@article {pmid41736165,
year = {2026},
author = {Wei, C and Chen, Z and Wang, Y and Huang, L and Chen, C},
title = {Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41736165},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Jumbo phages are phages with comparatively large genome sizes. Jumbo phages have been identified in various microbial communities. However, their diversity, genome structure, potential function, and their interactions with hosts and other phages are largely unknown due to insufficient genomic data.

RESULTS: We collected 59,652,008 putative viral genomes from seven habitats by using 38 public metagenome datasets, an integrated public viral genome database (IGN), and pig gut viral genome databases. We obtained 10,754 jumbo phage genomes with sizes ranging from 200 to 831 kb. Most (94.64%) of these jumbo phage genomes were classified into Caudoviricetes, and the results have expanded the known diversity of Caudoviricetes. We found 2,389 species-like operational genome clusters that contained 3,727 (34.69%) genomes without any known viral genomes in the IGN, suggesting potential novel species-like genomes. Genome analysis suggested the potential coevolution of jumbo phages with habitat types and highlighted the utilization of alternative genetic codes and their corresponding suppressor tRNAs for recoding stop codons. CRISPR spacer analysis revealed potential bacterial or archaeal hosts of jumbo phages and uncovered competitive networks among jumbo phages. Habitat type had an important effect on the variation in phage auxiliary metabolic genes.

CONCLUSIONS: This study provides an important resource and new knowledge for future studies on the interaction between jumbo phages and their bacterial or archaeal hosts.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00534-z.},
}

@article {pmid41917792,
year = {2026},
author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Panova, IA and Kadnikov, VV and Beletsky, AV and Mardanov, AV and Novikov, AA and Scherbakova, VA and Ravin, NV},
title = {A Novel Slowly Evolving Lineage of the Desulforudis Clade From the Deep Subsurface.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70293},
doi = {10.1111/1462-2920.70293},
pmid = {41917792},
issn = {1462-2920},
support = {24-14-00396//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; },
mesh = {Phylogeny ; Genome, Bacterial ; Siberia ; RNA, Ribosomal, 16S/genetics ; Evolution, Molecular ; DNA, Bacterial/genetics ; },
abstract = {Endemic to the deep subsurface biosphere sulphate-reducing 'Desulforudis audaxviator' has been called a living microbial fossil due to the high nucleotide sequence identity of its genomes across continents. Evolutionary stasis of this bacterium was established based on the analysis of metagenome assembled genomes, single cell genomes and a single axenic culture. The lack of high-quality reference genomes necessitates efforts to cultivate and isolate pure cultures that could shed light on the hypothetical slow evolution of Desulforudis-clade bacteria deep underground. Molecular signatures demonstrated the presence of Desulforudis-like phylotypes in subsurface environments worldwide. Here we report the isolation of four novel strains of the Desulforudis-clade, all belonging to Desulfosceptrum tomskiensis gen. nov. sp. nov. Four strains of the new species were isolated from deep boreholes in Western Siberia, separated by hundreds of kilometres. Genome comparisons revealed minimal differences between these strains, with average nucleotide sequence identity (ANI) values above 99.9%, low number of SNPs, and near-identical CRISPRs. The bacterium, together with Desulforudis audaxviator BYF[T] gen. nov. sp. nov., deposited in international culture collections, provides a bases for understanding the slow evolution of Bacillota endemic to the deep biosphere.},
}

Phylogeny
Genome, Bacterial
Siberia
RNA, Ribosomal, 16S/genetics
Evolution, Molecular
DNA, Bacterial/genetics

@article {pmid41918091,
year = {2026},
author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J},
title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04921-z},
pmid = {41918091},
issn = {1471-2180},
support = {2022YFC26023002//National Key Research and Development Program of China/ ; },
}

@article {pmid41918132,
year = {2026},
author = {Gao, L and Fang, BZ and Yang, J and Lian, ZH and Chen, Y and Mohamad, OAA and Xu, QY and Liu, YH and Wu, D and Yuan, Y and Abdugheni, R and Li, MM and Wang, P and Ortúzar, M and Li, XY and Huang, JR and Liu, L and Jiang, HC and Shu, W and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02361-5},
pmid = {41918132},
issn = {2049-2618},
support = {2022B0202110001//Guangdong S&T Program/ ; },
abstract = {BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood.

RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis.

CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.},
}

@article {pmid41918376,
year = {2026},
author = {Yuan, H and Guan, T and Yuan, Q and Zeng, Q and Yu, J and Cai, Y and Liu, E and Li, Q and Wang, Y},
title = {Molecular-Microbial Cascades Regulate Organic Phosphorus Mineralization in Lake Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15353},
pmid = {41918376},
issn = {1520-5851},
abstract = {Organic phosphorus (Po) mineralization is a major internal source of soluble reactive phosphorus (SRP) in lakes, yet the molecular and microbial mechanisms governing this transformation remain poorly understood. Here, we aim to elucidate these mechanisms by integrating excitation-emission fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), and metagenomics across two contrasting ecological niches in Taihu Lake, namely the Cyanophyta-dominated and macrophyte-dominated regions. We also supplement our results with the findings from a global meta-analysis. We found that fulvic-associated Po (Fu-Po) dominated sedimentary Po inventories, whereas Po extracted with NaHCO3 (NaHCO3-Po) and microbial biomass Po (biomass-Po) exhibited higher decomposition potential. Fluorescence indices indicated increasing lability with depth, and humic-like materials exhibited a higher tendency to be decomposed under anoxia, accompanied by the accumulation of fulvic-like fractions. FT-ICR-MS revealed proteins and lignins as key constituents of humic-associated Po and Fu-Po, supporting their bioavailability, while NaHCO3-Po was enriched in compounds with lipid-like CHOSP formulas, suggesting greater lability. Metagenomics identified phoD as the most abundant phosphatase-encoding gene, with rare but highly connected phoD-harboring taxa emerging as potential keystone regulators alongside abundant functional groups. Across global lake sediments, alkaline phosphatase activity, Po content, and phoD abundance were found to covary positively, and structural equation modeling highlighted Fu-Po as a disproportionate indirect driver of SRP replenishment via phoD-mediated phosphatase activity. These findings reveal a mechanistic cascade linking molecular composition to phoD-mediated enzymatic potential in Po mineralization, identifying Po bioavailability, rather than inorganic phosphorus pools alone, as a critical driver for reducing internal loading. Targeting this pathway could modulate Po mineralization mechanisms in sediments worldwide, offering valuable insights into the management of lake eutrophication under accelerating nutrient pressures.},
}

@article {pmid41918527,
year = {2026},
author = {Yang, K and Huang, Y and Gu, L and Li, J and Ma, Y and Gao, P and Qiu, W and Liu, K and Zhang, Y and Liu, H and Xu, J and Xu, J and Liu, T},
title = {Er-Chen Decoction ameliorates metabolic dysfunction-associated steatotic liver disease via gut microbiota-barrier axis-driven hepatic metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768664},
pmid = {41918527},
issn = {1664-302X},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) constitutes a critical global health challenge, with gut-liver axis dysfunction and metabolic endotoxemia serving as key drivers. The traditional Chinese medicinal formula Er-Chen Decoction (ECD) has proven effective in treating metabolic disorders, yet the specific mechanisms by which it modulates gut-liver crosstalk have not been fully elucidated.

METHODS: A mouse model of MASLD was established via a high-fat diet (HFD). The therapeutic effects of ECD were evaluated using the glucagon-like peptide-1 (GLP-1) receptor agonist semaglutide (SE) as a positive control. A comprehensive analysis of the underlying mechanisms of ECD treatment was conducted by integrating fecal metagenomic sequencing, untargeted serum metabolomic profiling, hepatic transcriptomic analysis, and molecular biology assays.

RESULTS: Treatment with ECD markedly ameliorated hepatic steatosis, insulin resistance, and hyperlipidemia, demonstrating a therapeutic efficacy comparable to that of SE. Fecal metagenomic analysis indicated that whereas SE predominantly enriched the genus Akkermansia, the relative abundance of Bifidobacterium and Lactobacillus was markedly and specifically elevated following ECD treatment. Serum metabolomic profiling revealed that ECD specifically activated the tryptophan-indole metabolic pathway, as evidenced by elevated concentrations of indoleacrylic acid and indole-3-acetic acid. Correlation analyses established a strong positive correlation between these indole derivatives and the bacterial genera enriched by ECD. Mechanistically, our findings suggest that elevated indoles activate the aryl hydrocarbon receptor (AHR) in the colon, upregulating tight junction proteins ZO-1 and Occludin and restoring intestinal barrier integrity, thereby significantly reducing serum lipopolysaccharide (LPS) levels. In hepatic tissue, the diminished LPS influx alleviated the suppression of DNA methyltransferase 3B (DNMT3B), thereby promoting the epigenetic silencing of the lipid droplet fusion protein CIDEA and inhibiting pathological hepatic lipogenesis.

CONCLUSION: Our findings elucidate a novel mechanism through which ECD may ameliorate MASLD via the distinctive "gut microbiota-indole-barrier" axis. In contrast to SE, ECD modulates gut microbiