without sequencing or bioinformatic analysis, the Multiplex assay showed no statistically significant difference in diagnostic accuracy from mNGS in this culture-positive cohort, without requiring library preparation or sequencing, representing a promising candidate for further evaluation as a routine NTM species-identification tool.},
}

@article {pmid42923215,
year = {2026},
author = {Luo, Y and Wang, Y and Shi, Z and Li, Z and Pu, T and Wang, Y and Ni, M and He, X and Li, J and Li, C and Li, X and Yang, P},
title = {Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco-safflower rotation fields.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1983930},
pmid = {42923215},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere microorganisms contribute to soil phosphorus (P) transformation and plant P acquisition, but P-cycling microbial communities and functional associations across tobacco-safflower rotation fields remain poorly characterized.

METHODS: Twenty-one safflower rhizosphere soil samples were collected from seven tobacco-safflower rotation fields in Lijiang, China. Soil physicochemical properties were measured, and shotgun metagenomics was used to characterize P-cycling bacterial communities and genes associated with P solubilization, mineralization, regulation, and transport. Culturable phosphate-solubilizing bacteria were isolated, preliminarily assigned taxonomically using 16S rRNA gene sequences, and evaluated by plate and liquid-culture assays.

RESULTS: Soil properties and P-cycling bacterial communities showed pronounced between-field variation. Metagenomic screening identified 6,019 non-redundant gene sequences assigned to 38 predefined P-cycling KO terms, with 460 genus-level bacterial taxa. Among 124 taxa shared across all fields, Nocardioides, Arthrobacter, Streptomyces, Gaiella, and Marmoricola were major dominant genera. PCoA and PERMANOVA showed significant field differences at the phylum (R [2] = 0.983, p = 0.001) and genus (R [2] = 0.964, p = 0.001) levels. Soil pH was associated with all four P-cycling functional modules. Exploratory random-forest analysis identified Sphingomonas, Streptomyces, Nocardioides, and Arthrobacter as candidate indicator taxa associated with variation in soil available P. Eighty-six culturable phosphate-solubilizing isolates representing 45 putative species-level taxa were obtained, with Streptomyces the most abundant genus (22.1%). Streptomyces isolates had solubilization index values of 1.10-1.89. The isolate with the highest SI, Streptomyces sp. LG-4, provisionally affiliated with S. endophyticus, reached a maximum net phosphate solubilization of 354.60 ± 7.22 mg L[-1] on day 3.

CONCLUSION: Soil physicochemical heterogeneity, particularly pH, was associated with between-field differences in P-cycling microbial communities and metagenomically inferred functional potential. Because no non-rotation or monoculture controls were included, these patterns should be interpreted as field-associated variation rather than effects of the rotation system itself. Both metagenomic and culture-dependent analyses highlighted Streptomyces as a candidate group of interest, while Streptomyces sp. LG-4 showed phosphate-solubilizing capacity under laboratory conditions and requires further taxonomic and functional validation.},
}

@article {pmid42923306,
year = {2026},
author = {Gao, X and Dong, Q and Shin, AS},
title = {Associations of colonic transit with the gut microbiota and short-chain fatty acids in health and irritable bowel syndrome.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1953842},
pmid = {42923306},
issn = {2296-861X},
abstract = {Gut bacteria are known to influence short-chain fatty acid (SCFA) levels through direct metabolic activity. Colonic transit also affects substrate contact time, fermentation duration, and SCFA absorption. But it is unclear whether some bacteria influence SCFA levels indirectly, by altering transit, rather than only directly, and whether this differs across health and irritable bowel syndrome (IBS) subtypes. Using data from 56 participants [17 healthy volunteers (HV), 15 IBS-C, 24 IBS-D] with concurrent stool metagenomes, stool SCFA, and segmental colonic transit measurements, we applied mediation analysis to test whether each bacterial taxon's association with SCFA levels may be transit-mediated statistically. Three taxa showed a potential transit-mediated association with at least one SCFA: Faecalibacterium prausnitzii in HV, Bacteroides thetaiotaomicron in IBS-C, and Phascolarctobacterium succinatutens in IBS-D. For F. prausnitzii, the transit-mediated pathway was the only detectable association with SCFA. The remaining two taxa, B. thetaiotaomicron and P. succinatutens, additionally showed a direct, transit-independent effect alongside the transit-mediated one. Separately, an analysis of direct, non-mediated effects identified 15 additional taxa (5 in HV, 2 in IBS-C, and 8 in IBS-D) whose associations with SCFA levels were not explained by colonic transit. Together, these findings suggest that colonic transit may potentially mediate specific associations between gut bacteria and SCFA levels, in addition to the direct metabolic effects of the bacteria. However, because the present study is cross-sectional, these findings should be interpreted as statistical associations rather than established biological or directional relationships. In addition, this was an exploratory post-hoc analysis of a single relatively small cohort, and independent validation will be required before the biological or clinical significance of these findings can be established.},
}

@article {pmid42923376,
year = {2026},
author = {Bai, H and Qiu, G and Shi, J and Xue, Y and Dai, W and Liu, Q and Zhou, X and He, K},
title = {Metagenomic and metabolomic analysis of the early gut microbiota development in Nipponia nippon.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1909232},
pmid = {42923376},
issn = {1664-302X},
abstract = {INTRODUCTION: The crested ibis (Nipponia nippon) is an endangered bird whose early gut microbiota development remains poorly understood. To address this gap, this study integrated metagenomics and metabolomics to investigate the dynamic succession of gut microbiota and metabolism in naturally hatched chicks during early development.

METHODS: Fecal samples were collected from naturally hatched crested ibis chicks aged 3 to 33 days and divided into groups Z3, Z8, Z13, Z18, Z23, Z28, and Z33. Integrated metagenomics and metabolomics were used to assess microbial gene richness, alpha and beta diversity, taxonomic composition, functional profiles, differentially expressed metabolites, pathway enrichment, and microbe-metabolite correlations.

RESULTS: Gut microbial gene richness and alpha diversity increased from Z3 to Z13, then fluctuated and stabilized, with Z13-Z18 representing a critical colonization window. Beta diversity analysis revealed progressive structural remodeling with age. At the phylum level, Pseudomonadota dominated early stages, while Bacillota increased over time. At the genus level, Plesiomonas, Clostridium, and Escherichia were prevalent; Enterobacter and Ligilactobacillus decreased by Z33, whereas Campylobacter, Cetobacterium and Proteus increased. Functional profiling indicated that Z3 exhibited high metabolic activity, including carbohydrate, amino acid, and energy metabolism, while Z33 showed reduced but more specialized functions. Metabolomics identified numerous differentially expressed metabolites across age groups, with pathway enrichment in cofactor biosynthesis, nucleotide metabolism, and amino acid metabolism. Correlation analysis revealed opposite metabolic associations: Corynebacterium was positively correlated with most metabolites, whereas Enterobacter, Citrobacter, and Klebsiella showed negative correlations.

DISCUSSION: These findings reveal dynamic succession of gut microbiota and metabolism during early development in crested ibises. The identification of a critical colonization window and age-related microbial and metabolic shifts provides fundamental insights for improving captive breeding and conservation of this endangered species.},
}

@article {pmid42923920,
year = {2026},
author = {Aji, N and Balati, T and Yang, Z and Jia, B},
title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid unravels brucellosis in a patient with chronic lung disease and venous thrombosis: A case report.},
journal = {IDCases},
volume = {46},
number = {},
pages = {e02786},
pmid = {42923920},
issn = {2214-2509},
abstract = {BACKGROUND: Brucellosis is a re-emerging zoonosis in Xinjiang, China. Pulmonary involvement and thrombotic complications are rare but can be life-threatening. In patients with idiopathic pulmonary fibrosis (IPF), unexplained respiratory worsening poses a diagnostic dilemma: is it an acute exacerbation of IPF, community-acquired pneumonia, or a zoonotic infection? We report a case of chronic brucellosis in an IPF patient who developed lower extremity venous thrombosis, diagnosed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), thereby resolving the clinical dilemma.

METHODS: A 57-year-old male farmer with IPF presented with progressive dyspnea and hypoxemia (SpO₂ 77% on room air). Serum Brucella agglutination test (SAT) and mNGS of BALF were performed.

RESULTS: SAT was positive at 1:800. mNGS of BALF detected 191 reads of Brucella spp. Lower extremity ultrasound revealed left calf muscular venous thrombosis. He was treated with doxycycline, rifampicin, and rivaroxaban. At one-month follow-up, his dyspnea had improved, and no recurrent thrombosis occurred.

CONCLUSION: In endemic areas, brucellosis should be considered in IPF patients with unexplained respiratory worsening, even without typical fever. mNGS of BALF is a valuable diagnostic tool when blood cultures are negative. Clinicians should also be aware that severe infection and hypoxemia are risk factors for venous thrombosis.},
}

@article {pmid42924103,
year = {2026},
author = {Xia, S and Yu, C and Cao, L and Bi, H and Lee, JK and Kalia, VC and Gong, C},
title = {Identification and Characterization of a Previously Uncharacterized Metagenome-Derived Chitinase and Its Application in N‑Acetyl‑d‑Glucosamine Production from Crayfish Shell Waste.},
journal = {ACS omega},
volume = {11},
number = {41},
pages = {63866-63876},
pmid = {42924103},
issn = {2470-1343},
abstract = {The generation of agricultural and food-processing byproducts has increased rapidly, highlighting the importance of their high-value utilization. In this study, a putative chitinase gene was identified from a metagenome-assembled genome. The enzyme plays a key role in chitin hydrolysis and was heterologously expressed in Escherichia coli as a recombinant protein with a molecular weight of approximately 39.2 kDa. The chitinase exhibited optimal activity toward colloidal chitin at pH 6.0 and 40 °C. Enzyme activity was significantly enhanced by Mn[2+], Mg[2+], and Sr[2+], remained largely unaffected by Ca[2+], and was strongly inhibited by Co[2+] and Fe[3+], while Zn[2+] and Cu[2+] completely abolished activity. Site-directed mutagenesis confirmed the conserved catalytic motif G-DG-D-D-E. Furthermore, the enzyme was applied to the direct hydrolysis of crayfish shell waste without conventional acid-alkali pretreatment, resulting in the formation of N-acetyl-d-glucosamine at a concentration of 3.26 mg/g. This approach eliminates the requirement for conventional acid-alkali pretreatment and enables the efficient valorization of crustacean shell waste. The developed enzymatic strategy provides a sustainable route for producing functional amino sugars with potential applications in food and related industries.},
}

@article {pmid42925049,
year = {2026},
author = {Creencia, AR and Arguelles, EDLR and Tan Gana, NH and Capanzana, RMAD and Martinez, JP and Lanceras, JC and Salaan, CAM and Del Castillo, RAM and Cadao, DFB},
title = {Bacterial community profiles of soils from the Mount Makiling Forest Reserve, Philippines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0093626},
doi = {10.1128/mra.00936-26},
pmid = {42925049},
issn = {2576-098X},
abstract = {The Mount Makiling Forest Reserve harbors diverse microorganisms with potential biotechnological applications, yet bacterial taxonomic profiling across its watersheds remains limited. Amplicon metagenome sequencing targeting the 16S rRNA gene revealed Proteobacteria and Acidobacteriota as dominant phyla, with Actinobacteriota, Verrucomicrobiota, Chloroflexi, Myxococcota, Methylomirabilota, Bacteroidota, Nitrospirota, and Planctomycetota present at varying abundances.},
}

@article {pmid42925311,
year = {2026},
author = {Abad-Recio, IL and Garate, L and Filker, S and Rubel, V and Stoeck, T and Logares, R and Lanzén, A},
title = {Modeling association networks from metagenome time series - a proof-of-concept from two contrasting estuaries.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag117},
pmid = {42925311},
issn = {1574-6941},
abstract = {Understanding microbial responses to environmental gradients is important for ecosystem assessment in estuarine environments. Here, we integrated time-series samples and shotgun metagenomics with association network inference, to examine patterns of taxonomic and functional co-variation. We collected and sequenced eDNA from two sediment time series from neighbouring but environmentally contrasting Basque estuaries, and compared the resulting taxonomic and functional association networks, based on Metagenome Assembled Genomes (MAGs) and KEGG Orthologous Groups (KOs), respectively. Networks inferred using 16S rRNA gene metabarcoding data were also included in this comparison. Several topology-based network properties differed strongly between the two sites, although differences were not always consistent when comparing the networks based on MAGs, KOs and metabarcoding. KO-based networks revealed distinct sets of associated Ortholog groups between sites, consistent with known environmental differences. Contrary to our expectations, metabolically related genes rarely formed complete pathway modules in gene networks, likely due to functional redundancy, gene copy number variation, synchronized pathway dynamics, or algorithmic constraints of correlation-based inference. Overall, the results illustrate both the potential and interpretative limitations of metagenome-based time association networks for functional ecosystem assessment, and support their use as hypothesis-generating tools that require further validation across a larger range of sites following environmental gradients.},
}

@article {pmid42925342,
year = {2026},
author = {Hercouët, K and Tardy, F and Marois-Créhan, C},
title = {The Palatine Tonsil Bacterial Microbiota in Pigs: Diverse, Underexplored, Yet Functionally Relevant.},
journal = {Current microbiology},
volume = {83},
number = {12},
pages = {},
pmid = {42925342},
issn = {1432-0991},
mesh = {Animals ; *Palatine Tonsil/microbiology ; *Microbiota ; Swine/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Swine Diseases/microbiology ; Metagenomics ; },
abstract = {The palatine tonsils play a pivotal role in porcine upper respiratory tract immunity by acting as an interface between the host and the external environment. As such, the tonsillar microbiota represents a critical yet insufficiently characterized microbial ecosystem. This review provides an overview of current knowledge on the porcine tonsillar microbiota, beginning with a description of sampling strategies and laboratory approaches, including metabarcoding, shotgun metagenomics, and culturomics. The development of the tonsillar microbiota over time and the main environmental, host-related, and management factors shaping its composition are examined. Particular emphasis is placed on the core bacterial communities commonly identified in the palatine tonsils, which are largely dominated by members of the Pasteurellaceae, Streptococcaceae, and Moraxellaceae families. The review further discusses how infectious and non-infectious diseases can disrupt tonsillar microbial homeostasis, as well as the effects of antimicrobial treatments, vaccination, and other prophylactic interventions on microbial structure and function. Finally, methodological biases inherent to current studies are highlighted, key knowledge gaps are identified, and future research directions are proposed to advance metagenomic investigations and better elucidate the role of the tonsillar microbiota in swine health and disease.},
}

Animals
*Palatine Tonsil/microbiology
*Microbiota
Swine/microbiology
*Bacteria/classification/genetics/isolation & purification
Swine Diseases/microbiology
Metagenomics

@article {pmid42925575,
year = {2026},
author = {Yasen, G and Ma, L and Yan, P and Xie, R and Zhang, T and Li, T and Muhetaier, M and Meng, W and Fu, S},
title = {Multi-layer analysis of gut metagenomic functional potential in major depressive disorder.},
journal = {Psychoneuroendocrinology},
volume = {195},
number = {},
pages = {108061},
doi = {10.1016/j.psyneuen.2026.108061},
pmid = {42925575},
issn = {1873-3360},
abstract = {BACKGROUND: Major depressive disorder (MDD) is associated with gut microbiota dysbiosis, but previous studies have mostly focused on species composition and are subject to confounding factors such as age and diet. Robust differences at the functional pathway level remain unclear.

METHODS: We included 98 indigenous residents of Xinjiang, China, whose families had resided there for three or more generations (49 MDD patients and 49 healthy controls) and performed shotgun metagenomic sequencing. Functional profiles were annotated with HUMAnN3 across seven levels: GBM, GMM, KO, EC, Module, Pathway, and PathAbundance. Features were transformed using the centered log-ratio (CLR) method. After controlling for 10 covariates (age, sex, BMI, bowel movement frequency, diet, gastrointestinal symptoms, years of smoking, alcohol consumption, physical activity, and sleep), OLS regression was performed with Benjamini-Hochberg FDR correction (q < 0.05). Complementary analysis was conducted using MaAsLin2, together with age caliper matching (52 participants), recurrent/first-episode subgroup analyses, and sensitivity analyses for treatment history. Overall functional profiles were evaluated by PERMANOVA based on Aitchison distance.

RESULTS: After covariate adjustment, overall functional profiles did not differ significantly between groups (PERMANOVA R²=1.9%, p = 0.071; PERMDISP p = 0.98). After FDR correction, 33 significant features were detected across five levels: EC, Pathway, Module, GMM, and PathAbundance (no significant signals at the GBM or KO levels). Key biologically meaningful signals included: propionate CoA-transferase (EC 2.8.3.1, β=-1.42, q = 0.022)↓, teichoic acid biosynthesis (map00552, β=-0.34, q = 0.045)↓, vancomycin resistance module (M00651, β=-1.28, q = 0.014)↓, galacturonate degradation II (MF0023, β=+1.82, q = 0.048)↑, and heme b biosynthesis I (PathAbundance, β=+0.93, q = 0.033)↑. MaAsLin2 effect sizes were correlated with the main OLS results at the Pathway level (R²=0.84) with consistent direction. GRSA independently confirmed downregulation of the phosphotransferase system (map02060, padj<0.001) and teichoic acid biosynthesis. The propionate CoA-transferase and teichoic acid biosynthesis signals were directionally consistent in the main model and recurrent subgroup, but did not survive correction in the matched subset; the first-episode subgroup (n = 11) was underpowered and its results are reported as exploratory.

CONCLUSIONS: Gut microbiota functional potential in MDD patients shows a mild but directionally consistent shift after controlling for confounders, involving short-chain fatty acid production, Gram-positive bacterial cell wall metabolism, and cofactor metabolism. This study measures functional potential and requires validation by metabolomics.},
}

@article {pmid42916994,
year = {2026},
author = {Cao, M and Wang, F and Wang, F and Huang, H and Ma, S and Li, J and Xiao, N and Xie, R and Sun, K},
title = {Divergent Shifts in Sediment Dissolved Organic Matter Stability and Microbial Carbon Metabolic Potential Induced by Biodegradable and Conventional Microplastics.},
journal = {Environmental science & technology},
volume = {60},
number = {39},
pages = {27867-27878},
doi = {10.1021/acs.est.6c10516},
pmid = {42916994},
issn = {1520-5851},
support = {310432104//Fundamental Research Funds for the Central Universities/ ; 42125703//National Science Fund for Distinguished Young Scholars/ ; 41822706//National Natural Science Foundation of China (NSFC)/ ; 42277371//National Natural Science Foundation of China (NSFC)/ ; T2421005//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Microplastics ; *Geologic Sediments/chemistry ; *Dissolved Organic Matter ; Carbon/metabolism ; Biodegradation, Environmental ; Polyesters ; },
abstract = {Biodegradable polymers are promoted as alternatives to conventional plastics, but their effects on sediment dissolved organic matter (DOM) and microbial communities remain unclear. Here, we estimated impacts of two nonbiodegradable (low-density polyethylene (LDPE) and poly(ethylene terephthalate) (PET)) and two biodegradable (polylactide (PLA) and poly(butylene succinate) (PBS)) polymers on DOM composition and microbial functional profiles using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing. The tested nonbiodegradable polymers shifted DOM toward recalcitrance. In contrast, biodegradable polymers exhibited divergent trajectories: PLA shifted from labile at day 30 to recalcitrant by day 60, whereas PBS showed the opposite trend toward instability. Microbial communities shifted from high-abundance Deltaproteobacteria (∼12%) at day 30 to Alphaproteobacteria (∼16%) and Actinomycetia (∼15%) at day 60. Glycolysis genes were less abundant under LDPE and PET, while fatty acid β-oxidation genes were enriched under LDPE, PET, and PLA. Spearman correlation and Mantel tests revealed that MP-driven DOM changes were associated with microbial community restructuring and bacterial diversity. This study highlights that biodegradable polymers cannot be assumed to have negligible sediment ecological impacts simply because of their degradable classification.},
}

*Microplastics
*Geologic Sediments/chemistry
*Dissolved Organic Matter
Carbon/metabolism
Biodegradation, Environmental
Polyesters

@article {pmid42917022,
year = {2026},
author = {Xiong, Y and Zheng, J and Ni, B and Wang, P and Wu, M and Kang, S and Li, S and Chen, Q and Zhu, D and Pan, B},
title = {Beyond the Dominant Geological Metal(loid): Co-Occurring Metal(loid)s Are Linked to Microbial Assembly and Resistomes in Mercury-Enriched Soils.},
journal = {Environmental science & technology},
volume = {60},
number = {39},
pages = {27660-27673},
doi = {10.1021/acs.est.6c13010},
pmid = {42917022},
issn = {1520-5851},
support = {2025J08123//Natural Science Foundation of Fujian Province/ ; 2023YFC3709100//National Basic Research Program of China (973 Program)/ ; 42130711//National Natural Science Foundation of China (NSFC)/ ; 42307027//National Natural Science Foundation of China (NSFC)/ ; 42477245//National Natural Science Foundation of China (NSFC)/ ; 42507556//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Mercury ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants ; Bacteria ; },
abstract = {High geological background regions are naturally enriched with multiple, typically low bioavailability metal(loid)s. Superimposed mining, smelting, and agricultural inputs create complex yet poorly studied environments. Using metagenomics, we profiled bacterial community assembly and life history strategies in a mercury (Hg)-enriched geological area with elevated co-occurring metal(loid)s. Bacterial composition, structure, and community assembly, as well as the abundances of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs), were independent of Hg concentration. Instead, cadmium (Cd), ammonium nitrogen (NH4+-N), soil organic matter (SOM), and available potassium (AK) were significantly associated with ARG/MRG variation (p < 0.05). Moreover, elevated Cd intensified heterogeneous selection (HeS) while suppressing homogeneous selection (HoS) (p < 0.05). This shift also led communities enriched in "nutrient recycling" traits adopted a resource acquisition strategy together with competitor traits (MRGs and ARGs), and nitrogen metabolism. These traits likely reflect a strategy prioritizing resource use efficiency and nutrient competitiveness. Moreover, elevated Cd exacerbated the codissemination risks of resistance genes and pathogenicity (p < 0.001). Thus, Cd was more strongly associated than Hg with bacterial community and resistome variation in Hg-enriched geological soils, underscoring the need to consider co-occurring metal(loid)s when assessing ecological responses in high-background regions.},
}

Mercury
Soil/chemistry
Soil Microbiology
Soil Pollutants
Bacteria

@article {pmid42918121,
year = {2026},
author = {Musta, K and Ojanen, MJT and Stensland, M and Kankaanranta, J and Lehtimäki, T and Karhunen, PJ and Nyman, TA and Hytönen, VP},
title = {Toward Optimized Proteomics Analysis to Detect Bacterial and Host Proteins in Calcified Coronary Artery Plaques.},
journal = {Journal of proteome research},
volume = {25},
number = {10},
pages = {5611-5623},
pmid = {42918121},
issn = {1535-3907},
support = {NA//Yrj? Jahnssonin S??ti?/ ; 755320//H2020 Health/ ; 848146//H2020 Health/ ; 201668//FP7 Health/ ; 322098//Research Council of Finland/ ; 331946//Research Council of Finland/ ; 356405//Research Council of Finland/ ; NA//Jane ja Aatos Erkon S??ti?/ ; NA//Juho Vainion S??ti?/ ; NA//Tampereen Teknillinen Yliopisto/ ; NA//Pirkanmaan Rahasto/ ; NA//Syd?ntutkimuss??ti?/ ; NA//Sigrid Jus?liuksen S??ti?/ ; NA//Tampereen Tuberkuloosis??ti?/ ; NA//Tays/ ; NA//Suomen kliinisen kemian yhdistys/ ; },
mesh = {Humans ; *Proteomics/methods ; *Bacterial Proteins/isolation & purification/analysis ; *Plaque, Atherosclerotic/microbiology/metabolism/pathology ; *Coronary Vessels/pathology/microbiology ; *Proteome/isolation & purification ; *Coronary Artery Disease/microbiology/metabolism/pathology ; },
abstract = {Coronary calcification is the final stage in coronary heart disease, associated with significantly increased morbidity and mortality. The molecular pathology of calcification and especially events triggering calcification are poorly understood. Metagenomic and molecular microbial techniques have identified the presence of oral biofilm-producing and dental calculus-forming bacteria in atherosclerotic plaques, suggesting that they may be involved in calcification. To enable studying this at the proteome level, we compared four different protein extraction methods to find a robust and reliable method for the identification and quantification of human and bacterial proteins from 10 calcified arterial plaques. We identified 3 913 human proteins and 24 bacterial proteins. These findings provide further support for the presence of bacterial proteins in calcified areas of coronary artery plaques, with Fusobacteria being the most abundant bacterial protein source. Comparisons of the extraction methods showed that the urea-based extraction method was most optimal due to its simplicity and reproducible identification of a high number of proteins, which makes it suitable for further large-scale analysis of coronary artery plaque samples.},
}

Humans
*Proteomics/methods
*Bacterial Proteins/isolation & purification/analysis
*Plaque, Atherosclerotic/microbiology/metabolism/pathology
*Coronary Vessels/pathology/microbiology
*Proteome/isolation & purification
*Coronary Artery Disease/microbiology/metabolism/pathology

@article {pmid42918447,
year = {2026},
author = {Ortega-Yago, A and Rubio, P and Ulldemolins, P and Baeza-Oliete, J and Bas, P and Bas, T},
title = {[Translated article] What's new in spinal instrumentation-related infections.},
journal = {Revista espanola de cirugia ortopedica y traumatologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.recot.2026.10.016},
pmid = {42918447},
issn = {1988-8856},
abstract = {Infections associated with spinal instrumentation represent one of the most complex complications in spine surgery and frequently involve biofilm-forming pathogens that compromise the effectiveness of antimicrobial therapies. Diagnosis - particularly in chronic cases - requires the use of advanced microbiological techniques, such as implant sonication, next-generation metagenomic sequencing, and prolonged culture incubation. Therapeutic strategies depend on the chronicity of the infection and the stability of the implant, ranging from surgical debridement with retention of osteosynthesis material to staged delayed re-instrumentation. Empirical antibiotic therapy should be initiated promptly and subsequently adjusted according to microbiological results. Prevention remains a fundamental pillar and includes strict perioperative optimization. Favorable outcomes rely on early detection, a multidisciplinary team approach, and individualized surgical and antimicrobial management based on accurate clinical and radiological assessment.},
}

@article {pmid42918601,
year = {2026},
author = {Tian, H and Liu, J and Zhang, Y},
title = {Metagenomic Insights into Microplastic Micro-interfaces: Transforming Pollutants and Spreading Resistance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129408},
doi = {10.1016/j.envpol.2026.129408},
pmid = {42918601},
issn = {1873-6424},
abstract = {Microplastic micro-interfaces (MPMI) in wastewater treatment plants (WWTPs) serve as critical hubs for microbial colonization, pollutant transformation, and antibiotic resistance gene (ARG) dissemination. In this study, a large-scale genome-resolved metagenomic approach was employed to reconstruct 463 high-quality metagenome-assembled genomes (MAGs) from biofilms established on polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) within a municipal WWTP. Taxonomic profiling revealed that MPMI selectively enriched strict anaerobes and uncultured taxa, driving a profound ecological shift from the surrounding water and indicating the formation of localized hypoxic micro-niches. Functionally, the MPMI microbiome constructed a highly integrated metabolic network. Key dominant lineages were found to synergistically couple aromatic hydrocarbon degradation (via the shikimate pathway and β-oxidation) with complex carbon, nitrogen, and sulfur cycling, while deploying energy-efficient nucleotide salvage strategies to ensure biofilm stabilization under nutrient stress. Crucially, horizontal gene transfer (HGT) emerged as a fundamental mechanism for functional diversification, facilitating the active cross-genomic exchange of key adaptive traits associated with pollutant metabolism and biofilm regulation. Furthermore, MPMI harbored a highly diverse resistome comprising 36 ARG categories and 289 subtypes, highlighted by the critical genomic co-localization of mobile elements and clinical resistance markers (e.g., mcr-5.1, mupA) in core colonizers. Ultimately, these genomic insights elucidate the MPMI as a profound ecological hotspot driving the concurrent adaptation of metabolic networks and the resistome, thereby exacerbating the risks of ARG dissemination in aquatic environments.},
}

@article {pmid42918750,
year = {2026},
author = {Xiao, L and Liu, J and Tanentzap, AJ and Duarte, CM and Fu, C and Zhou, L and Dang, R and Zhou, M and Luo, M and Zhang, P and Yu, J and Xu, Y and Rosentreter, J and Spencer, RGM and Lichtfouse, E and Luo, Y and Han, G},
title = {Resilience of blue carbon microbiomes in response to ecological and anthropogenic filtering.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918750},
issn = {2041-1723},
support = {U2106209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42077025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277236//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991330//National Natural Science Foundation of China (National Science Foundation of China)/ ; U2106209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; },
mesh = {Phylogeny ; *Carbon/metabolism ; *Microbiota/genetics ; *Ecosystem ; Metagenome ; *Anthropogenic Effects ; Bacteria/genetics/classification/metabolism ; Carbon Cycle ; },
abstract = {Global change is threatening the microbial consortia that sustain the services and functions of blue carbon ecosystems (BCEs), but little is known about how the composition and functioning of these consortia will respond to ecological and anthropogenic stressors. Here, we construct a continental-scale microbial genome catalog from 116 representative habitats, including mangrove forests, saltmarshes, and seagrass meadows, and recover 1954 non-redundant metagenome-assembled genomes (MAGs). We find that BCE microbiomes are taxonomically distinct from terrestrial, marine, and marginal sea ecosystems, with ecosystem type and spatial distribution further differentiating community composition. Environmental filtering constrains taxonomic composition, yet functional composition is largely invariant to taxonomic turnover. Specialist KEGG orthologues underpin over 90% of metabolic functions conserved across all BCEs. Notably, for carbon fixation, phylogenetically divergent functional lineages provide functional redundancy that can mitigate the effects of species replacement. Collectively, our study quantifies the vulnerability of BCEs to future species loss while providing a scientific basis for confidence that blue carbon ecosystems, supported by phylogenetic redundancy, may sustain functional stability despite environmental change.},
}

Phylogeny
*Carbon/metabolism
*Microbiota/genetics
*Ecosystem
Metagenome
*Anthropogenic Effects
Bacteria/genetics/classification/metabolism
Carbon Cycle

@article {pmid42918757,
year = {2026},
author = {Song, K and Wang, Y and Li, L and Deng, M and Wu, F and Xia, Z and Zhao, X and Greening, C and Lücker, S and Guo, J},
title = {Niche specialization and prevalence of comammox Nitrospira in the alkaline sediments of thermokarst lakes on the Tibetan Plateau.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918757},
issn = {2041-1723},
support = {DP230101340//Department of Education and Training | Australian Research Council (ARC)/ ; 42222709//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42107277//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307505//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Tibet ; *Lakes/microbiology/chemistry ; *Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Hydrogen-Ion Concentration ; *Geologic Sediments/microbiology/chemistry ; *Ammonia/metabolism ; Nitrification ; Oxidation-Reduction ; Nitrogen Cycle ; Metagenomics ; },
abstract = {Complete ammonia-oxidizing (comammox) Nitrospira are recognized as key players in the nitrogen cycle, yet their ecological roles in extreme environments remain poorly understood. Here, we show that comammox Nitrospira occupy distinct ecological niches in Tibetan Plateau thermokarst lakes (pH 7.5-10.2) using stable isotope probing, metagenomics, and metatranscriptomics. While gross nitrification rates are significantly higher in subalkaline lakes due to the active presence of ammonia-oxidizing archaea (AOA) and bacteria (AOB), these canonical nitrifiers are inhibited under elevated pH. In contrast, comammox Nitrospira activity is significantly higher in alkaline than in subalkaline lakes, becoming the predominant nitrifiers with activities exceeding those of AOA and AOB by over 6- and 15-fold, respectively. This niche transition, coupled with the inherently low N2O yield of comammox, results in significantly attenuated nitrous oxide (N2O) production in alkaline lakes. Under saline-alkaline stress, these bacteria maintained high expression of carbon fixation and sulfur metabolism genes while upregulating compatible solute biosynthesis, cation transporters, and protein chaperones. Altogether, these findings identify comammox bacteria as key mediators of nitrogen cycling in permafrost-affected thermokarst lakes, expanding their known physiological range and providing mechanistic insights into their adaptations to extreme environments.},
}

Tibet
*Lakes/microbiology/chemistry
*Archaea/metabolism/genetics/classification
*Bacteria/metabolism/genetics/classification/isolation & purification
Hydrogen-Ion Concentration
*Geologic Sediments/microbiology/chemistry
*Ammonia/metabolism
Nitrification
Oxidation-Reduction
Nitrogen Cycle
Metagenomics

@article {pmid42918805,
year = {2026},
author = {Liu, P and Lv, Y and Zhang, Y and Wang, Y and Zhu, K and Cao, Z and Dong, L and Xiao, X and Pan, Y and Li, J},
title = {Extensive horizontal gene transfer drives microbial adaptation and diversification in Kermadec Trench hadal microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918805},
issn = {2041-1723},
support = {42225402//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Metagenome ; *Adaptation, Physiological/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; },
abstract = {Hadal trenches, plunging beyond six kilometers depth, harbor a dynamic yet enigmatic microbial biosphere. From ~10 km depth Kermadec Trench sediments, we integrated metagenomics, in situ metatranscriptomics, and phylogenetics to reconstruct 300 prokaryotic species and 186,496 viral populations. In hadal sediment metagenomes analyzed here, we detect distant horizontal gene transfer (DHGT) across phyla/domains and estimate that it contributes on average ~13% of each genome and accounting for >46.7% of multi-copy gene expansions, with four phyla acquiring more than 30% of their genes via DHGT. These DHGT genes encode critical adaptations, including reactive oxygen species detoxification, aromatic compound degradation, and fatty acid/heme biosynthesis, which help microbes survive extreme pressure, low temperatures, and oligotrophy. While classical mechanisms such as conjugation (~0.27%), transduction (~2.1%), and transformation account for a fraction of events, additional potential gene flow conduits are proposed: magnetotaxis-mediated encounters by magnetotactic bacteria (~17.4% of DHGT events), possibly increasing opportunities for gene exchange. These findings suggest that DHGT can contribute substantially to metabolic diversification in the hadal genomes, representing an evolutionary mode distinct from gradualist Darwinian inheritance and consistent with the idea that episodic acquisition of functional modules can contribute to rapid metabolic diversification.},
}

*Gene Transfer, Horizontal
Phylogeny
*Microbiota/genetics
*Bacteria/genetics/classification
Metagenome
*Adaptation, Physiological/genetics
*Geologic Sediments/microbiology
Metagenomics

@article {pmid42918922,
year = {2026},
author = {Trebše, N and Hyvärinen, S and Šket, R and Kovač, J and Trebše, R and Pokorn, M},
title = {Diagnostic accuracy and clinical considerations of metagenomic next-generation sequencing in prosthetic joint infection: a systematic review and meta-analysis.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42918922},
issn = {1435-4373},
abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) has emerged as a promising complementary method for pathogen detection in prosthetic joint infection (PJI). This systematic review and meta-analysis evaluated the diagnostic accuracy of mNGS and conventional microbiological culture.

METHODS: A systematic review and bivariate diagnostic accuracy meta-analysis were conducted in accordance with the PRISMA-DTA guidelines. PubMed, Ovid MEDLINE, Embase, WoS and the CNKI database were searched. Eligible studies evaluated shotgun mNGS in suspected or confirmed PJI, used a recognized reference standard for diagnosis, and reported sufficient data to construct 2 × 2 contingency tables for mNGS and conventional culture. Pooled sensitivity and specificity were estimated using a bivariate random-effects Reitsma model.

RESULTS: Fourteen studies comprising 1,579 cases were included, of which 982 were classified as PJI and 597 as non-PJI. When pooled separately, mNGS had a sensitivity of 84.3% (95% CI 77.3-89.4%) and specificity of 91.5% (95% CI 88.4-93.9%), compared with 66.0% (95% CI 60.1-71.4%) and 95.6% (95% CI 92.8-97.4%), respectively, for conventional culture. The area under the summary receiver operating characteristic (SROC) curve was 0.941 for mNGS and 0.930 for culture. Sensitivity analyses did not change the overall findings.

CONCLUSION: When analysed separately, mNGS demonstrated higher pooled sensitivity than conventional culture. Overall diagnostic performance assessed by SROC was comparable between the two methods. These findings suggest that mNGS may provide complementary microbiological information. Nevertheless, microorganisms detected exclusively by mNGS should be interpreted cautiously and in conjunction with other clinical and laboratory findings.},
}

@article {pmid42919172,
year = {2026},
author = {Jorquera, R and Ejsmentewicz, T and Lagos, R and Bravo, N and Issotta, F and Hernández-Oliveras, A and Villarroel-Espíndola, F and González-Stegmaier, R},
title = {Evaluating 16S metagenomics data analysis pipelines using an Ion Torrent sequencer for human gut microbiome research.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42919172},
issn = {1471-2180},
support = {internal grant ID FALP-LMT-2021//Fundacion Arturo Lopez Perez/ ; internal grant ID FALP-LMT-2022//Fundacion Arturo Lopez Perez/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Software ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: High-throughput 16S rRNA gene amplicon sequencing is essential for characterizing gut dysbiosis in translational research. However, microbiome profiles vary widely across sequencing platforms, library preparation protocols, targeted hypervariable regions (HVRs), and bioinformatics workflows. For users of the Ion Torrent S5 platform, there is currently no consensus methodology for performing open-source analyses as an alternative to proprietary frameworks. This study evaluates the proprietary Ion Reporter™ software against eight open-source pipelines based on QIIME2 and the SILVA database, accounting for data compositionality. Benchmarking was performed using a commercial human fecal reference material (ZymoBIOMICS™ D6323) characterized via DNA-shotgun sequencing (the ZB-Shotgun profile), as the reference standard.

RESULTS: Poisson regression modeling showed that using two primer sets for library preparation yielded a 30 % lower expected read count than a single primer set (IRR = 0.6986, p < 0.001). Across all configurations, the choice of denoising algorithm (DADA2 vs. Deblur) significantly affected alpha diversity calculations. At the phylum level, hierarchical clustering of Bayes factors (BFs) indicated that multi-region Ion Reporter workflows produced stable consensus predictions. Conversely, at the species level, single-HVR open-source pipelines significantly outperformed multi-region approaches.

CONCLUSIONS: Open-source pipelines that combine targeted HVR2 or HVR4 inputs with state-of-the-art denoisers outperform proprietary Ion Reporter options, providing superior taxonomic resolution and precision for species-level microbiome profiling. This study establishes a traceable, reproducible, and cost-effective framework that empowers independent researchers to maximize the utility of Ion Torrent 16S rRNA data in healthcare and gastrointestinal research without relying on restrictive software ecosystems.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Software
*High-Throughput Nucleotide Sequencing/methods
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Computational Biology/methods
Sequence Analysis, DNA/methods
DNA, Bacterial/genetics

@article {pmid42919413,
year = {2026},
author = {Moreno, ML and Taft, DH and Tompkins, TA and Dahl, WJ},
title = {Efficacy of yeast mannan supplementation on increasing stool frequency in adults: a randomized controlled trial.},
journal = {Trials},
volume = {27},
number = {1},
pages = {},
pmid = {42919413},
issn = {1745-6215},
support = {PRO00067834//Lallemand/ ; },
mesh = {Humans ; *Mannans/administration & dosage/adverse effects ; Double-Blind Method ; Feces/microbiology ; *Dietary Supplements ; *Defecation/drug effects ; *Saccharomyces cerevisiae/chemistry ; Gastrointestinal Transit/drug effects ; Treatment Outcome ; Adult ; Time Factors ; Quality of Life ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Yeast mannans are microbial-available substrates that may improve laxation and specifically modulate gut microbiota composition. The aim of this study is to determine the effect of yeast mannan supplementation on stool frequency in adults. Secondary aims will assess gastrointestinal tolerance and quality of life, whole gut transit time, fecal microbiota composition, and fecal and urinary levels of microbial-generated metabolites.

METHODS: A 6-week, double-blinded, parallel, randomized trial will evaluate the effect of 12 g of yeast mannan (Saccharomyces cerevisiae cell wall fraction containing mannan-oligosaccharides and mannoproteins) or control (maltodextrin and yeast protein) supplementation on mean daily stool frequency in adults (n = 60). Participants will complete a daily survey of stool frequency, gastrointestinal symptoms, and quality of life, any adverse events, and compliance with supplement intake during the 2-week baseline and 4-week intervention periods; gastrointestinal tolerance will be assessed weekly. Capsules containing radiopaque markers will be administered, and all stools will be collected during the last 3 days of baseline and intervention. Whole gut transit time will be estimated using the 80% recovery of radiopaque markers method. Per period, 24-h urine will be collected, and metabolomics will be determined by LC-MS/MS. For the primary outcome, change from baseline daily stool frequency between groups will be compared, and between-group comparisons of secondary outcomes using appropriate generalized linear regression models, and for those outcomes with repeated measures, linear mixed effect models. Fecal microbiome using whole metagenome sequencing data will be processed using metaphlan4, Braken, or another tool appropriate for estimating the relative abundance of microbial species. Additional analysis using tools such as humann3 will enable functional assignment of reads. Resulting relative abundance and normalized functional data will be further analyzed using a combination of tools in R software, including phyloseq and vegan packages.

DISCUSSION: In accordance with our pilot open-label study, the hypothesis is that yeast mannans will increase daily stool frequency, be highly tolerable, and demonstrate specific modulation of the microbiota, supporting its prebiotic properties. Additionally, yeast mannan supplementation may decrease whole gut transit time and mitigate the microbial production of inflammatory microbial-generated metabolites.

TRIAL REGISTRATION: NCT ID NCT06911177. Registered on 04 April 2025.},
}

Humans
*Mannans/administration & dosage/adverse effects
Double-Blind Method
Feces/microbiology
*Dietary Supplements
*Defecation/drug effects
*Saccharomyces cerevisiae/chemistry
Gastrointestinal Transit/drug effects
Treatment Outcome
Adult
Time Factors
Quality of Life
*Gastrointestinal Microbiome/drug effects

@article {pmid42919998,
year = {2026},
author = {Chen, K and Li, J and Zhou, L and Ge, R and Zheng, K and Xu, C and Su, Y and Sun, S and Liang, Y and Xing, J and Wang, M},
title = {Isolation and genomic characterization of a Teetrevirus phage infecting Klebsiella quasipneumoniae with a putative SAMase gene.},
journal = {Archives of virology},
volume = {171},
number = {11},
pages = {},
pmid = {42919998},
issn = {1432-8798},
support = {LSKJ202203201//the National Key Research and Development Program of China/ ; 42120104006 and 42176111//the National Natural Science Foundation of China/ ; 202172002//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {Phylogeny ; *Genome, Viral ; *Bacteriophages/genetics/isolation & purification/classification/enzymology ; *Klebsiella/virology ; *Viral Proteins/genetics/metabolism/chemistry ; Wastewater/virology/microbiology ; Genomics ; Models, Molecular ; Molecular Docking Simulation ; },
abstract = {Phages regulate bacterial populations in engineered ecosystems. However, wastewater associated phage lineages remain uncultured and poorly characterized. Here, we describe vB_KquP_T1, a bacteriophage infecting Klebsiella quasipneumoniae and exhibiting a lytic growth phenotype, isolated from urban wastewater. Genome-based phylogenomic analyses revealed that vB_KquP_T1 represents a distinct species-level lineage within the Teetrevirus of the Autotranscriptaviridae, closely related to uncultured viral genomes. Metagenomic recruitment from 234 global wastewater datasets reveals that vB_KquP_T1-like phages are widespread, with pronounced regional variation. Notably, the vB_KquP_T1 genome encodes a putative S-adenosyl-L-methionine hydrolase (SAMase)-like protein. Structural modeling and comparative analysis revealed a conserved structural architecture, while molecular docking predicted potential interactions with SAM-related ligands. These findings link an uncultured viral lineage to a cultivated representative and support the conservation of SAM metabolism-related auxiliary genes across tailed phages.},
}

Phylogeny
*Genome, Viral
*Bacteriophages/genetics/isolation & purification/classification/enzymology
*Klebsiella/virology
*Viral Proteins/genetics/metabolism/chemistry
Wastewater/virology/microbiology
Genomics
Models, Molecular
Molecular Docking Simulation

@article {pmid42920530,
year = {2026},
author = {Huang, F and Jin, X and Xu, J and Wu, H and Gan, M and Chang, W and Tan, Q and Wang, Y and Li, R and Li, D and Zhang, X},
title = {Gut microbiome-driven longevity mechanisms in giant pandas: age-associated gut microbial shifts, functional pathways, and probiotic insights.},
journal = {Current zoology},
volume = {72},
number = {5},
pages = {616-638},
pmid = {42920530},
issn = {1674-5507},
abstract = {Microbiome-mediated longevity mechanisms in conservation wildlife remain largely uncharacterized, particularly in species with specialized diets where host-microbe coevolution plays essential compensatory roles. We conducted cross-sectional metagenomic profiling of gut microbiota in 82 captive giant pandas (Ailuropoda melanoleuca) spanning juvenile, adult, and geriatric cohorts. The cohort included 14 long-lived individuals (≥25 years). Our approach integrated enterotype analysis, functional pathway characterization, and lactic acid bacteria (LAB) isolation. Age-specific compositional shifts occurred throughout the lifespan, characterized by reciprocal dominance between Bacillota (declining from 84.77% to 10.26%) and Pseudomonadota (increasing from 12.74% to 81.86%). Streptococcus dominated adolescent microbiomes, followed by a transition to cellulose-degrading taxa in young adults. Enterotype analysis revealed 4 distinct community types with age-dependent succession patterns. Long-lived pandas exhibited elevated abundance of Akkermansia muciniphila, Bifidobacterium longum, Lactobacillus intestinalis, and Ruminococcus gnavus. Functional profiling revealed age-dependent shifts from nucleotide and amino acid biosynthesis in young animals to lipid metabolism and amino acid degradation in aged individuals. Carbohydrate-active enzyme analysis demonstrated enrichment of cellulolytic enzymes (such as GH3, GH5, and GH9) in long-lived adults. Biosynthetic gene cluster profiling revealed progressive age-associated accumulation of genes encoding NRPS, RiPP-like, arylpolyene, and terpene biosynthetic pathways. Culture-based isolation from fecal samples of long-lived giant pandas yielded 98 LAB strains representing 8 species (Lactobacillus johnsonii, Limosilactobacillus reuteri, L. intestinalis, among others), including 89 non-hemolytic strains that were sensitive to 6 common antibiotics. These findings suggest potential cross-species conservation of microbiome-longevity mechanisms, with implications for understanding physiological adaptations in specialist herbivores and applications in conservation medicine.},
}

@article {pmid42920578,
year = {2026},
author = {Barak, H and Brenner, A and Kushmaro, A},
title = {Genome-resolved metagenomics reveals potential biochemical capabilities of a microbial community in an industrial wastewater membrane bioreactor during performance deterioration and recovery.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1908813},
pmid = {42920578},
issn = {1664-302X},
abstract = {This study investigates the microbial community composition and biochemical capabilities within a membrane bioreactor (MBR) system treating industrial wastewater during two operational states: a period of marked performance deterioration and a subsequent early recovery phase. The MBR system experienced a prolonged decline in treatment performance, with Total Organic Carbon (TOC) removal efficiency decreasing from approximately 90% to approximately 70% and effluent Biochemical Oxygen Demand (BOD) increasing to more than 70 mg/L. Metagenomic sequencing and subsequent analysis unveiled distinct shifts in microbial community composition and functional potential during these operational states. A total of 51 Metagenome-Assembled Genomes (MAGs) were reconstructed and characterized, revealing microbial populations associated with Pseudomonadota and Bacteroidota. These populations exhibited putative metabolic capabilities associated with nitrogen cycling, sulfur metabolism, and degradation of recalcitrant aromatic compounds. Key taxa enriched during the early recovery condition contained genes associated with nitrogen fixation and sulfur oxidation. These findings provide genome-resolved insights into microbial community composition and predicted functional potential during contrasting MBR operational states and may inform future investigations of industrial wastewater treatment systems.},
}

@article {pmid42920641,
year = {2026},
author = {Zhou, Y and Zhang, Y and Zhang, R and Zhang, Y and Cui, Y},
title = {Case Report: Cytomegalovirus-associated granulomatous lung disease in an immunocompetent preterm infant.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2000675},
pmid = {42920641},
issn = {1664-3224},
mesh = {Humans ; Male ; *Cytomegalovirus Infections/diagnosis/virology/immunology/complications ; *Cytomegalovirus/genetics ; Infant, Premature ; Infant ; Immunocompetence ; Tomography, X-Ray Computed ; },
abstract = {Granulomatous lung disease caused by cytomegalovirus (CMV) has not been described in immunocompetent infants. We report a 5-month-old boy, born at 31[+5] weeks of gestation, with a 2-month history of isolated cough and normal growth. Contrast-enhanced chest computed tomography showed a multiloculated cystic mass in the right upper lobe. CMV DNA was detected in whole blood (1.41 × 10[4] copies/mL) and urine (1.44 × 10[6] copies/mL). Intravenous ganciclovir for 2 weeks produced no radiological change; because a tumor could not be excluded, video-assisted thoracoscopic right upper lobectomy was performed. Histology showed extensive necrosis with well-formed epithelioid granulomas and multinucleated giant cells. Stains for acid-fast bacilli and fungi and Epstein-Barr virus-encoded RNA in situ hybridization were negative. To exclude an infectious granulomatous disease, metagenomic next-generation sequencing (mNGS) of the resected tissue identified CMV at 1,143 reads per million as the only pathogen. The postoperative course was uncomplicated, with no recurrence at 6 months. CMV produced a localized granulomatous mass mimicking a congenital lung lesion or neoplasm, and tissue mNGS provided the decisive microbiological evidence. When a preterm infant has an unexplained chronic pulmonary lesion, CMV should be considered, and mNGS of pathological tissue can establish the diagnosis.},
}

Humans
Male
*Cytomegalovirus Infections/diagnosis/virology/immunology/complications
*Cytomegalovirus/genetics
Infant, Premature
Infant
Immunocompetence
Tomography, X-Ray Computed

@article {pmid42920753,
year = {2026},
author = {Meski, S and Mojsoska, B and Krogfelt, KA and Cruz-Paredes, C},
title = {Bridging soil resistome and clinical inference: A four-tier evidentiary framework.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117815},
pmid = {42920753},
issn = {2589-0042},
abstract = {Soils support a varied range of microbial communities and are important repositories of antimicrobial resistance genes. Sequence-based techniques, such as quantitative polymerase chain reaction and shotgun metagenomics, have substantially aided soil-resistome cataloging. Nevertheless, discovery alone does not indicate activity, transferability, exposure, or clinical relevance. This review contends that better clinical inference requires tying presence-based signals to function, mobility, and exposure routes, rather than just increasing survey volume. We offer a four-tiered evidentiary paradigm that distinguishes between detection, functional or expression-based evidence, mobile genetic element context, and exposure-linked evidence in environmental, animal, and human compartments. Because activity, mobility, and cross-compartmental similarity support several claims, layered, claim-aligned approaches are required for careful One Health interpretation.},
}

@article {pmid42920917,
year = {2026},
author = {Myburgh, DA and da Silva, NA and Romeyer-Dherbey, JH and Grefen-Peters, S and Jöns, H and Peek, C and Nebel, A and Krause-Kyora, B},
title = {Paleogenomics reveals leprosy at the late antique burial site of Fallward in northern Germany.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117877},
pmid = {42920917},
issn = {2589-0042},
abstract = {The coastal settlement of Fallward in northwestern Germany (3[rd]-5[th] century CE) is renowned for exceptionally preserved wooden and textile grave goods, yet the genetic and pathogen landscape of its inhabitants has remained unstudied. We conducted metagenomic analyses on skeletal samples from 11 individuals to investigate their genetic affinities and infectious disease history. Three individuals yielded sufficient data for population genetic analysis: two clustered with northwestern European Iron Age and Anglo-Saxon groups, while one adult male might have originated from a Roman frontier population. This man was also infected with a strain of Mycobacterium leprae belonging to phylogenetic branch 4 and was buried in a boat accompanied by Roman-influenced grave goods, including carved furniture and a military belt. Together, these findings point to possible long-distance connections linking remote communities, such as Fallward, to the wider Roman world during Late Antiquity.},
}

@article {pmid42921440,
year = {2026},
author = {Cotella, D},
title = {Gene, microbiome, and anti-aging doping in sport: molecular mechanisms, detection strategies, and implications for sports rehabilitation medicine.},
journal = {Frontiers in sports and active living},
volume = {8},
number = {},
pages = {1984895},
doi = {10.3389/fspor.2026.1984895},
pmid = {42921440},
issn = {2624-9367},
abstract = {Advances in gene transfer have created legitimate opportunities for tissue repair, but the same tools raise the prospect of illicit use to enhance athletic performance ("gene doping"). Evidence that elite athletes harbour a distinctive gut microbiota has raised a parallel concern that microbiome manipulation, including faecal microbiota transplantation (FMT) from high-performing donors, could be used as a form of biological enhancement ("microbiome doping"). A third, related frontier is anti-aging gene therapy (telomerase and Klotho gene delivery and partial cellular reprogramming) which targets the same muscle- and stem-cell-regenerative pathways relevant to injury recovery and has already reached unregulated human self-experimentation. This narrative review summarises the principal gene-doping targets relevant to performance and recovery (erythropoietin, myostatin/activin inhibitors, insulin-like growth factor 1, PPAR-δ/AMPK reprogramming), their delivery vectors, and current detection strategies. It then reviews athlete-associated gut microbiota signatures, notably the lactate-metabolising bacterium Veillonella atypica, and the feasibility and detection challenges of microbiota transplantation, before examining the rationale, targets, and governance challenges of anti-aging gene therapy. Attention is given to the overlap between all three frontiers and legitimate regenerative, microbiota-directed, or aging-biology therapies under investigation for musculoskeletal, metabolic, and gastrointestinal conditions, an overlap that places rehabilitation clinicians in a sensitive position, particularly with older or master athletes; across all three frontiers, the same biological pathways and delivery technologies are simultaneously being developed for legitimate therapeutic use, creating a recurring dual-use dilemma for clinicians and regulators alike. I review safety risks, the regulatory framework administered by the World Anti-Doping Agency (WADA) and its gaps regarding microbiome and longevity interventions, and the practical responsibilities of rehabilitation professionals. I conclude that interdisciplinary collaboration between molecular biologists, microbiome and aging researchers, anti-doping scientists, and clinicians is essential to keep detection methods and clinical governance aligned with the pace of innovation in these three areas, and we outline specific priorities, including clarification of the regulatory status of microbiota transfer and anti-aging gene constructs, strain-level metagenomic monitoring, and biological-age biomarkers, for achieving this alignment.},
}

@article {pmid42922426,
year = {2026},
author = {Kabbashi, S and Chetty, M},
title = {Periodontal Infectogenomics in Africa: The Biological Case for a Population-Centred Research Agenda.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70186},
pmid = {42922426},
issn = {1600-0765},
support = {//South African Medical Research Council/ ; //University of the Western Cape/ ; },
abstract = {African populations harbour the greatest human genetic diversity on earth and carry the highest global burden of severe periodontitis, yet their absence from periodontal infectogenomics represents a biological limitation of the field with profound implications for host-microbe interaction research. This Perspective builds the biological case for African populations as an urgent research priority and proposes a research roadmap integrating genomics, metagenomics and multiomics approaches.},
}

@article {pmid42922467,
year = {2026},
author = {Mortimer, K and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of a shovel-head worm, Maea johnstoni (Fiege, Licher & Mackie, 2000) (Spionida: Magelonidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {461},
pmid = {42922467},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Maea johnstoni (Fiege, Licher & Mackie, 2000) (shovel-head worm; Annelida; Polychaeta; Spionida; Magelonidae). The genome sequence has a total length of 881.61 megabases. Most of the assembly (97.37%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.47 kilobases. From the metagenome data, we recovered two Spirochaetota bins, one of which was a MAG.},
}

@article {pmid42922524,
year = {2026},
author = {Tantry, A and Long, W and Tran, J and Rohatgi, S and Cyphert, EL},
title = {Exploratory multi-omics analysis reveals sex-specific differences in microbial response to antibiotic exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.01.748584},
pmid = {42922524},
issn = {2692-8205},
abstract = {UNLABELLED: Antibiotic exposure is a major driver of microbiome disruption and antimicrobial resistance gene (ARG) expansion. Yet, the role of biological sex in shaping these responses remains poorly understood. Most studies do not stratify antibiotic-induced microbiome changes by sex or integrate multi-omics datasets, limiting our understanding of how microbial, metabolic, and immune responses interact. Therefore, there remains a critical need for an integrative systems-level approach to determine how sex-specific disruptions under antibiotic pressure are paralleled across microbial, metabolic, and host immune layers. The objective of this work was to perform an exploratory study investigating how continuous antibiotic exposure reshaped the gut microbiome across sexual maturation and how these perturbations influenced downstream host responses in a sex-specific manner using an integrative multi-omics framework. Male and female mice that were exposed to continuous antibiotics were profiled over sexual maturation using shotgun metagenomics, untargeted metabolomics, and bulk RNA sequencing of the spleen to assess microbial composition, ARG dynamics, metabolic profiles, and immune responses. Overall, our results demonstrated sex-specific correlations at a systems-level that help provide valuable context to the differences observed in males and females upon antibiotic exposure.

IMPORTANCE: Antimicrobial resistance is a major global threat, and it remains unclear how continuous antibiotic exposure shapes the gut microbiome across sexual maturation and influences the host response in a sex-specific manner. In this work, we used an integrative multi-omics framework to demonstrate sex-specific correlations at a systems-level across several biological layers including taxonomic and resistome composition, host-microbe interactions through cecal metabolomic profiles, and host splenic gene expression. These results provide valuable context to understand systems-level differences in males and females following antibiotic exposure and inform sex-specific antibiotic strategies to contribute to more effective antimicrobial stewardship.},
}

@article {pmid42922537,
year = {2026},
author = {Fiamenghi, MB and Kyrpides, NC},
title = {Discovery of novel enzybiotic candidates targeting human bacterial pathogens through large-scale viral-host profiling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.01.748673},
pmid = {42922537},
issn = {2692-8205},
abstract = {UNLABELLED: The rise of antibiotic-resistant bacteria demands alternative therapeutic strategies, with bacteriophage (phage) therapy and phage-derived enzybiotics emerging as promising approaches. However, identifying candidate phages against specific pathogens has historically been a bottleneck due to the need for cultivation methods to assess host range and lytic activity. Advances in metagenomic sequencing and the emergence of large-scale viral genome databases now provide an opportunity to accelerate this process computationally. Here, we present a large-scale mining of the MetaVR database to identify phages targeting human bacterial pathogens. By integrating direct host associations with CRISPR-spacer evidence, we linked 196,472 high-quality and complete viral genomes, representing 42,360 vOTUs, to 618 species of pathogenic and opportunistic bacteria. Functional enrichment analysis revealed distinct genomic signatures with viral lifestyle and host-range breadth: virulent phages were enriched in replication and structural functions, whereas temperate and broad host-range phages were enriched in anti-defense and regulatory modules. To characterize their lytic potential we annotated lysis-related protein families and their structural diversity, identifying 76 structurally novel lysis-associated proteins, including candidates targeting WHO priority pathogens. Focused analysis of endolysins revealed 592 structural clusters, with extensive sharing of endolysin repertoires among ESKAPE pathogens, suggesting candidates for broad-spectrum enzybiotic development. Selection analysis identified 167 endolysin families with sites under positive selection within functional domains, highlighting evolutionary diversification potentially associated with phage-host interactions. Together, our results establish a large-scale framework for connecting human bacterial pathogens to phages and their lytic machinery, providing a resource for prioritizing phage therapy and enzybiotic development.

IMPORTANCE: Antibiotic resistance is a growing global health crisis, and phage therapy represents a promising alternative to conventional antibiotics. By leveraging a large-scale viral genomic database to computationally link almost 200,000 phage genomes to 618 human pathogen species, we substantially expand the catalog of known phage-pathogen interactions. Additionally, we characterize the lysis machinery encoded by these phages, including holins, spanins and endolysins uncovering structurally novel enzymes, associated with phages targeting WHO priority pathogens that could serve as starting points for enzybiotic development. We also reveal extensive sharing of endolysin repertoires among pathogen species, indicating opportunities for developing broad-spectrum enzybiotic strategies. By providing a systematic, genomics-driven framework for identifying and prioritizing phage-derived therapeutic candidates, this work translates large-scale viral genomic data into a resource for developing new therapeutic strategies against drug-resistant bacterial infections.},
}

@article {pmid42922792,
year = {2026},
author = {Pruss, KM and Chang, ZL and Hossain, MS and Rahman, MM and Mahfuz, M and Coskun, R and Sharmin, R and Rezwan, AHM and Sarker, SA and Das, S and Fahim, SM and Gazi, MA and Hudson, KA and Rodríguez, AM and Liu, H and Kitchen, R and Byrne, AE and Kao, C and Brodrick, BB and Rose, A and Bhattarai, B and Khantakova, D and Fachi, J and Colonna, M and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Functional characterization of duodenal microbiota and associated enteropathy in undernourished Bangladeshi women and gnotobiotic mice.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.14.26360472},
pmid = {42922792},
abstract = {UNLABELLED: Undernutrition is an intergenerational global health challenge. Environmental enteric dysfunction (EED) is a small intestinal (SI) disorder characterized by villous atrophy, gut barrier dysfunction, malabsorption and systemic inflammation. To examine its pathogenesis and role in undernutrition, we performed esophagogastroduodenoscopy on undernourished Bangladeshi women with EED and their healthy counterparts. Histologic characterization of duodenal mucosal biopsies, aptamer-based proteomic analyses of their duodenal mucosa and plasma, plus metagenomic analyses of their duodenal and fecal microbiota, revealed associations between bacterial taxa and duodenal tissue and plasma proteomes indicative of EED. Colonization of germ-free female mice with consortia of cultured duodenal bacteria from these women, followed by measurements of SI bacterial abundances, SI cellular patterns of gene expression (single nucleus RNA-seq), plus proteomic and flow cytometric analyses disclosed bacterial, epithelial, and immune features of EED in dams and their offspring resembling those in the women. These findings have diagnostic and therapeutic implications.

ONE SENTENCE SUMMARY: Bacteria-protein associations in the small intestine underlying pathogenesis of environmental enteric dysfunction in undernourished Bangladeshi women.},
}

@article {pmid42922855,
year = {2026},
author = {Song, Y and Jia, Z},
title = {Pathway-level analysis suggests a maintenance-oriented transcriptional response of the ammonia-oxidizing bacterium Nitrosospira sp. NT to acidic pH.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1957381},
pmid = {42922855},
issn = {1664-302X},
abstract = {Acidic environments impose energetic constraints on ammonia-oxidizing bacteria (AOB), although some acid-tolerant lineages remain capable of ammonia oxidation at low pH. The transcriptional responses of acid-tolerant AOB to low-pH conditions remain poorly resolved. Here, we characterized the pathway-level response of Nitrosospira sp. NT by integrating a reconstructed metagenome-assembled genome with comparative metatranscriptomic data from cultures incubated for 24 h at pH 5.0 or pH 8.0. Transcript abundance was not uniformly reduced among the metabolic pathways examined at pH 5.0. Genes associated with the Calvin-Benson-Bassham cycle, the oxidative tricarboxylic acid cycle, nucleotide and deoxyribonucleotide biosynthesis, glycogen metabolism, and septal peptidoglycan synthesis generally showed lower transcript abundance, indicating reduced expression of pathways linked to biomass production and cell proliferation. By contrast, transcripts associated with selected oxidative pentose phosphate pathway enzymes, cell-envelope homeostasis, membrane-protein quality control, c-di-GMP-associated surface functions, stored-iron mobilization, and c-type cytochrome maturation showed comparable or higher transcript abundance. Iron-dependent cofactor pathways also responded differently: transcripts related to bacterioferritin-associated iron mobilization and Ccm-dependent cytochrome c maturation were higher, whereas those involved in heme a/o synthesis and SUF-mediated Fe-S cluster assembly were lower. Collectively, these patterns support a maintenance-oriented transcriptional model in which transcripts associated with cellular integrity, redox support, envelope homeostasis, and intracellular iron reutilization were relatively more abundant than those associated with biomass accumulation at pH 5.0. This study provides a pathway-level framework for understanding the transcriptional response of acid-tolerant AOB to acidic conditions.},
}

@article {pmid42922915,
year = {2026},
author = {Singh, P and Sharma, A and Kumar Sarmah, B and Arivaradarajan, P and Nath, T and Nandi, SP},
title = {Dominance of ascomycota and ubiquity of Trichoderma in Argemone mexicana microbiomes across Assam, India.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1868321},
pmid = {42922915},
issn = {2673-6128},
abstract = {INTRODUCTION: In India, Argemone mexicana is known for its pharmaceutical value. The plant hosts many endophytes. Plant-associated microbes also help plants with development and protection.

MATERIAL AND METHODS: A metagenomic study of rhizospheric soil, roots, and shoots was conducted to investigate variation in the organization and diversity of fungal communities from two different locations (Amlighat and Dergaon, Assam, India) for the first time. Illumina sequencing was used for the fungal metagenomic analysis. The DNA library was constructed using primers specific for the fungal internal transcribed spacer 2 (ITS2) region.

RESULTS AND DISCUSSION: Next-generation sequencing identified a total of 5 phyla, 32 classes, 39 orders, 68 families, 125 genera, and 273 fungal species (including unknown and unidentified taxa) in triplicate samples. The fungal taxa were mostly similar in both locations but occurred at varying relative abundances. The fungal community richness was higher in the root samples from Dergaon than in the other samples. Ascomycota (37.47%-75.84%) was the dominant phylum across all samples, followed by Basidiomycota (3.53%-6.95%). Beta diversity analyses, including principal component analysis, cluster analysis, unweighted pair group method with arithmetic mean (UPGMA), and network analysis, also showed a close relationship between the fungi of both locations. We observed mostly similar fungal diversity, with some differences, among the roots and shoots of A. mexicana and its rhizospheric soil. Trichoderma species were detected in all samples at varying relative abundances. These findings suggest that this fungus may modulate acaricide production in A. mexicana.},
}

@article {pmid42922957,
year = {2026},
author = {Jiang, F and Shen, T},
title = {Case Report: VV-ECMO rescue of severe pneumonia with polymicrobial mNGS detections and uncertain EBV significance in obesity.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1915648},
pmid = {42922957},
issn = {2296-858X},
abstract = {Severe pneumonia with multiple microbial detections can make etiologic attribution and rescue decisions difficult. We report a 42-year-old man with obesity (body mass index, 36.3 kg/m[2]) who was admitted with rapidly progressive pneumonia, sepsis, acute hypoxemic respiratory failure, and multiorgan dysfunction [Sequential Organ Failure Assessment (SOFA) score, 9]. Despite invasive ventilation, one approximately 28-h prone-positioning session, and broad-spectrum antimicrobials, oxygenation deteriorated; immediately before extracorporeal support, PaO2 was 52 mmHg on FiO2 1.0 (PaO2/FiO2, 52 mmHg). The course included blood-tinged secretions, suspected alveolar hemorrhage without a documented progressively bloody serial lavage pattern, and complete left lung atelectasis. Bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Legionella pneumophila, and a high Epstein-Barr virus (EBV) sequence burden. Admission blood cultures and conventional sputum culture showed no bacterial growth. On hospital day 3, venovenous extracorporeal membrane oxygenation (VV-ECMO) was initiated at 3,510 rpm, with blood flow 5.0 L/min and sweep gas flow 4.5 L/min. Adjunctive intravenous acyclovir (0.75 g every 8 h for 7 days) was administered because of the high EBV burden, although its clinical benefit in EBV pulmonary disease is unproven. VV-ECMO was discontinued on hospital day 18, extubation occurred on hospital day 24, and the patient subsequently returned to normal daily life. The clinical value of this case lies in management of a compound, potentially reversible phenotype rather than proof of any single microbial cause: severe pneumonia with polymicrobial mNGS detections, high EBV burden of uncertain significance, suspected hemorrhagic lung injury, unilateral atelectasis, and obesity-related respiratory mechanics successfully bridged with VV-ECMO.},
}

@article {pmid42922991,
year = {2026},
author = {Chen, R and Xu, Z and He, T and Liu, X and Ding, Y and Hou, X},
title = {Pathogen spectrum and triple-criteria interpretation algorithm of BALF-targeted NGS in children with refractory severe community-acquired pneumonia in mountainous Northeastern Sichuan: a single-center retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1929990},
pmid = {42922991},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Pneumonia/microbiology ; Retrospective Studies ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Male ; Coinfection/microbiology/diagnosis/virology ; *Algorithms ; Infant ; Bacteria/isolation & purification/genetics/classification ; *Community-Acquired Infections/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) causes substantial pediatric hospitalization and respiratory failure in mountainous western China. Conventional microbial assays show limited sensitivity for fastidious pathogens and mixed infections. Targeted next-generation sequencing (tNGS) using bronchoalveolar lavage fluid (BALF) enables broad-spectrum pathogen detection at lower cost than whole-metagenomic sequencing. However, many previous tNGS studies directly equate multiple microbial nucleic-acid signals with true coinfection, which may lead to unnecessary combined anti-infective therapy.

METHODS: This single-center retrospective study enrolled 86 children aged < 14 years with refractory SCAP who underwent BALF-tNGS testing at Guangyuan Central Hospital between March 2023 and September 2024. We developed a triple-criteria interpretive algorithm combining an exploratory empirical pathogen-load cut-off (>1.0 × 10[6] copies/mL), inflammatory biomarkers (CRP, PCT), and chest imaging to discriminate genuine active coinfection from airway colonization. This load threshold was empirical and not internally validated by ROC analysis in our dataset. Patients were stratified into four age subgroups; diagnostic concordance was assessed among 34 patients with parallel routine microbial tests.

RESULTS: In total, 229 pathogen isolates were identified. Viruses predominated (58.9%, 135/229), followed by bacteria (32.8%, 75/229). The three most frequent pathogens were Haemophilus influenzae (32.56%), Streptococcus pneumoniae (30.23%), and respiratory syncytial virus A (RSV-A, 18.60%). While 82.6% (71/86) of patients harbored ≥2 pathogen nucleic-acid signals, only 17.4% (15/86) fulfilled criteria for clinical coinfection, dominated by virus-bacterial dual infection. Viral detection rates tended to decline with increasing age, whereas bacterial positivity was higher among preschool- and school-age children. A prominent spring epidemic peak was observed during May-June 2023. Only 22.86% of paired routine microbial tests showed full concordance with tNGS. These single-center data cannot be generalized to all pediatric severe-pneumonia populations. Most abundant multi-pathogen tNGS signals represented colonization or residual dead-microbe nucleic acid instead of true active infection.

CONCLUSION: Our triple-criteria interpretive framework offers standardized rules for grassroots mountain hospitals to reduce over-prescription of combined antibiotics and antivirals when interpreting BALF-tNGS results for children with refractory SCAP.},
}

Humans
*Community-Acquired Pneumonia/microbiology
Retrospective Studies
China/epidemiology
*High-Throughput Nucleotide Sequencing/methods
Child
Child, Preschool
*Bronchoalveolar Lavage Fluid/microbiology/virology
Female
Male
Coinfection/microbiology/diagnosis/virology
*Algorithms
Infant
Bacteria/isolation & purification/genetics/classification
*Community-Acquired Infections/microbiology
Adolescent

@article {pmid42923033,
year = {2026},
author = {Zhang, C and Chen, Q and Sun, Z and Wu, T and Zhang, Y and Huang, B and Huang, S and Zhang, Y and Han, M},
title = {Tripterygium wilfordii ameliorates complete freund adjuvant-induced rheumatoid arthritis through modulating the gut-joint axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828110},
pmid = {42923033},
issn = {1664-3224},
mesh = {Animals ; *Tripterygium/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Rheumatoid/drug therapy/chemically induced/immunology/metabolism ; Rats ; *Arthritis, Experimental/drug therapy/immunology/metabolism ; Cytokines/metabolism/blood ; *Joints/drug effects/metabolism/immunology ; Male ; *Plant Extracts/pharmacology ; Synovial Membrane/metabolism ; *Drugs, Chinese Herbal/pharmacology ; Signal Transduction/drug effects ; Metabolomics ; },
abstract = {INTRODUCTION: Although Tripterygium wilfordii (TW) is a classical Chinese herbal medicine for the treatment of rheumatoid arthritis (RA), the mechanism by which it alleviates inflammation through modulation of the gut microbiota remains unclear.

METHODS: To elucidate the mechanism underlying the therapeutic effects of TW on RA, we first employed network pharmacology to predict the relevant pathways and core targets. Subsequently, an integrative multi-omics approach was applied, including gut metagenomics, gut metabolomics, serum metabolomics, and synovial transcriptomics, to investigate the alterations in gut microbiota, intestinal and serum metabolites, and synovial gene expression in a rat model of RA.

RESULTS: Our findings revealed that TW supplementation lowered serum concentrations of IL-6, IL-1β, TNF-α, and IL-10 and modulated the Th17/Treg balance in intestinal tissue. TW treatment altered gut microbiota (GM) composition, marked by increased abundance of Prevotella sp PCJ2 and Psychrobacter pasteurii, and decreased Adlercreutzia equolifaciens and Schaedlerella arabinosiphila, synergizing with keystone species (Bifidobacterium animalis, Phocaeicola sartorii, Blautia faecis) to promote gut health. Concurrently, TW elevated tryptophan metabolites (tryptophol, tryptamine, 5-hydroxykynurenamine) while reducing 4-(2-aminophenyl)-2,4-dioxobutanoic acid, restoring tryptophan metabolism. This regulation coincided with upregulated Inmt mRNA in synovium, activating the tryptophan pathway. Correlation and mediation analyses indicated that gut-derived circulating metabolites such as N-myristoyl arginine and lauramidoxide were positively correlated with synovial Jun expression, potentially participating in the modulation of the IL-17-NF-κB cascade. Consistently, upregulated synovial Socs3 may exert negative feedback suppression on JAK-STAT signaling to alleviate inflammatory responses.

DISCUSSION: These findings point to the gut microbiome and tryptophan pathway as a new therapeutic avenue for RA.},
}

Animals
*Tripterygium/chemistry
*Gastrointestinal Microbiome/drug effects
*Arthritis, Rheumatoid/drug therapy/chemically induced/immunology/metabolism
Rats
*Arthritis, Experimental/drug therapy/immunology/metabolism
Cytokines/metabolism/blood
*Joints/drug effects/metabolism/immunology
Male
*Plant Extracts/pharmacology
Synovial Membrane/metabolism
*Drugs, Chinese Herbal/pharmacology
Signal Transduction/drug effects
Metabolomics

@article {pmid42923064,
year = {2026},
author = {Galaras, A and Chasapi, IN and Aplakidou, E and Chasapi, MN and Lamari, E and Diplari, S and Georgakopoulos-Soares, I and Karatzas, E and Baltoumas, FA and Kyrpides, NC and Pavlopoulos, GA},
title = {WasteFams: a database of protein families from global wastewater microbiomes.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {4},
pages = {lqag127},
pmid = {42923064},
issn = {2631-9268},
mesh = {*Wastewater/microbiology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; *Databases, Protein ; *Bacterial Proteins/genetics ; },
abstract = {Wastewater surveillance has emerged as a critical tool for global epidemiology, yet the functional diversity of wastewater microbiomes remains poorly characterized at the protein level. Here, we present WasteFams, the first comprehensive database dedicated to the systematic exploration of protein families in wastewater metagenomic and metatranscriptomic studies worldwide. Integrating data from 580 metagenomes, 132 metatranscriptomes, and 1709 reference genomes (504 metagenomes, 129 metatranscriptomes, and 1151 reference genomes after filtering), WasteFams catalogs 3887 non-redundant protein families (containing ⪰100 members) derived from over 105 million predicted proteins. Each protein family is enriched with multi-layered annotations, including AlphaFold3 structural predictions, taxonomic classifications, and biome-specific metadata. To further expand their functional annotation, we integrated deep genomic context analysis to link protein families to mobile genetic elements, biosynthetic gene clusters, antibiotic resistance genes, and CRISPR elements. Accessible through the EnvoFams portal, WasteFams provides a user-friendly interface featuring advanced search capabilities, sequence and structural similarity tools, and interactive visualization modules. As global initiatives increasingly leverage wastewater for public health and environmental insights, WasteFams can serve as a critical resource for discovering novel microbial functions, monitoring resistance mechanisms, and exploring the biotechnological potential of secondary metabolites within wastewater-engineered ecosystems.},
}

*Wastewater/microbiology
*Microbiota/genetics
Metagenome
Metagenomics
*Databases, Protein
*Bacterial Proteins/genetics

@article {pmid42923070,
year = {2026},
author = {Nawaz, F and Barkaat, M and Khan, MN and Kanwal, H and Tabassum, M and Rauf, N and Malik, TSS and Imran, M},
title = {Impact of microbial composition on nutritional and organoleptic quality of an Indigenous fermented milk product (Dahi).},
journal = {Journal of food science and technology},
volume = {63},
number = {11},
pages = {2065-2076},
pmid = {42923070},
issn = {0022-1155},
abstract = {UNLABELLED: Dahi, a traditionally fermented milk product, is renowned for its unique nutritional, physicochemical, and organoleptic properties, underpinned by complex and largely unexplored microbial ecosystem. This study employed culturable and metagenomic approaches to investigate microbial profile and its influence on nutritional and organoleptic properties of Dahi. The average pH of Dahi was 4.3, with 37.11% solids, 6.11% crude protein, 3.59% fat, and 0.5% ash. Among macronutrients, potassium (567.2 mg/L) was predominant, alongside calcium, sodium, and magnesium, while iron (5.42 mg/L) and zinc (2.94 mg/L) enhanced its nutritional value. Microbial analysis revealed Firmicutes (87%) as the dominant bacterial phylum and Lactobacillus (51%) as the leading genus, with Ascomycota (95%) and Kluyveromyces (70%) prevailing among fungi. Functional profiling identified key metabolic pathways including homolactic fermentation and glycolysis, essential for flavor, texture, and sensory enhancements. Enzymes like L-lactate dehydrogenase and acetyl-CoA carboxylase contributed to lactic acid production, fatty acid metabolism, and exopolysaccharide synthesis, improving texture and syneresis properties. Sensory evaluation linked microbial diversity to attributes such as creamy texture, fruity aroma, and sour taste, furthermore Lactobacilli was also positively correlated with desirable traits. Alpha diversity indices and functional analysis highlighted the correlation between microbial diversity and sensory attributes underscoring Dahi's microbial and metabolic uniqueness, emphasizing its potential as a functional food.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13197-025-06342-8.},
}

@article {pmid42906136,
year = {2026},
author = {Cheng, J and Hui, M and Yu, M and Wang, M and Sha, Z},
title = {Early holobiont-level divergence and adaptation across seafloor geochemical contrasts in the deep-sea squat lobster Shinkaia crosnieri.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag262},
pmid = {42906136},
issn = {1537-1719},
abstract = {Deep-sea hydrothermal vents and methane seeps host unique animal communities sustained by chemosynthetic symbioses, yet how biological diversification proceeds across these geochemically distinct and geographically fragmented habitats remains poorly understood. Previous studies have largely focused on either host genomic adaptation or symbiont diversity as drivers of isolation, leaving unresolved how environmental geochemistry and host-microbe associations jointly shape evolutionary trajectories in chemosynthetic ecosystems. Here, we addressed this gap by combining chromosome-level host genomics, population resequencing, and episymbiont metagenomics in the deep-sea chemosynthetic lobster Shinkaia crosnieri, a dominant species inhabiting both hydrothermal vents and methane seeps. Genomic innovations-including sensory trade-offs (vision loss versus chemosensory expansion), metabolic compensation for pigment loss, and positive selection on respiratory protein-underpin deep-sea colonization of S. crosnieri. Populations from the Okinawa Trough vent and the South China Sea seep exhibit pronounced genetic divergence, potentially driven by Pleistocene vicariance and reinforced by divergent selection across sulfur-enriched (vent) versus sulfur-depleted, methane-dominated (seep) environments. This selection target host genes involved in chemoreception and immunity, with coordinated signatures in both sequence evolution and structural variation. Crucially, holobiont-level adaptation is amplified by habitat-specific recruitment of episymbionts: sulfur-oxidizing Campylobacterales/Thiotrichales dominate vent-associated lobsters, while methanotrophic Methylococcales prevail at seep counterparts. These symbionts partition energy niches metabolically, with seep-associated communities enhancing biosynthesis of key cofactors (e.g., coenzyme Q, tetrahydrofolate). Host transporters for these nutrients are concurrently upregulated, demonstrating functional synergy. Our findings establish that diversification in extreme environments operates holobiont-wide, where geochemical gradients synergistically shape host genomic plasticity and symbiont metabolic specialization to drive early-stage divergence.},
}

@article {pmid42906345,
year = {2026},
author = {Liu, L and Tong, B and Cui, Y and Cao, X and Zhai, Y},
title = {Dissolved organic matter drives fraction-specific mobilization and transformation of redox-sensitive constituents in groundwater.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127169},
doi = {10.1016/j.watres.2026.127169},
pmid = {42906345},
issn = {1879-2448},
abstract = {The anomalous mobilization of redox-sensitive elements (Fe, Mn, N, As, and P) in riparian groundwater is frequently associated with dissolved organic matter (DOM) influx; however, the contrasting roles of labile protein-like and recalcitrant humic-like DOM remain poorly resolved. Here, we employed tyrosine (Tyr) and humic acid (HA) as model compounds for labile, protein-like DOM and recalcitrant, humic-like DOM, respectively, and conducted gradient incubation experiments (0, 20, and 100 mg/L) under both sterile and non-sterile conditions. By integrating hydrochemical time-series, solid-phase speciation, fluorescence parallel-factor analysis, amplicon sequencing, and metagenomic functional profiling, we distinguished the biotic and abiotic drivers governing elemental coupling. Our results reveal that DOM substantially altered redox-driven elemental mobilization, with effects that were strongly dependent on DOM type, concentration, and incubation stage. In biotic treatments, Tyr profoundly stimulated microbial loops, enriching Fe/Mn-reducing and N-cycling taxa (relative abundances of 32.25% and 26.13% at 20 mg/L, versus 11.70% in controls) and upregulating genes involved in dissimilatory nitrate reduction and extracellular electron transfer. Notably, low-concentration Tyr (20 mg/L) favored Mn release, whereas high-concentration Tyr (100 mg/L) promoted late-stage Fe oxide dissolution and concomitant P liberation. In stark contrast, HA exerted a dualistic influence: although it weakly stimulated canonical metal reducers and even suppressed gene abundance at elevated loads, it facilitated Fe, As, and P migration via abiotic pathways-electron shuttling, ligand complexation, and competitive adsorption-as evidenced by sustained release in sterilized systems. Intriguingly, the decoupling of As from Fe after mid-term release suggests rapid re-adsorption or secondary mineral sequestration, complicating risk prognostics. Collectively, this work not only advances a conceptual framework for multi-element coupling at the DOM-mineral-microbe triple interface, but also provides critical insights for predicting groundwater quality trajectories under shifting DOM input regimes.},
}

@article {pmid42906382,
year = {2026},
author = {Haonan, Q and Shihong, Y and Guangmei, W and Jie, Z and Yi, X and Morellos, A and Xiaoling, L and Shide, D and Zewei, J and Hanwen, L and Jiazhen, H and Vázquez-Arellano, M and Mouazen, AM},
title = {Irrigation regime modulates the effects of organic amendments on soil quality and microbial carbon-degrading gene composition in saline-alkali soils.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131204},
doi = {10.1016/j.jenvman.2026.131204},
pmid = {42906382},
issn = {1095-8630},
abstract = {Soil salinization severely constrains agricultural productivity, highlighting the need to understand how irrigation regimes and organic amendment types jointly influence soil quality in salt-affected agroecosystems. However, their interactive effects on microbial communities and carbon-degradation-related functional potential remain poorly understood. Here, a two-year field experiment combined two irrigation regimes, W1 (irrigation triggered at -30 kPa soil matric potential for maize; 100 mm applied at jointing and grain-filling period for wheat) and W2 (-60 kPa; 60 mm), with three organic amendments (straw, manure, and biochar). Soil physicochemical properties, extracellular enzyme activities, microbial communities, metagenomic carbohydrate-active enzyme (CAZyme) profiles, and a soil quality index (SQI) were analyzed to characterize water-carbon coupling (the interaction between irrigation regime and organic amendment input). Irrigation regime strongly influenced amendment performance. In the 0-20 cm soil layer, W1B and W2M consistently exhibited higher microbial biomass carbon (MBC), carbon-cycling enzyme activities, and SQI than W1M and W2B in both years, whereas straw showed smaller differences between irrigation regimes for most indicators. Treatment effects were limited in the 20-40 cm layer. Water-carbon coupling did not significantly alter bacterial or fungal community composition but affected the abundance of nine carbon-degrading enzyme families. Families reaching significance occurred mainly in hemicellulose degradation (five of six families) and microbial-residue recycling (three of five), whereas few cellulose and no pectin- or starch-degrading families responded. The interaction-responsive families were correlated with MBC and with two of the five measured carbon-cycling enzymes, indicating that the treatment effects were reflected in functional gene composition rather than community composition. Based on soil indicators, the effectiveness of organic amendments is strongly governed by the irrigation regime, with biochar preferred under adequate irrigation and manure under deficit irrigation. Amendment selection should therefore follow water availability, providing practical guidance for the sustainable utilization of organic amendments in salt-affected agricultural systems.},
}

@article {pmid42906596,
year = {2026},
author = {Dos Anjos, TMC and Macedo, DB and Ferreira, VBC and Dantas, CWD and de Los Santos, EFF and Cardenas-Alegria, OV and Ramos, RTJ},
title = {Metagenomic Bioprospecting of Bioremediation-Related Genes in Amazonian Aquatic Ecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {},
pmid = {42906596},
issn = {1758-2229},
support = {//Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal do Pará/ ; //Universidade Federal do Pará/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 312316/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Secretaria de Estado de Ciência, Tecnologia, Educação Superior, Profissional e Tecnológica do Pará/ ; },
mesh = {*Biodegradation, Environmental ; *Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Brazil ; *Metagenome ; *Rivers/microbiology ; Ecosystem ; Mercury/metabolism ; Metals, Heavy/metabolism ; Copper/metabolism ; Hydrocarbons/metabolism ; },
abstract = {Environmental monitoring of contaminated freshwater systems still lacks curated genomic resources tailored to bioremediation-oriented screening. In this study, we developed a curated catalogue of 546 genes from 80 microbial species associated with heavy-metal resistance, hydrocarbon degradation, detoxification and related functions and applied it to river metagenomes from four municipalities in Pará, Brazilian Amazon: Altamira, Bragança, Marabá and Paragominas. Functional annotation was performed using eggNOG-mapper and metagenomic reads were aligned against the curated catalogue with Bowtie2. Mercury- and copper-related genes were the most frequently represented functional categories across all river systems, a pattern that may reflect both sequence representation in the metagenomes and the unequal composition of the curated reference catalogue. Bragança showed the largest detected gene repertoire, whereas diversity, Jaccard, UpSet and Dunn-based analyses revealed marked spatial heterogeneity and sites of localized functional enrichment. Recurrently associated bacterial taxa included Acinetobacter, Enterobacter, Pseudomonas, Stenotrophomonas, Cupriavidus and Sphingopyxis. These findings indicate that the catalogue provides a targeted genomic reference for environmental screening and bioprospecting, although metagenomic detection represents functional potential rather than experimentally confirmed remediation activity.},
}

*Biodegradation, Environmental
*Metagenomics
*Bacteria/genetics/classification/metabolism/isolation & purification
Brazil
*Metagenome
*Rivers/microbiology
Ecosystem
Mercury/metabolism
Metals, Heavy/metabolism
Copper/metabolism
Hydrocarbons/metabolism

@article {pmid42907021,
year = {2026},
author = {Lisboa, HM and Lima, J and Martins, ME and Monteiro, SS and Schnorr, C and Pasquali, MAB},
title = {CAZyme-guided modification of cactus and regional polysaccharides for food hydrocolloid applications.},
journal = {Carbohydrate polymers},
volume = {392},
number = {},
pages = {125895},
doi = {10.1016/j.carbpol.2026.125895},
pmid = {42907021},
issn = {1879-1344},
mesh = {*Opuntia/chemistry ; Colloids/chemistry ; *Pectins/chemistry/metabolism ; *Polysaccharides/chemistry ; Xylans/chemistry ; Plant Mucilage/chemistry ; },
abstract = {Food-hydrocolloid performance depends on polymer architecture and processing history rather than ingredient name alone. This critical narrative review evaluates CAZyme-guided modification of cactus-derived pectic materials and related regional polysaccharides for food hydrocolloid applications. Opuntia mucilage and pectic fractions are the focal substrates; non-cactus pectins provide the closest mechanistic evidence, and arabinoxylan is retained only as a bounded comparison for substitution and oxidative crosslinking. Starch is considered only as a limited process benchmark and is not used to infer cactus-polysaccharide behavior. The evidence is organized as four incomplete links: candidate selection, enzyme-to-edit, edit-to-property, and application validation. No study yet completes this chain for a food hydrocolloid, and cactus-associated microbiomes have not been shown to be superior CAZyme reservoirs. Candidate selection therefore requires reaction-specific annotation, multidomain and genomic-context analysis where relevant, expression, real-substrate kinetics, edit-state measurement, side-activity testing, and comparison with conventional hydrocolloids. Metagenomic discovery is treated as one prospective route to new catalysts, not as the evidentiary foundation of the current enzyme-to-material literature or as a validated production platform.},
}

*Opuntia/chemistry
Colloids/chemistry
*Pectins/chemistry/metabolism
*Polysaccharides/chemistry
Xylans/chemistry
Plant Mucilage/chemistry

@article {pmid42907460,
year = {2026},
author = {Khatib, L and Oles, R and Hernández, AR and Myers, T and Zhao, J and Kumar, M and Laroya, A and Tolosa-Enguis, V and Matsunami, N and Suzuki, D and Chiba, N and Gilbert, KE and Das, P and Sanders, JG and Patel, L and Litwin, N and Nowinski, B and Birmingham, A and Farmer, S and Brennan, C and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Cowart, C and Nizet, O and Diaz, EA and Veiga, P and Shetty, SA and Knol, J and Lay, C and Koutnikova, H and Chaumont, S and Tap, J and Cotillard, A and Derrien, M and Laiola, M and González, A and Tovar, AR and Torres, N and Sanz, Y and Yamada, T and McDonald, D and Song, SJ and Bartko, A and Knight, R},
title = {Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42907460},
issn = {2041-1723},
support = {T32 GM154642/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Mexico ; *Diet ; *Gastrointestinal Microbiome/genetics ; United States ; Japan ; Spain ; United Kingdom ; Metagenomics ; Geography ; Genetic Variation ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Male ; },
abstract = {Human diet and lifestyle vary widely across cultures, shaping global diversity in gut microbiome composition and function. However, comparable cross-population studies have been limited by methodological heterogeneity. The Human Diets and Microbiome Initiative (THDMI) integrates standardized recruitment, dietary assessment, and shotgun metagenomics across 1,976 participants from the United States, United Kingdom, Spain, Mexico, and Japan to disentangle biological from technical variation. We observed pronounced geographic differences in nutrient intake, food consumption, and microbial composition, with both shared and country-specific features linked to diet. Sparse canonical correlation and machine-learning analyses revealed that microbiome-diet associations were largely population-specific, with limited cross-country generalization. Strain-level analyses further uncovered significant genomic differentiation of gut microbes, consistent with localized dietary and ecological differences. Together, these results show that while core microbial responses to healthy eating exist, the structure and function of the human gut microbiome varies strongly with culture, geography, and long-term dietary practices.},
}

Humans
Mexico
*Diet
*Gastrointestinal Microbiome/genetics
United States
Japan
Spain
United Kingdom
Metagenomics
Geography
Genetic Variation
Female
Bacteria/classification/genetics/isolation & purification
Metagenome
Male

@article {pmid42907565,
year = {2026},
author = {Wu, XJ and Han, WX and Liang, C and Chen, J and Nicol, G and Rillig, MC and Zhu, D and Liu, BB and Wang, FH and Xiao, KQ and Zhu, YG},
title = {Soil viruses as key regulators of the microbial carbon pump in deep soils.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {42907565},
issn = {2397-334X},
abstract = {Deep soils store over half of terrestrial organic carbon, yet the viral mechanisms governing carbon persistence in subsurface contexts remain unclear. Here, by conducting a soil profile survey (0-700 cm) across four agroecosystems and a global synthesis of subsurface metagenomes, we established the Deep Soil Viral Resources Database, comprising 50,949 viral operational taxonomic units and 3,902 auxiliary metabolic genes (AMGs). Viral richness increased significantly with depth, accompanied by a shift towards lysogeny driven by declining carbon availability. The deep-soil virome carried AMGs and lysozymes involved in polymer degradation and cell endolysis. Viral endolysin significantly promoted necromass carbon accumulation, which contributed to increases in mineral-associated organic carbon. A synthesis of 138 global soil profiles further revealed a positive effect of viral abundance on soil organic carbon. Our findings establish a framework where viruses strengthen the microbial carbon pump in deep soils by facilitating host carbon scavenging via AMGs and promoting necromass formation via endolysin activity.},
}

@article {pmid42907919,
year = {2026},
author = {Danthanarayana, N and O'Dwyer, J and Goi, J and Latimore, S and Stevens, V and Pal, M and McSharry, BP and Hernandez-Jover, M and Pomat, W and Karl, S and Roby, JA and Forwood, JK and Neave, MJ and Williams, DT},
title = {Diversity of insect-specific viruses in Culex mosquitoes from Papua New Guinea.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42907919},
issn = {1743-422X},
mesh = {Animals ; *Culex/virology ; Papua New Guinea ; Genome, Viral ; Female ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; Virome ; Metagenomics ; Biodiversity ; *Mosquito Vectors/virology ; Genetic Variation ; Metagenome ; RNA Viruses/genetics/classification/isolation & purification ; },
abstract = {Insect-specific viruses (ISVs) are integral components of mosquito viromes, influencing virus evolution, vector competence, and arbovirus ecology. Papua New Guinea (PNG) is a region of exceptional biodiversity, yet ISVs in local mosquito populations remain poorly characterized. Here, we present the first comprehensive metagenomic survey of ISVs in Culex mosquitoes collected across five provinces of PNG between 2019 and 2021. Using unbiased shotgun metagenomic sequencing, 13,871 female Culex mosquitoes representing five species were analyzed across 86 samples. Approximately 1.6 billion paired-end reads were generated, yielding ∼20 million viral read pairs. Overall, 231 viral species representing 38 viral families were detected. Of these, 120 were ISV species spanning 25 viral families, and ISVs accounted for 93.8% of species-assigned viral reads, with RNA viruses predominating. The most abundant families included Partitiviridae, Birnaviridae, Rhabdoviridae, and Iflaviridae. Approximately 40% of viral reads corresponded to viruses that are not currently assigned to recognized ICTV families. More than 150 complete viral genomes or genome segments were recovered, including divergent sequences that share <90% amino acid identity with known references. Phylogenetic analyses revealed several divergent viral lineages across major ISV groups. Within the Partitiviridae, previously unrecognized RNA-dependent RNA polymerase (RdRP)-capsid pairings enabled reconstruction of complete genome architectures for Broome partiti-like virus 1 and Sonnbo virus for the first time, together with additional divergent partitivirus lineages. Cambodia Culex birnavirus sequences from PNG, clustered within the known lineage but formed a distinct regional clade. Rhabdovirus analyses identified host-restricted lineages, including Culex tritaeniorhynchus rhabdovirus-like sequences confined to Culex annulirostris. Within the Iflaviridae, several viruses were detected for the first time in PNG. Hubei virga-like virus 2 was the most abundant ISV detected and formed a PNG-specific clade, suggesting local diversification. ISVs were detected in both blood-fed and unfed mosquitoes, indicating that they are stable constituents of the mosquito virome. Multiple viral species from the same family were detected within pooled samples, consistent with either co-infection of individual mosquitoes or heterogeneous infections among pooled individuals. Overall, this study reveals a diverse ISV landscape in PNG Culex mosquitoes, expanding the known geographic range and genetic diversity of multiple viral groups and providing a baseline for future investigations into ISV ecology and evolution in the Indo-Pacific region and mosquito-virus interactions globally.},
}

Animals
*Culex/virology
Papua New Guinea
Genome, Viral
Female
Phylogeny
*Insect Viruses/genetics/classification/isolation & purification
Virome
Metagenomics
Biodiversity
*Mosquito Vectors/virology
Genetic Variation
Metagenome
RNA Viruses/genetics/classification/isolation & purification

@article {pmid42908097,
year = {2026},
author = {Silva, LHDSE and da Silva, SP and da Silva, FS and Hernández, LHA and Dias, DD and da Silva, SLS and Reis, LAM and Reis, HCF and do Nascimento, BLS and Brandão, RCF and Vieira, DBR and Nunes, BTD and Cruz, ACR and Nunes Neto, JP},
title = {Metagenomic detection and characterization of RNA viruses associated with Rhipicephalus linnaei (Audouin, 1826) ticks from the Amazon, Pará, Brazil.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70128},
pmid = {42908097},
issn = {1365-2915},
support = {88887.756798/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 314563/2026-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {In recent years, tick-borne viruses (TBVs) have gained significant prominence in public and veterinary health due to reports of fatal cases associated with vertebrates and the identification of a wide diversity of viruses in ixodid ticks through molecular techniques, particularly high-throughput sequencing. This study aims to investigate RNA viruses in Rhipicephalus linnaei ticks from two distinct regions of the state of Pará, in the Amazon, using a metagenomic approach. Specimens of Rhipicephalus linnaei were confirmed based on the COXI gene of their mitochondrial genome. We report the first record of Brown dog tick mivirus 1 (Mivirus rhipicephali; Family Chuviridae) and Brown dog tick phlebovirus 2 (Uukuvirus tobagoense; Family Phenuiviridae) in Brazil, as well as partial fragments of Uukuvirus tobagoense, Castanhal tick orthomyxovirus (Family Orthomyxoviridae), Guangdong tick quaranjavirus (Family Orthomyxoviridae), Alpharicinrhavirus taishun (Family Rhabdoviridae) and Zhangye Rhabd tick virus 1 (Family Rhabdoviridae). This research identified viruses with potential relevance to public and animal health and expands knowledge about the geographic distribution of viruses in tick populations, especially species of vector importance. In this context, studies on ixodid populations are essential to elucidate viral ecology, identify potential emerging agents and assess risks to public and animal health, contributing to the improvement of disease surveillance and prevention strategies.},
}

@article {pmid42908401,
year = {2026},
author = {Alekhin, D and Alon, M and Sidi, T and Mazeh, SP and Carmi, G and Finkel, OM and Erez, A},
title = {Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT.},
journal = {Nucleic acids research},
volume = {54},
number = {19},
pages = {},
pmid = {42908401},
issn = {1362-4962},
support = {1001577560//Israel Ministry of Science and Technology/ ; 101077278/ERC_/European Research Council/International ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Soil Microbiology ; Bacteria/classification/genetics ; Shotgun Sequencing ; *Software ; Algorithms ; },
abstract = {Shotgun metagenomes from complex environments such as soil uncover vast biodiversity. Yet most short reads produced by shotgun sequencing cannot be taxonomically or functionally annotated, as they lack a sufficiently comprehensive reference, obscuring the true structure and function of microbial communities. We introduce BBERT, a nucleotide large language model optimized for short reads. Testing on a large cohort of soil metagenomes, we found that BBERT identifies bacterial sequence syntax without relying on reference databases, enabling accurate assignment of taxonomic domain, coding potential, and reading frame directly from reads as short as 100 bp. BBERT is small and fast enough to analyze metagenomes using a modest GPU and can be used to convert short metagenomic reads directly to bacterial amino acid sequences for downstream applications. BBERT also improves de novo metagenomic assembly, reducing mismatches and gaps while accelerating runtime. Using metagenomes from wild legume nodules, we demonstrate that BBERT filtering improves bin quality while significantly accelerating de novo assembly. By providing fast, reference-free classification of short reads, BBERT unlocks large metagenomic archives for more accurate ecological and evolutionary analyses.},
}

*Metagenomics/methods
*Metagenome
Soil Microbiology
Bacteria/classification/genetics
Shotgun Sequencing
*Software
Algorithms

@article {pmid42908433,
year = {2026},
author = {Manciulea Profir, M and Ionescu, RF and Popescu Roşu, OA and Stancu, AC and Cucu, I and Cretoiu, SM and Pavelescu, LA},
title = {From Clinical Question to Defensible Inference: A Decision Framework for Integrated Gut Microbiome-Metabolome Studies.},
journal = {Romanian journal of internal medicine = Revue roumaine de medecine interne},
volume = {},
number = {},
pages = {},
doi = {10.2478/rjim-2026-0022},
pmid = {42908433},
issn = {2501-062X},
abstract = {The rapid expansion of microbiome and metabolome technologies has transformed the study of host-microbial interactions, but methodological choices are still often driven by technical availability rather than by the question and intended claim. This review examines how biological compartment, microbiome profiling, metabolomics platform, data-integration strategy and validation determine the strength of inference in integrated gut microbiome-metabolome research. We distinguish descriptive association from functional interpretation, clinical prediction and causal evidence, and identify the analytical safeguards required for credible biomarker development. We then propose a five-stage decision framework that begins with definition of the intended scientific or clinical claim, links that claim to compartment and analytical resolution, selects integration according to purpose, and limits interpretation to the achieved validation level. Building on recent calls for question-driven multi-omics integration, its practical contribution is to connect prospective design choices to the intended claim and make the weakest validated component of the analytical chain - rather than technology choice alone - the explicit ceiling for the permissible claim, illustrated by two worked design examples. This question-driven approach is intended to improve design transparency, reproducibility and the responsible clinical translation of integrated microbiome-metabolome studies.},
}

@article {pmid42908571,
year = {2026},
author = {Yang, X and Li, M and Zhu, Y and Tao, X and Cheng, Y},
title = {Case Report: Delayed-onset and recurrent infectious endophthalmitis after intravitreal dexamethasone implant.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1962200},
pmid = {42908571},
issn = {2296-858X},
abstract = {PURPOSE: To report a rare case of delayed-onset infectious endophthalmitis occurring 33 days after an intravitreal dexamethasone implant (Ozurdex®), with recurrence 20 days after complete pars plana vitrectomy and implant removal.

METHODS: Case report with clinical findings, diagnostic workup, management, and literature review.

RESULTS: A 51-year-old male with recurrent anterior uveitis received a dexamethasone implant for refractory cystoid macular edema. Thirty-three days post-injection, he developed acute hypopyon and severe vitritis. Emergent 25-gauge pars plana vitrectomy with implant removal was performed. Aqueous humor metagenomic next-generation sequencing (mNGS) confirmed Staphylococcus epidermidis (24,904 reads; 99.96% relative abundance), with no resistance genes detected. Postoperatively, inflammation initially resolved; however, hypopyon recurred 20 days after vitrectomy. A 6-day course of intravenous vancomycin achieved complete resolution. At final follow-up, best-corrected visual acuity improved to 20/33, with no further recurrence.

CONCLUSION: Endophthalmitis following corticosteroid implants may present with delayed-onset and can recur even after complete surgical removal. Systemic antimicrobial therapy may play a crucial role in eradicating residual infection in such challenging cases.},
}

@article {pmid42908594,
year = {2026},
author = {Ma, Y and Lu, Y and Geng, M and Wang, Y and Chen, WH},
title = {Baseline co-occurrence of Faecalibacterium prausnitzii and Ruminococcus bromii is associated with greater increases in selected short-chain fatty acid-related pathways following resistant starch type 2 intervention across diverse populations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1959463},
pmid = {42908594},
issn = {1664-302X},
abstract = {Type 2 resistant starch (RS2) can be fermented by the gut microbiota and contribute to short-chain fatty acid (SCFA) production; however, microbial responses to resistant starch vary substantially across individuals and populations, and the role of baseline microbiota in this variability remains incompletely understood. In this study, we integrated four publicly available paired metagenomic datasets representing diverse experimental and host contexts and performed cross-dataset analyses of taxonomic and functional responses. Faecalibacterium prausnitzii was among the taxa consistently enriched after resistant starch-related intervention or exposure across multiple datasets. Exploratory baseline stratification further suggested that the presence of F. prausnitzii was associated with changes in selected SCFA- and carbohydrate metabolism-related pathways. We subsequently examined its relationships with the representative resistant starch degraders Ruminococcus bromii and Bifidobacterium adolescentis. Baseline association analyses identified a reproducible positive association between R. bromii and F. prausnitzii. In cohort-adjusted analyses of mutually exclusive microbial configurations, the Fp + Rb configuration was associated with greater increases in the acetate/lactate-related pathways P41-PWY and PWY-5100 than the Fp + Rb + Ba configuration, whereas no significant differences were observed for the other selected SCFA-related pathways. Continuous abundance analyses provided no significant evidence for abundance-dependent effects of Rb or Fp or for an Rb × Fp interaction. These findings identify baseline Fp + Rb co-occurrence as a hypothesis-generating microbial configuration associated with responses in selected SCFA-related pathways and provide a basis for independent experimental validation.},
}

@article {pmid42908611,
year = {2026},
author = {Li, J and Liao, Y and Li, X and Lin, L and Liu, Y and Li, W and Huang, Z and Wu, Z and Fang, X and Zhang, W},
title = {Metagenomic next-generation sequencing in tuberculous periprosthetic joint infection: pathogen-detection yield and clinical characteristics compared with common bacterial PJI.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1935713},
pmid = {42908611},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis ; Female ; Retrospective Studies ; Male ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Aged ; *Metagenomics/methods ; Middle Aged ; Aged, 80 and over ; },
abstract = {OBJECTIVE: To compare the pathogen-detection yield of metagenomic next-generation sequencing (mNGS) and conventional culture in tuberculous periprosthetic joint infection (TB-PJI) and common bacterial PJI (CB-PJI), and to characterize clinical differences and exploratory associations with TB-PJI.

METHODS: A retrospective cohort included 197 patients with periprosthetic joint infection treated between January 2016 and June 2024 who underwent both conventional culture and mNGS during the same diagnostic or surgical episode. Patients were classified as CB-PJI (n=178) or TB-PJI (n=19). Paired pathogen-detection rates were compared using McNemar's test. Exploratory multivariable associations with TB-PJI were assessed using Firth penalized logistic regression with the Charlson Comorbidity Index (CCI) modeled continuously.

RESULTS: In CB-PJI, mNGS showed a higher pathogen-detection rate than conventional bacterial culture (94.4% vs. 78.1%, P<0.001). In TB-PJI, Mycobacterium tuberculosis complex (MTBC) was detected by mNGS in 17/19 cases (89.5%) and recovered by mycobacterial culture in 5/19 cases (26.3%; P<0.001); 12/19 cases were mNGS-positive/mycobacterial-culture-negative. In the primary exploratory Firth model, each 1-point increase in CCI was associated with higher odds of TB-PJI (aOR=2.39, 95% CI: 1.51-4.10, P<0.001), whereas each 10% increase in SF PMN% was associated with lower odds (aOR=0.722, 95% CI: 0.564-0.917, P = 0.009); BMI was not statistically significant. Drug-related complications were more frequent in TB-PJI (42.1% vs. 11.8%, P = 0.002), while the 2-year infection recurrence rate did not differ significantly (15.8% vs. 7.9%, P = 0.216).

CONCLUSION: In this selected retrospective cohort, mNGS provided a higher pathogen-detection yield than conventional culture, particularly for TB-PJI. Higher CCI and lower SF PMN% were exploratory clinical associations with TB-PJI and should not be interpreted as validated diagnostic thresholds. mNGS should be considered an adjunct to mycobacterial culture, molecular testing, and histopathology rather than a stand-alone diagnostic test.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Prosthesis-Related Infections/microbiology/diagnosis
Female
Retrospective Studies
Male
*Mycobacterium tuberculosis/genetics/isolation & purification
Aged
*Metagenomics/methods
Middle Aged
Aged, 80 and over

@article {pmid42908641,
year = {2026},
author = {Li, L and Xing, Z and Liu, L and Mu, X and Zhai, Y and Luan, S and Li, J and Guo, Q},
title = {Mycobacterium mageritense submandibular lymphadenitis in children: diagnostic challenges and the role of metagenomic next-generation sequencing: two case reports and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1936269},
pmid = {42908641},
issn = {2296-858X},
abstract = {Mycobacterium mageritense is an extremely rare, rapidly growing nontuberculous mycobacterium (NTM). Pediatric cases are rarely reported worldwide, and the non-specific clinical manifestations, low sensitivity of conventional microbiological tests, and limited specimen volume from children often lead to diagnostic delays. We describe the clinical data of two immunocompetent children with submandibular lymphadenitis caused by Mycobacterium mageritense, both diagnosed by metagenomic next-generation sequencing (mNGS). We also systematically reviewed the relevant literature and performed a pooled analysis of 36 eligible cases (the two new paediatric cases from the present study included). Case 1 involved a 6-year-old girl with dental caries and acute fever who was initially misdiagnosed with common bacterial infection and received ineffective empirical antibiotics for over two weeks; mNGS of aspirated pus confirmed the diagnosis. Case 2 involved a 9-year-old girl with dental caries who presented only with submandibular lymphadenopathy and normal laboratory findings, with a diagnostic delay of up to two months; mNGS of lymph node tissue identified the pathogen. Literature-pooled analysis of 36 patients revealed a mean diagnostic delay of 4.69 months (median 2.00 months, IQR: 0.81-5.75 months). Conventional culture had low sensitivity, often requiring prolonged incubation (≥96 h) or special media to obtain positive results. Initial misdiagnosis occurred in 17.6% of cases. Patients diagnosed by NGS achieved more rapid and accurate pathogen identification. This report suggests that mNGS, as a culture-independent, unbiased pan-pathogen detection technique, shows clear advantages in identifying rare and fastidious pathogens such as M. mageritense. For pediatric patients with dental caries, fever, and cervical lymphadenopathy unresponsive to conventional therapy, clinicians should suspect Mycobacterium mageritense infection, and mNGS is an effective tool for its rapid and accurate diagnosis.},
}

@article {pmid42908652,
year = {2026},
author = {Yang, Z and Yan, Y and Wang, H and Zhou, H and Zheng, M},
title = {Case Report: Klebsiella pneumoniae-associated pyogenic spondylitis and occult intrahepatic cholangiocarcinoma during calculous cholangitis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1967835},
pmid = {42908652},
issn = {2296-858X},
abstract = {BACKGROUND: Klebsiella pneumoniae is a common Gram-negative pathogen in biliary tract infections and may cause deep-seated infection following bacteremia, although vertebral involvement is uncommon. Severe biliary infection and stone disease may also complicate the recognition of coexisting hepatic malignancy.

CASE PRESENTATION: A 51-year-old woman presented with calculous acute obstructive suppurative cholangitis complicated by septic shock and multiorgan dysfunction. Blood and bile cultures yielded Klebsiella pneumoniae, and her condition improved after urgent biliary drainage and antimicrobial therapy. During a subsequent admission, she developed progressive low-back pain. Lumbar magnetic resonance imaging showed abnormalities involving the L3/4 vertebrae and adjacent paravertebral tissues, initially raising suspicion of spinal tuberculosis. Vertebral biopsy demonstrated focal suppurative inflammation, and metagenomic next-generation sequencing of the same tissue detected 33,735 K. pneumoniae-specific reads, with a relative abundance of 82.18% and genome coverage of 59.7%, together with multiple hypervirulence-associated determinants. These findings supported a diagnosis of K. pneumoniae-associated pyogenic spondylitis. Meanwhile, serial hepatobiliary imaging showed regression of the right hepatic abnormalities as the infection improved, whereas a focal lesion in the left liver persisted. Subsequent imaging raised suspicion of cholangiocarcinoma, and histopathologic examination after surgical resection confirmed poorly differentiated intrahepatic cholangiocarcinoma.

CONCLUSION: This case underscores the importance of maintaining diagnostic vigilance even after an initial diagnosis has been established. New focal symptoms or abnormalities that persist or follow a different clinical course should not be automatically attributed to the original disease process, and the possibility of additional coexisting diagnoses should remain under consideration.},
}

@article {pmid42908874,
year = {2026},
author = {Jie, Y and Yang, X and Lou, P and Chen, W},
title = {Pulsatilla decoction attenuates colorectal cancer progression in association with gut microbiota remodeling, T-cell immune restoration, and NF-κB/JAK2/STAT3 signaling suppression.},
journal = {American journal of cancer research},
volume = {16},
number = {9},
pages = {4170-4188},
pmid = {42908874},
issn = {2156-6976},
abstract = {Pulsatilla Decoction (PD) exhibits anti-inflammatory properties, but its impact on colorectal cancer (CRC) and the role of gut microbiota remain incompletely understood. This study investigated the antitumor effects of PD in a xenograft mouse model of HCT116 cells reconstituted with human peripheral blood mononuclear cells. We also analyzed corresponding changes in gut microbiota, T-cell immunity, inflammatory responses, and NF-κB/JAK2/STAT3 signaling. Tumor-bearing mice were treated for three weeks with low-, medium-, or high-dose PD, or with 5-fluorouracil. Gut microbiota composition and function were analyzed using 16S rRNA and metagenomic sequencing. Immune cell populations, cytokines, and pathway-related proteins were assessed via flow cytometry, immunofluorescence, ELISA, RT-qPCR, and western blotting. To further evaluate the involvement of microbiota, we performed antibiotic pretreatment followed by fecal microbiota transplantation (FMT). PD effectively reduced tumor volume and weight without causing significant body weight loss. High-dose PD partially restored microbial diversity and community structure, increased Akkermansia muciniphila, and modulated inflammation- and metabolism-related microbial pathways. Furthermore, PD enhanced peripheral and intratumoral CD4[+] and CD8[+] T-cell responses, improved the splenic Treg/Th17 balance, decreased TNF-α, IL-6, and IL-17A, increased IL-10, and suppressed NF-κB, JAK2, and STAT3 activation in tumor tissues. FMT from high-dose PD-treated donors partially transferred tumor inhibition, increased tumor CD8A and granzyme B, reduced Foxp3, and lowered NF-κB, JAK2, and STAT3 levels in recipient mice not directly treated with PD. These findings suggest that PD inhibits CRC progression by coordinately modulating gut microbiota, T-cell immunity, inflammation, and NF-κB/JAK2/STAT3 signaling, with the gut microbiota partially contributing to its antitumor effects.},
}

@article {pmid42908916,
year = {2026},
author = {Yang, L and Guo, C and Zhao, Q and Yang, J and Zhang, H and Zhai, Y and Ma, Y},
title = {Clinical validation of a novel multiplex real-time PCR for diagnosing community-acquired pneumonia in the emergency department: a promising diagnostic tool for Mycoplasma pneumoniae.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1979614},
pmid = {42908916},
issn = {1664-302X},
abstract = {Community-acquired pneumonia (CAP) is a global public health burden with high morbidity, but timely diagnosis is hindered by limitations of conventional methods. We validated a novel multiplex real-time PCR (mRT-PCR) for CAP diagnosis in the emergency department, focusing on Mycoplasma pneumoniae (M. pneumoniae). A retrospective cohort of 371 CAP patients (2019-2021) from the Chinese PLA General Hospital was enrolled. The panel targeted 85 pathogens (40 bacteria, 18 viruses, 17 fungi, 10 other) plus 8 resistance genes, with a turnaround time (TAT) under 4 h and a cost of approximately US$100 per test. mRT-PCR showed performance comparable to mNGS for common pathogens (concordance >69% for bacteria/fungi) and high concordance with the final clinical diagnosis. Notably, it detected M. pneumoniae in 36.7% (136/371) of cases, outperforming conventional methods by identifying 204 exclusive positives (55.0% of cohort), with M. pneumoniae (40%) and viruses (30%) predominating. Polymicrobial infections occurred in 36.1% of cases; M. pneumoniae co-infections (38 cases) showed elevated neutrophils and reduced lymphocytes vs. single infections. An independent reference standard analysis excluding both index tests showed that 24.1% (210/873) of calls were independently corroborated - high for influenza, SARS-CoV-2 and M. pneumoniae, lower for S. pneumoniae, consistent with the limited sensitivity of sputum culture. Unlike conventional syndromic panels such as FilmArray, which profile fewer targets without concurrent resistance-gene detection, this mRT-PCR combines broad coverage with rapid TAT and low cost, making it promising for timely CAP diagnosis, particularly in resource-limited settings and for targeted therapy.},
}

@article {pmid42908966,
year = {2026},
author = {Jiang, L and Wu, D and Li, E and Li, W and Liu, Y and Li, X and Yang, G and Lv, G},
title = {Differences in microbial composition and salt tolerance between rhizosphere and bulk soil of Kalidium foliatum.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1920612},
pmid = {42908966},
issn = {1664-462X},
abstract = {Salt is an important abiotic stress that affects plant growth. Research has shown that plants can recruit beneficial microorganisms from the surrounding soil. However, the ecological functions of the rhizosphere microbiome in salt tolerant plants have not been explored to a large extent. Based on this, this study took the halophyte K. foliatum as the research object, and used metagenomics technology to analyze the differences in microbial composition and salt tolerance functional genes between the rhizosphere and bulk soil of K. foliatum in different salt habitats, providing new theoretical basis for salt alkali management. The results showed that the dominant groups in the rhizosphere soil microbial community of K. foliatum under two salt habitats were Actinobacteria, Proteobacteria, Bacteroidetes, and Chloroflexi. The abundance of 49 genera in Actinobacteria in high salt rhizosphere were significantly higher than that in low salt rhizosphere. These microorganisms belong to soil salt tolerant and halophilic microorganisms, and have the ability to improve plant salt tolerance. In high salt habitat, the expression of genes related to ion transport (nqrA, nhaC, rnfC, chaA, and yrbG) and the synthesis of osmoregulatory substances (proP, ectA) was significantly increased. These genes are associated with Na[+], K[+], Mg[2+], proline and ectoine involved in transport or synthesis. The correlation indicates that halophilic archaea have a greater impact on functional genes than other microorganisms, suggesting that halophilic bacteria have a more prominent ability to regulate salt tolerance of K. foliatum.},
}

@article {pmid42909071,
year = {2026},
author = {Wang, T and Xie, Y and Liu, S and Xin, Y and You, J and Zeng, H and Wang, H and Li, Y and Li, B and Chen, X and Liu, X and Liang, J and Shi, C},
title = {Virome dynamics of Aedes albopictus during the 2025 chikungunya outbreak in Foshan.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100667},
pmid = {42909071},
issn = {2666-5174},
abstract = {Chikungunya virus (CHIKV) has re-emerged globally, yet little is known about how natural CHIKV transmission influences the resident virome of mosquito vectors under field conditions. Here, we combined continuous entomological surveillance, viral genomics and metagenomic sequencing to characterize CHIKV transmission and virome dynamics in Aedes albopictus during the 2025 chikungunya outbreak in Foshan, China. Mosquitoes were continuously collected throughout the outbreak using pooled and individual sampling strategies, and viral metagenomic sequencing was performed to compare virome composition between CHIKV-positive and CHIKV-negative mosquitoes. CHIKV-positive mosquitoes first appeared shortly after the onset of local human transmission and expanded geographically in parallel with the epidemic. Mosquito- and human-derived CHIKV genomes were nearly identical and belonged to a genetically homogeneous East/Central/South African (ECSA) lineage, supporting sustained local mosquito-human transmission. Despite widespread CHIKV circulation, the resident mosquito virome remained broadly stable, with sampling time contributing more to virome variation than CHIKV infection status. Only two resident viruses, Orthophasmavirus barstukorius and Guato virus, were significantly associated with CHIKV infection. Integration of pooled and individual sequencing further showed that pooled samples reliably represented the population-level core virome, whereas individual mosquitoes revealed substantial inter-individual heterogeneity. Five previously undescribed RNA viruses were also identified, expanding the known virosphere of Ae. albopictus. Together, our findings show that natural CHIKV emergence is accompanied by limited species-specific shifts rather than wholesale restructuring of the resident mosquito virome, and highlight the value of integrating genomic and metagenomic surveillance into vector-borne disease monitoring.},
}

@article {pmid42909078,
year = {2026},
author = {Sinha, A and Murmu, J and Singh, S and Pal, A and Mallick, U and Mishra, P and Sahoo, KC and Sahu, MC and Pati, S},
title = {Environmental occurrence and dissemination of colistin resistance in contaminated aquatic systems: a systematic review of eight observational studies.},
journal = {Frontiers in antibiotics},
volume = {5},
number = {},
pages = {1970443},
pmid = {42909078},
issn = {2813-2467},
abstract = {INTRODUCTION: Colistin is a last-resort antibiotic used against multidrug-resistant Gram-negative bacterial infections. The emergence of plasmid-mediated colistin resistance, particularly mcr genes, has raised concerns about the environmental persistence and dissemination of resistance determinants. Aquatic environments may serve as reservoirs and dissemination pathways for colistin resistance; however, the available evidence remains fragmented. This systematic review aimed to synthesize evidence on the occurrence, resistance mechanisms, and environmental and potential public health implications of colistin resistance in contaminated aquatic systems.

METHODS: A systematic literature search was conducted in five electronic databases up to December 2024 in accordance with PRISMA guidelines. Studies investigating colistin resistance in wastewater, surface water, aquaculture systems, and related aquatic environmental matrices were eligible for inclusion. Following screening and eligibility assessment, eight observational studies were included. Owing to substantial methodological and outcome heterogeneity, a narrative synthesis was performed. Isolate-level phenotypic resistance, sample- or site-level molecular positivity, and metagenomic relative gene abundance were analyzed as separate, non-comparable outcome strata.

RESULTS: A total of 26,740 records were retrieved, of which 20,691 unique records were screened after removal of duplicates. Eight studies met the predefined eligibility criteria. The studies investigated diverse aquatic environments, including slaughterhouse effluents, municipal wastewater, urban rivers, aquaculture systems, and wastewater-associated bioaerosols. Plasmid-mediated mcr genes were identified across several environmental settings and frequently occurred alongside other antimicrobial resistance determinants. Chromosomal mechanisms of colistin resistance were also reported. The reported resistance measures varied substantially between studies, ranging from isolate-level phenotypic resistance and sample/site-level molecular detection to metagenomic relative abundance.

DISCUSSION: The available evidence indicates that contaminated aquatic environments can harbor colistin resistance determinants and may contribute to their environmental dissemination. However, the limited number of eligible studies and substantial methodological heterogeneity prevent direct quantitative comparison or estimation of a common environmental prevalence. Standardized surveillance approaches integrating culture-based methods, molecular detection, and genomic/metagenomic characterization are needed to improve comparability and clarify the environmental pathways of colistin resistance within a One Health framework.

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024613277.},
}

@article {pmid42909159,
year = {2026},
author = {Erira, A and Robayo, DAG and Gamboa, FO and Chala Galindo, AI and Moreno Torres, A and Arregui, AC and Muñoz, E and Noguera Polania, JF and Tosse, FT},
title = {Bacterial metagenome in plaque, saliva, and tumor samples from individuals with and without OSCC by next-generation sequencing.},
journal = {GigaByte (Hong Kong, China)},
volume = {2026},
number = {},
pages = {gigabyte189},
pmid = {42909159},
issn = {2709-4715},
abstract = {BACKGROUND: Oral dysbiosis has been associated with oral squamous cell carcinoma (OSCC); however, most microbiome studies rely on 16S ribosomal RNA (rRNA) gene sequencing, limiting species-level taxonomic resolution.

METHODS: Dental plaque, saliva, and tumor tissue samples from 10 patients with OSCC and dental plaque and saliva samples from 10 healthy controls were analyzed in this exploratory cross-sectional study. DNA was extracted and subjected to shotgun metagenomic sequencing using the Illumina MiSeq platform. Sequence reads were quality filtered with fastp, taxonomically classified using Kraken2 v2.1.3, and species-level abundances were re-estimated with Bracken v2.9 following the removal of human reads and low abundance taxa. Relative abundances were compared using the Mann-Whitney U test with the Benjamini-Hochberg false discovery rate correction, while the Bray-Curtis principal coordinate analysis was used as an exploratory approach to visualize microbial community patterns.

RESULTS: Shotgun metagenomic sequencing revealed distinct bacterial community profiles across the oral microenvironment. Dental plaque exhibited the highest taxonomic diversity and relative abundance. The control plaque was enriched in Streptococcus koreensis, Capnocytophaga sp. oral taxon 878, Treponema sp. Marseille Q4132, and Leptotrichia sp. oral taxon 498, whereas the plaque from patients with OSCC showed a higher relative abundance of Pyramidobacter piscolens, Parvimonas parva, and Gemella sanguinis. Salivary samples displayed lower diversity and a more homogeneous composition, predominantly comprising Capnocytophaga endodontalis, Prevotella jejuni, Aggregatibacter aphrophilus, and Gemella sanguinis. The tumor tissue showed relatively higher abundance of Sellimonas catena, Escherichia coli, Solobacterium moorei, and Lacrimispora sp. HJ-01.

CONCLUSIONS: This exploratory study provides species-level characterization of the oral microbiome across multiple oral microenvironments in OSCC and generates hypotheses for future integrative metagenomic and functional studies investigating the potential contribution of oral bacterial communities to OSCC pathogenesis.},
}

@article {pmid42909340,
year = {2027},
author = {Tian, H and Zhu, L and Zhang, Y and Chen, M and Zuo, X and Wu, Y and Wang, H and Lv, Z and Huang, Q and Wu, M and Wu, E and Zeng, J and Wang, X},
title = {Gut microbial histamine and serotonin promote cerebrovascular angiogenesis: Evidence from moyamoya disease.},
journal = {Genes & diseases},
volume = {14},
number = {2},
pages = {102306},
pmid = {42909340},
issn = {2352-3042},
abstract = {Moyamoya disease (MMD) is a progressive cerebrovascular disorder characterized by arterial stenosis and compensatory neovascularization, but its upstream drivers remain poorly defined. Here, we identify Bifidobacterium pseudocatenulatum (B. pseudocatenulatum), a traditionally probiotic species, as a context-dependent pathobiont. Integrated metagenomic and metabolomic analyses revealed enrichment of B. pseudocatenulatum in MMD, closely associated with elevated microbial-derived histamine and serotonin. In mice, chronic oral administration of B. pseudocatenulatum disrupted intestinal barrier integrity and increased gut microbial production and systemic levels of histamine and serotonin. These changes were accompanied by systemic inflammation and activation of angiogenic pathways, which together promoted MMD-relevant cerebrovascular remodeling in experimental models. Notably, direct administration of histamine or serotonin to mice reproduced key MMD-like vascular phenotypes, supporting the conclusion that these microbial metabolites are sufficient to induce selected MMD-relevant vascular changes in experimental models. Our findings propose a microbial-metabolite-vascular axis and suggest that the role of specific Bifidobacterium strains may be more nuanced than previously recognized. These results provide a mechanistic framework for understanding the gut-brain axis in neurovascular pathology and nominate the microbiome and its metabolic products as potential targets for non-invasive diagnostics and precision therapeutic interventions in MMD.},
}

@article {pmid42909663,
year = {2026},
author = {Chaves, VA and Martins, DT and Dantas, CWD and da Silva, SM and da Silva, JAG and Queiroz Cavalcante, AL and Macedo, DB and Fernandes, ALL and Tiwari, S and Ramos, RTJ and Cardenas-Alegria, OV},
title = {Prospecting for efflux pump and repressor genes in rivers of the Amazon region of Brazil.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42909663},
issn = {1573-4978},
support = {312316/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Brazil ; *Rivers/microbiology ; Bacteria/genetics ; Bacterial Proteins/genetics ; *Membrane Transport Proteins/genetics ; *Repressor Proteins/genetics ; Water Microbiology ; Metagenomics/methods ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: The spread of multidrug-resistant bacteria in water bodies poses a significant public health concern. Efflux pumps represent critical mechanisms of antimicrobial resistance, regulated by genetic repressors that aid bacterial adaptation to environmental stress. This study profiles the diversity of efflux pump genes and genetic repressors in the surface waters of the Cereja (Bragança) and Uraim (Paragominas) rivers in the Amazon region of Brazil.

METHODS AND RESULTS: Surface water samples were collected along a gradient of anthropogenic impact, and environmental DNA was sequenced on the Illumina platform. The resulting sequencing data were subsequently subjected to metagenomic analysis, which identified a higher abundance of efflux pump genes in the Cereja River compared to the Uraim River, dominated by the RND and SMR families. Additionally, two-component system (TCS) repressor genes, particularly cbrB, were successfully recovered and modeled using Swiss-Model homology modeling.

CONCLUSIONS: The higher coverage of the cbrB repressor gene in anthropogenically impacted sites underscores its regulatory role in bacterial stress responses, suggesting its potential application as a novel biomarker of environmental pollution and antibiotic resistance spread in aquatic ecosystems.},
}

Brazil
*Rivers/microbiology
Bacteria/genetics
Bacterial Proteins/genetics
*Membrane Transport Proteins/genetics
*Repressor Proteins/genetics
Water Microbiology
Metagenomics/methods
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid42909692,
year = {2026},
author = {da Silva E Silva, LH and da Silva, SP and de Castro, PHG and Maurício, KD and da Silva, FS and Dias, DD and Hernández, LHA and da Silva, SLS and Reis, HCF and Dos Santos, LEC and do Nascimento, BLS and Brandão, RCF and Vieira, DBR and Nunes, BTD and Cruz, ACR and Nunes Neto, JP},
title = {Detection, characterization, and evolutionary inferences regarding a novel virus identified in Amblyomma dissimile Koch, 1844 (Acari: Ixodidae) from the Amazon, Pará, Brazil.},
journal = {Archives of virology},
volume = {171},
number = {11},
pages = {},
pmid = {42909692},
issn = {1432-8798},
support = {88887.756798/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 314563/2026-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Brazil ; Phylogeny ; *Amblyomma/virology ; RNA, Viral/genetics ; *Rhabdoviridae/genetics/isolation & purification/classification ; Genome, Viral ; Evolution, Molecular ; *Ixodidae/virology ; Metagenomics ; },
abstract = {Ticks are among the primary vectors of infectious agents of medical and veterinary importance, second only to mosquitoes in the number of pathogens transmitted to humans. These arthropods are capable of transmitting a wide diversity of microorganisms, including protozoa, bacteria, and viruses. Notable among tick-borne viruses are those associated with viral encephalitis, which cause severe acute and chronic neurological infections in humans. This study aimed to characterize the RNA virome of an Amblyomma dissimile specimen collected from a Boa constrictor rescued in the municipality of Ananindeua, Pará state, in the Brazilian Amazon, using an RNA metagenomic sequencing approach. A total of eleven viral sequences were identified, distributed across five families: Chuviridae (n = 2), Rhabdoviridae (n = 2), Orthomyxoviridae (n = 5), Nodaviridae (n = 1), and Orthototiviridae (n = 1). A key finding was the identification of Dissimile tick rhabdovirus a potential new member of the Rhabdoviridae family described here for the first time, with no prior records in the scientific literature. Additionally, segments of Granville quaranjavirus were detected in Brazil for the first time, expanding the known geographic distribution of this virus. These results highlight the underrepresentation of viral diversity associated with Brazilian ticks in reference databases, underscoring the need to expand metagenomic surveillance and virological characterization efforts in the country, particularly given the potential impacts of climate change on tick distribution and virus circulation dynamics.},
}

Animals
Brazil
Phylogeny
*Amblyomma/virology
RNA, Viral/genetics
*Rhabdoviridae/genetics/isolation & purification/classification
Genome, Viral
Evolution, Molecular
*Ixodidae/virology
Metagenomics

@article {pmid42909972,
year = {2026},
author = {Becker, CC and Cauvin, AR and Neely, KL and Dennison, CE and Baker, AC and Walker, BK and Meyer, JL},
title = {Markers of resilience to stony coral tissue loss disease and putative probiotic functions in the microbiomes of the coral, Orbicella faveolata.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag278},
pmid = {42909972},
issn = {2730-6151},
abstract = {Stony coral tissue loss disease (SCTLD) is widespread within the Caribbean and affects at least 22 species of reef-building coral. Bacteria have been implicated in the etiology of SCTLD, but the community of bacteria and archaea may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to SCTLD resistance, we sequenced metagenomes from 41 colonies of the threatened coral, Orbicella faveolata, in the lower Florida Keys. All colonies were fate-tracked for 4 to 5 years, treated with amoxicillin if needed to prevent SCTLD-related mortality, and categorized into 4 health status categories following the monitoring period: never diseased (20%), diseased before sampling but recovered (10%), apparently healthy during sampling but eventually diseased (22%), and diseased (49%). Within the coral microbiome, diseased and yet-to-be diseased colonies exhibited higher variability in functional genes. In contrast, corals that remained unaffected or recovered had less variable microbiomes with greater abundances of vitamin and antibiotic biosynthesis, secretion system, and quorum-sensing genes that may support host health and resilience to pathogens. Despite repeated antibiotic treatments on some colonies, there was no effect on the diversity of beta-lactamases, antibiotic resistance genes that may confer amoxicillin resistance. Additional potentially probiotic gene clusters for the production of antimicrobial and bioactive compounds were present in many colonies regardless of fate. Taken together, we find significant putative probiotic functions in the coral microbiome to armor host O. faveolata corals against SCTLD infection, which may underpin intraspecific variation in stony coral tissue loss disease resilience and susceptibility.},
}

@article {pmid42909991,
year = {2026},
author = {Viera Heredia, FJ and Zambrano Narváez, EJ and Yánez Pilco, AM and Escudero Andino, TM and Fernández Gómez, DA and Gallardo Larreina, NA and Fuentes Lara, PA and Salazar Heredia, LA},
title = {Chronic Complications Following Dengue Infection: A Scoping Review.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e116633},
pmid = {42909991},
issn = {2168-8184},
abstract = {Dengue virus infection has increased substantially in Latin America, prompting epidemiological alerts from regional health authorities in recent years. While most published research focuses on the acute phase, chronic multisystemic sequelae remain poorly characterized. This scoping review aimed to identify and describe chronic complications in adult patients following dengue infection, as reported in the available scientific literature. A scoping review was conducted following the PRISMA-ScR guidelines. A structured Population, Concept, Context (PCC) question guided searches of PubMed (National Library of Medicine, Bethesda, Maryland), Scopus (Elsevier, Amsterdam, the Netherlands), Google Scholar (Google, Mountain View, California), EMBASE (Elsevier, Amsterdam, the Netherlands), Cochrane Library (John Wiley & Sons, Hoboken, New Jersey), and LILACS (BIREME, São Paulo, Brazil), and gray literature from January 2005 to June 15, 2026. Articles were screened independently by eight reviewers using Rayyan; inter-rater reliability was assessed using Fleiss' kappa (κ = 0.81, 95% CI: 0.74-0.88), and disagreements were resolved by consensus. Of the 222 identified records, 62 studies met the inclusion criteria after deduplication and full-text screening. Neurological complications were the most frequently represented category among the included publications (30.6%, n = 19), followed by ophthalmological (19.4%, n = 12), heterogeneous persistent symptoms (12.9%, n = 8), fatigue (9.7%, n = 6), multisystemic (9.7%, n = 6), psychiatric (9.7%, n = 6), cardiological (4.8%, n = 3), and immunological (3.2%, n = 2) complications. These proportions reflect the distribution of the published literature rather than the clinical prevalence of complications among dengue patients, given that approximately one-third of the included studies were case reports or case series. The evidence base includes the largest population-based cohort of post-acute dengue sequelae to date (n = 55,870, Singapore), a two-year disability-adjusted life-year (DALY) burden analysis from the same registry, the first systematic review of dengue-associated Guillain-Barré syndrome, the first reported case of chronic dengue encephalitis with brain-tissue DENV RNA confirmed by metagenomic sequencing, and two narrative reviews that substantially expanded the evidence base on psychiatric sequelae. Dengue infection is associated with a broad and heterogeneous spectrum of chronic complications affecting multiple organ systems, including elevated post-acute cardiovascular, neuropsychiatric, and autoimmune risks, as well as a measurable disease and healthcare cost burden. The absence of a consistent relationship between acute severity and chronic outcomes supports structured, evidence-based, long-term post-dengue follow-up, particularly for patients with persistent symptoms or clinically relevant risk factors and for underrepresented Latin American populations.},
}

@article {pmid42910101,
year = {2026},
author = {Espinosa, A and Pavloudi, C and Shlafstein, MD and Ray, S and Sen, P and Noell, SE and Saw, JH},
title = {Dataset of amplicons, metagenomes, and metagenome-assembled genomes from geothermal biofilms four years after a volcanic eruption in Hawai'i.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113316},
pmid = {42910101},
issn = {2352-3409},
abstract = {This data report presents sequence data (16S rRNA gene amplicon sequences, metagenomes, and metagenome-assembled genomes - MAGs) from biofilms and geothermally heated soils (temperatures between 32.6 - 57.6°C) in Fissures 8 and 24 in Hawai'i, USA, 4 years after they were formed by a lava flow during the 2018 Lower Puna eruption. Using DNA extracted from these samples, we generated 587 Mbp and 363 Mbp of raw data from 16S rRNA gene sequencing using universal and archaeal-specific primers, respectively, and 62.7 Gbp of raw data from metagenome sequencing. Using the amplicon sequence data, we produced 276 ASVs from the universal primers and 576 ASVs from the archaeal-specific primers. Using the metagenome data, we reconstructed 82 medium-quality (>50% completeness and <10% contamination) and 61 high-quality (>90% completeness and <5% contamination) prokaryotic MAGs. Fastq files of the raw 16S rRNA gene amplicon sequences and metagenomes, as well as MAG sequences are publicly available on NCBI under BioProject PRJNA1459608. The amplicon sequence data indicated a strong effect of temperature, with communities dominated by Cyanobacteriota, Armatimonadota, and Pseudomonadota. The MAGs were primarily from domain Bacteria, having 142 MAGs, and 1 MAG from Archaea, with most abundance from phyla Chloroflexota, Proteobacteria and Acidobacteriota . These sequencing data provide a valuable resource for researchers interested in the colonization of geothermally heated soils as well as those interested in the microbial diversity and functionality of microorganisms inhabiting geothermally heated soils globally.},
}

@article {pmid42910237,
year = {2026},
author = {Tan, B and Zafra, C and Ng, C},
title = {Comparative genomics of the Smithellaceae: reductive evolution and a mobile alkane-activation module in Smithella.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag275},
pmid = {42910237},
issn = {2730-6151},
abstract = {Smithella are repeatedly implicated as primary alkane activators in methanogenic hydrocarbon-degrading communities, yet the propionate-oxidizing type species and many relatives cannot activate alkanes, and the genus's diversity and functional differentiation remain poorly resolved. Here, we present genus-scale comparative genomics of Smithella across 108 Smithellaceae metagenome-assembled genomes from three genera. The 74 Smithella genomes resolve into 23 species, 15 of them unnamed. Alkylsuccinate synthase occurs as two paralogous families, A and B. They differ by a third of their residues and coexist in the same genome. Both reject the species topology, family B decisively. assA has been gained and lost independently in several lineages. The families differ in mobility: family A is single-copy, confined to two species and in a conserved neighbourhood, whereas family B duplicates within genomes, spans four species and occupies a far less conserved context, most often beside a 2-hydroxyisobutanoyl-CoA mutase. Reductive specialization is pervasive, including genus-wide loss of flagellar motility, dissimilatory sulfite reduction, and de novo cobamide (vitamin B12) biosynthesis. In consortium models, both lineages behaved equivalently on propionate, the substrate they share, and a hydrogenotrophic partner was obligatory for alkane oxidation, for which H2 and formate are the only electron acceptors. The genus appears to favour propionate dismutation, thermodynamically preferred when hydrogen removal is incomplete; both lineages have largely lost the methylmalonyl-CoA epimerase most sister genomes retain. Alkane activation is therefore a mobile accessory on an otherwise conserved syntrophic core. Acquiring it widens the substrate range while tightening the requirement for a hydrogenotrophic partner.},
}

@article {pmid42910239,
year = {2026},
author = {Xu, TZ and Hu, CQ and Zhu, B and Xie, YR},
title = {Disseminated Mycobacterium colombiense Disease in a Person Living with HIV: Diagnostic and Therapeutic Considerations.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {628257},
pmid = {42910239},
issn = {1178-6973},
abstract = {BACKGROUND: Disseminated non-tuberculous mycobacterial (NTM) disease is an uncommon but serious complication in people living with HIV. Rare species such as Mycobacterium colombiense are infrequently reported, and guidance on diagnosis and treatment remains limited. This case illustrates challenges in identifying and managing disseminated M. colombiense infection.

DESCRIPTION: A middle-aged man living with HIV presented with disseminated Talaromyces marneffei infection complicated by hemophagocytic lymphohistiocytosis. He received antifungal therapy, immunomodulatory treatment, and antiretroviral therapy. During immune recovery, he developed progressive hepatic lesions and systemic inflammation, followed by osteoarticular involvement. Conventional microbiological tests were repeatedly negative, while metagenomic next-generation sequencing of liver tissue identified Mycobacterium colombiense. The patient was treated with prolonged macrolide-based combination antimycobacterial therapy, alongside corticosteroids for immune reconstitution inflammatory syndrome. Due to focal bone involvement, surgical debridement was performed. Following combined medical and surgical management, clinical symptoms resolved, inflammatory markers improved, and imaging demonstrated regression of lesions.

CONCLUSION: Disseminated M. colombiense infection should be considered in people living with HIV who develop unexplained visceral or skeletal lesions during immune recovery. Early use of molecular diagnostic tools is critical when routine investigations are inconclusive. Prolonged individualized multidrug therapy, combined with selective surgical intervention for focal disease, may improve clinical outcomes in rare NTM infections.},
}

@article {pmid42910241,
year = {2026},
author = {Wang, L and He, Z and Li, N},
title = {Deep Spinal Infection Caused by Corynebacterium simulans: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {637375},
pmid = {42910241},
issn = {1178-6973},
abstract = {Corynebacterium simulans is a commensal coryneform bacterium that commonly colonizes human skin and mucosal surfaces. Owing to limitations in conventional microbiological identification, it is often regarded as a contaminant, and clinically significant deep-seated infections caused by this organism are rarely reported. Here, we describe a case of lumbar infectious spondylitis caused by C. simulans in a 62-year-old male farmer who presented with a 2-month history of persistent low back pain accompanied by pain in both lower limbs. The patient had several potential predisposing factors including repeated unregulated needle-pricking bloodletting therapy, previously unrecognized hyperglycemia, and a family history of psoriasis. Lumbar magnetic resonance imaging and computed tomography revealed destructive infectious lesions involving the L3 and L4 vertebral bodies and L3/4 intervertebral disc. Blood culture initially yielded coryneform bacilli from a single anaerobic bottle, whereas repeated blood cultures were subsequently negative, supporting the possibility of contamination. However, given the compatible clinical manifestations, elevated inflammatory markers, and imaging evidence of spinal infection, percutaneous vertebral biopsy was performed. Routine bacterial culture of the deep-tissue specimen showed no growth, whereas metagenomic next-generation sequencing identified C. simulans with high sequence reads and relative abundance, supporting its etiological relevance in the appropriate clinical context. The patient was treated with intravenous vancomycin combined with glycemic control, followed by oral linezolid as step-down therapy. His symptoms gradually improved, inflammatory markers decreased toward the normal range, and follow-up magnetic resonance imaging showed reduced paravertebral soft tissue edema. No recurrence was observed during the 3-month follow-up period. This case highlights that Corynebacterium species detected in the blood or deep tissue specimens should not be readily dismissed as contaminants in patients with compatible evidence of infection. Deep tissue sampling combined with metagenomic next-generation sequencing (mNGS) may improve the detection of rare opportunistic pathogens and facilitate timely targeted antimicrobial therapy.},
}

@article {pmid42911143,
year = {2026},
author = {Das, S and Jain, M and Khapuinamai, A and Joseph, J},
title = {The evolving landscape of fungal keratitis: from emerging pathogens to precision diagnostics and novel therapeutics.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/17460913.2026.2751606},
pmid = {42911143},
issn = {1746-0921},
abstract = {Fungal keratitis (FK) remains a major cause of vision-threatening corneal infection, especially in tropical and subtropical regions, with an expanding epidemiological spectrum driven by environmental, climatic, occupational and host-related factors. Fusarium and Aspergillus were the most common pathogens reported. Greater etiological diversity is reflected by increasing recognition of dematiaceous fungi, uncommon molds, and cryptic species. The literature search was performed by searching bibliographic databases (PubMed and Google Scholar), covering publications from January 2000 to August 2026. Additional relevant studies were identified by screening the reference lists of key publications. This review provides an overview of the current state of FK including changing epidemiology, established diagnostic approaches, emerging technologies, and evolving therapeutic approaches. Conventional microscopy and culture remain central to diagnosis, with molecular methods, sequencing, MALDI-TOF and noninvasive imaging offering advantages in sensitivity, speed and species-level identification. Novel diagnostic methods such as CRISPR-based tests, genome sequencing, artificial intelligence, biosensors and point-of-care diagnostics may provide rapid and accessible precision diagnosis. Therapeutic challenges include poor corneal drug penetration, antifungal resistance and prolonged treatment. Hence, the exploration of new antifungals, nanotechnology-based delivery systems, photoactivated therapies and antimicrobial peptides. These advances support a transition to integrated, rapid and precision-based management of FK collectively.},
}

@article {pmid42911222,
year = {2026},
author = {Popowitch, EB and Tran, TH and Escapa, IF and Bhatt, E and Sozat, AK and Ahmed, N and Deming, C and Roberts, AQ and Program, NCS and Segre, JA and Kong, HH and Conlan, S and Lemon, KP and Kelly, MS},
title = {Description of Corynebacterium nasorum sp. nov. and Corynebacterium hallucis sp. nov. isolated from human nasal passages and skin.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {10},
pages = {},
pmid = {42911222},
issn = {1466-5034},
mesh = {Humans ; *Corynebacterium/classification/genetics/isolation & purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry/analysis ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Base Composition ; Sequence Analysis, DNA ; *Skin/microbiology ; *Nose/microbiology ; Whole Genome Sequencing ; Genome, Bacterial ; },
abstract = {Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the USA and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain-heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were C18 : 1 ω9c (oleic acid), C16 : 0 (palmitic acid) and C18 : 0 (stearic acid). Analysis of the 16S rRNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with average nt identities of <95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallucis sp. nov., with the type strain CTNIH22[T] (=ATCC TSD-435[T]=DSM 117774[T]), and Corynebacterium nasorum sp. nov., with the type strain KPL3804[T] (=ATCC TSD-439[T]=DSM 117767[T]). These data also indicate that 'Corynebacterium kefirresidentii' is designated C. nasorum sp. nov.},
}

Humans
*Corynebacterium/classification/genetics/isolation & purification
*Phylogeny
RNA, Ribosomal, 16S/genetics
Fatty Acids/chemistry/analysis
Bacterial Typing Techniques
DNA, Bacterial/genetics
Base Composition
Sequence Analysis, DNA
*Skin/microbiology
*Nose/microbiology
Whole Genome Sequencing
Genome, Bacterial

@article {pmid42912803,
year = {2026},
author = {Jiang, H and Peng, Y and Lam, B and Yang, K and Lin, Y and Mak, JWY and Tse, YK and Chan, FKL and Xu, Z and Ng, SC},
title = {Gut virome remodeling after fecal microbiota transplantation is associated with virus-bacteria co-variation and metabolic response in obesity and type 2 diabetes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746820},
doi = {10.1080/19490976.2026.2746820},
pmid = {42912803},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/therapy/metabolism/microbiology/virology ; *Fecal Microbiota Transplantation ; *Obesity/therapy/metabolism/microbiology/virology ; *Virome ; Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {Fecal microbiota transplantation (FMT) modifies gut bacterial composition and improves metabolic outcomes in subjects with obesity and type 2 diabetes (ObT2), but bacterial changes alone do not fully explain the heterogeneity in clinical response. We performed virus-like particle (VLP)-enriched metagenomic sequencing coupled with bulk-DNA metagenomic sequencing on longitudinal fecal samples from a randomized controlled FMT trial in ObT2. Using random forest classification, post-FMT virome changes showed accuracy comparable to bacteriome changes (84.8% vs 81.4%) in distinguishing LDL responders from non-responders. Donor-derived viral contig engraftment was detected in 64.7% (11/17) of recipients receiving FMT alone and 58.8% (10/17) receiving FMT with lifestyle intervention (LSI), versus 5.6% (1/18) in the sham with LSI group. FMT was associated with increased virome diversity, compositional shifts toward the donor virome, and coordinated virus-bacteria associations, with most responsive viral contigs classified as Caudoviricetes. FMT-responsive viral contigs that were shared between the two FMT groups were predicted to infect Roseburia and Bifidobacterium, while contigs associated with clinical responses were predicted to infect Escherichia, Roseburia, Blautia, and Enterococcus. These findings suggest that the gut virome is a complementary ecological component associated with FMT responses and metabolic outcomes in ObT2.},
}

Humans
*Diabetes Mellitus, Type 2/therapy/metabolism/microbiology/virology
*Fecal Microbiota Transplantation
*Obesity/therapy/metabolism/microbiology/virology
*Virome
Feces/microbiology/virology
*Bacteria/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
*Viruses/classification/genetics/isolation & purification

@article {pmid42913303,
year = {2026},
author = {Lee, G and Rosa, BA and Ndao, IM and Martin, J and Anzà, S and Luby, JL and Smyser, CD and Rogers, CE and Barch, DM and Kimmel, MC and Hall-Moore, C and Bryant, RE and Warner, BB and Mitreva, M},
title = {Infant gut microbiome neuroactive pathways link to social disadvantage, toddler neurodevelopment, cognitive and behavioural outcomes: a longitudinal cohort study.},
journal = {EBioMedicine},
volume = {133},
number = {},
pages = {106533},
doi = {10.1016/j.ebiom.2026.106533},
pmid = {42913303},
issn = {2352-3964},
abstract = {BACKGROUND: Early life is a critical window for co-development of the brain and gut microbiome (GM). Evidence supports a role for the GM in brain development, but longitudinal human data remain limited, particularly regarding the influence of social disadvantage (SD), a powerful determinant of child mental health and neurodevelopment. Here, we examine longitudinal relationships between the GM and neurodevelopmental outcomes over the first three years of life, and the impact of SD on them.

METHODS: We sequenced and analysed stool samples of 187 children, collected at 5 timepoints over 4-36 months of life (MOL; 905 samples) using a whole-metagenome sequencing approach. Associations between GM-derived Gut-Brain Modules (GBM) and neuroactive potential were assessed using generalised linear mixed models, adjusting for covariates. Neurodevelopmental outcomes were evaluated by Bayley-III (cognitive, language, and motor), and neurobehavioural dysregulation and externalising/internalising-behaviour by the Infant-Toddler Social and Emotional Assessment (ITSEA) and Preschool Age Psychiatric Assessment (PAPA).

FINDINGS: Temporal changes were observed in GBMs, including glutamate/GABA synthesis and degradation pathways, as well as short-chain fatty acids. GM community structure and GBMs were significantly associated with concurrent and later Bayley-III outcomes, most consistently for cognition and language (FDR < 0.10). Several GBMs were associated with both neurobehavioural outcomes and SD, including S-adenosylmethionine (SAM) synthesis, butyrate synthesis, and glutamate and GABA synthesis II (FDR < 0.10). A partial mediating effect between SD and 36 MOL language outcomes was observed using SAM synthesis at 4 MOL (β = -0.042, P = 0.048).

INTERPRETATION: This longitudinal cohort study of GM neuroactive metabolic capacity across early transitional developmental windows reveals a dynamic pattern of GM-derived neuroactive metabolic pathways and identifies specific pathways associated with later neurodevelopmental (cognitive, language) and neurobehavioural outcomes, even after controlling for important covariates. These pathways are shaped by the socioeconomic status of mothers, starting with in-utero exposure, and GBMs partially mediated this effect. The study identifies microbial pathways associated with both SD and neurodevelopmental outcomes, highlighting potential biological processes that may contribute to neurodevelopmental risk and warrant further investigation.

FUNDING: This work was supported by the National Institute of Mental Health, March of Dimes, Children's Discovery Institute, National Institute of Diabetes and Digestive and Kidney Diseases, and National Center for Advancing Translational Sciences.},
}

@article {pmid42913490,
year = {2026},
author = {Chen, N and Yuan, Y and Zhan, Y and Cao, W and An, N and Xiao, Q and Feng, C and Liu, T and Wu, S and Guo, H},
title = {Convergent Biogenic Magnetite Formation from Diverse Iron (Oxyhydr)oxide Precursors Drives Cr(VI) Reduction via an Environmental Battery Mechanism.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c05850},
pmid = {42913490},
issn = {1520-5851},
support = {2024YFC3712600//National Basic Research Program of China (973 Program)/ ; 42277041//National Natural Science Foundation of China (NSFC)/ ; 52200031//National Natural Science Foundation of China (NSFC)/ ; },
abstract = {Iron (oxyhydr)oxides mediate electron flux across coupled biogeochemical cycles in anoxic environments, yet whether their biogenic transformation feeds back to reshape interfacial electron transfer efficiency remains unresolved. Here, five structurally distinct iron (oxyhydr)oxide precursors (ferrihydrite, goethite, magnetite, wüstite, and hematite) were exposed to anaerobic sulfur-oxidizing bioreactors under Cr(VI) stress, and their transformation trajectories were tracked using synchrotron EXAFS spectroscopy, electrochemical impedance spectroscopy, DFT calculations, and metagenomic profiling. Mineral bioavailability decreased in the order ferrihydrite > goethite > magnetite > wüstite > hematite, a hierarchy governed by lattice iron-leaching energetics quantified via DFT (Efev from -8.96 eV for ferrihydrite to 5.76 eV for hematite). Despite this wide disparity in precursor lability, all biotransformation trajectories converged on magnetite as the thermodynamically stable end point. In the ferrihydrite system, biogenic magnetite reached 60% of the final solid phase and operated as an in situ "environmental battery" (storing and releasing electrons through reversible Fe(II)/Fe(III) lattice cycling), lowering interfacial charge transfer resistance and producing a 4.77-fold higher pseudo-first-order Cr(VI) reduction rate constant than the mineral-free biotic control (C-S). Metagenomic analysis revealed mineral-specific restructuring of the microbial community toward a tightly coupled sulfur-iron redox network. These results reframe precursor mineralogy from a determinant of intrinsic reactivity to a kinetic regulator of biogenic electron-buffer formation, providing a mechanistic basis for mineral-informed bioremediation design.},
}

@article {pmid42913813,
year = {2026},
author = {Zhang, W and Li, X and Zhang, X and Zhang, W and Gu, L and Chen, Y and Ai, H},
title = {Intermittent illumination enables reversible carbon buffering by Rhodopseudomonas palustris for enhanced methane recovery from food waste anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136115},
doi = {10.1016/j.biortech.2026.136115},
pmid = {42913813},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) of food waste (FW) is vulnerable to acidification when fermentation outpaces syntrophic oxidation and methanogenesis. To address this temporal imbalance, we introduced Rhodopseudomonas palustris (R. palustris), which can assimilate fermentation-derived volatile fatty acids (VFAs) and store carbon as polyhydroxyalkanoates (PHAs). Intermittent illumination reduced VFA accumulation and end-cycle H2 partial pressure, while yielding the highest mean daily methane production (589.0 mL d[-1]) and fraction of carbon recovered as methane (37.2 %). A pure-culture assay showed that PHA accumulated during illumination and declined in darkness, indicating reversible intracellular carbon storage and remobilization. The PHA turnover pattern paralleled reactor methane dynamics, which was consistent with a temporal association between carbon storage and downstream methanogenesis. Intermittent illumination yielded the lowest NADH/NAD[+] ratio while maintaining high ATP availability. Community analysis revealed a more balanced distribution of functional guilds between the liquid and reactor-wall fractions, while metagenomic analysis indicated functional potential for PHA turnover and methanogenesis. Together, these findings support a carbon-buffering model in which light-dark cycling is associated with transient carbon storage and subsequent remobilization, potentially improving the temporal coupling between acidogenesis and methane formation and enhancing AD stability and methane recovery.},
}

@article {pmid42913844,
year = {2026},
author = {Costa, BG and Rutschke, S and Endres, MI and Gomez, A and Heins, BJ},
title = {Effects of social rearing systems on the gut microbiome of dairy calves before and after weaning.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28497},
pmid = {42913844},
issn = {1525-3198},
abstract = {Social housing may offer behavioral benefits for dairy calves but may also increase exposure to diverse microbes, including pathogens. Pre-weaned dairy calves are susceptible to gastrointestinal diseases, and it is unknown how social contact may impact the gut microbiome composition of dairy calves before and after weaning. This study aimed to investigate the effects of social rearing systems on the fecal microbiome of dairy heifer calves before and 3 d after weaning. The study was conducted at the University of Minnesota West Central Research and Outreach Center dairy in Morris, Minnesota. Dairy calves born from September to November 2020 were randomly assigned to one rearing system at birth: individual (IND, n = 18); group (GRP, n = 21); or dam-reared (DAM, n = 15). Calves were weaned at 63 d and housed in groups and comingled with other calves from the different treatments. Fecal samples were collected before and 3 d after weaning and sent for 16S rRNA short amplicon sequencing (V4 region). Gut microbiome sequence data were analyzed with Qiime2 and the R statistical interface for ecological analyses. Results showed a significant effect of the rearing system, weaning, and an interaction between the housing system and weaning on the calf fecal microbiome. Even though all treatments had different fecal microbiome compositions before weaning, particularly for analyses of presence/absence of taxa (Jaccard index), DAM raised calves showed the most distinctive microbiome and lower α diversity when compared with GRP and IND calves before weaning. DAM calves showed enrichment of Firmicutes, particularly before weaning, and enrichment of genera associated the fermentative metabolism and gut maturation, such as, Butyricicoccus, Megasphaera, Ruminococcus, Collinsella, and Sphaerochaeta. The GRP and IND calves had an enrichment of bacteria associated with solid feed intake, such as members of Prevotellaceae family before weaning. All calves showed a shift in their microbiome over weaning. After weaning, there were fewer microbiome compositional and diversity differences between treatments. Nevertheless, DAM calves maintained the most distinctive microbiome and unique features, such as lower enrichment of Prevotella and Bifidobacterium when compared with IND and GRP calves. In summary, results indicated that rearing calves in full contact with dams (therefore, having access to adult cattle and their environmental resources), may impact gut microbiome colonization and potentially accelerate gut maturation. However, those effects were less pronounced after weaning. The results also indicated the presence of beneficial bacteria in all treatment calves. Therefore, contact with adult cattle and their environmental resources appears to influence gut microbiome composition and maturation of dairy calves. Nevertheless, further studies, including functional analyses (shotgun metagenomics and metatranscriptomics, metabolomics, immune performance) considering different weaning strategies, feed intake, and environmental samples, as well as disease challenge models postweaning, would help elucidate the effects of social contact on the gut microbiome and health of dairy calves.},
}

@article {pmid42914000,
year = {2026},
author = {Maartens, LH and Thompson, PN and Grewar, JD and Picard, JA and Gummow, B},
title = {Bovine keratoconjunctivitis: a review of the bovine ocular surface microbiome and related epidemiological risk factors.},
journal = {Veterinary journal (London, England : 1997)},
volume = {320},
number = {},
pages = {106947},
doi = {10.1016/j.tvjl.2026.106947},
pmid = {42914000},
issn = {1532-2971},
abstract = {Bovine keratoconjunctivitis (BK) is a common inflammatory condition of the ocular surface (OS) of cattle, with a complex epidemiology. This review summarises current knowledge about the bovine ocular surface microbiota (OSMt) and discusses how it integrates with agent, host and environmental factors involved in BK epidemiology. A comprehensive literature review, from 1950 to 2026, was conducted to identify known constituents of the OSMt and symbionts with pathogenic potential within this community. Information about key epidemiological factors associated with BK was simultaneously collected. After applying a structured literature search and selection criteria, 321 papers remained. A directed acyclic graph was used to construct a conceptual framework that visualised the role of the bovine OSMt in BK within the epidemiological web. The graph indicated that cattle are exposed to six injurious environmental factors acting from outside the ocular surface microbiome (OSMe)-(i) ultraviolet B, (ii) lachryphagous insects, (iii) desiccation stress, (iv) nutritional deficiencies, (v) large particulate matter, and (vi) small particulate matter-and two factors acting from within the microbiome-(vii) pathogenic stages of Thelazia spp. and (viii) pathogenic viruses. Metagenomic analyses revealed marked diversity within the bovine OSMt and symbionts of both high (e.g., Moraxella bovis) and low pathogenic potential (e.g., Mesomycoplasma bovoculi). The symbiotic relationship is influenced by damaging or disruptive environmental influences impacting on barrier integrity. Integrating the OSMe within a network of agent, host, and environmental factors provides a new perspective on BK that may inform future control strategies.},
}

@article {pmid42914022,
year = {2026},
author = {Shibata, SS and Oki, H and Kawahara, K and Kokame, K and Masuda, R and Fujii, KK and Koide, T},
title = {Triple-helical ligands selectively targeting the closed αI domain of integrin α2β1.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113692},
doi = {10.1016/j.jbc.2026.113692},
pmid = {42914022},
issn = {1083-351X},
abstract = {Integrins α1β1, α2β1, α10β1, and α11β1 are known to recognize the GxxGEx motif of the collagen triple helix through their αI domains, with the Glu residue engaging the domain via a divalent metal cation. The binding amino acid sequences containing these motifs, identified from native collagen, exhibit low subtype selectivity. Here we identify novel triple-helical peptides that selectively bind the α2I domain independently of Glu and metal ions. Yeast two-hybrid screening of randomized triple-helical peptide libraries yielded non-natural sequences in which the canonical Glu was replaced by aliphatic residues such as Met. X-ray crystal structural analysis of the representative variant GFOGMR in complex with the α2I domain revealed a new binding mode. In this mode, peptides are recognized by the closed, inactive conformation of the α2I domain without metal coordination. This cryptic interaction, likely unused by native ligands, provides a new basis for the design of subtype-specific ligands targeting collagen-binding integrins.},
}

@article {pmid42914073,
year = {2026},
author = {Huang, B and Chen, B and Li, Z and Yang, E and Lu, J and Hu, L and Hou, X and Chao, Y and Luan, T and Yuan, K},
title = {Fates and Characteristics of Antibiotic Resistance Genes Carried by Viruses during a Full-Scale Anaerobic Sludge Digestion.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125980},
doi = {10.1016/j.envres.2026.125980},
pmid = {42914073},
issn = {1096-0953},
abstract = {The transmission of antibiotic resistance genes (ARGs) mediated by viruses in sludge represents an emerging concern for antibiotic resistance dissemination. This study investigated the virus-carried ARGs (vARGs) profiles and potential risks in sludges collected from an entire anaerobic sludge digestion plant. A total of 79 unique vARGs spanning 10 antibiotic resistance classes were identified, with trimethoprim resistance genes being the most diverse. Although most vARGs (94.9%) exhibited low sequence similarity (< 70%) to known ARGs, the representative functional validation showed that virus-carried dfr genes could confer trimethoprim resistance to Escherichia coli. Thermal hydrolysis reduced the levels and diversity of vARGs, whereas subsequent anaerobic digestion led to substantial enrichment. More than 90% of vARGs in sludge viromes were removed after all treatment processes, but a significant number of ARG-carrying viruses (10[5] - 10[6] VLPs/g) still remained in the final sludges. In the metagenomes, the levels of vARGs increased approximately 7-fold, suggesting that vARGs were more difficult to be moved than plasmid-associated ARGs and chromosome-associated ARGs. The host prediction suggested associations between some vARG-carrying viruses and potential pathogenic bacteria, which worthing further experimental validation. In summary, the persistence of vARGs in sludge remains a concern, even after the implementation of sludge treatment processes.},
}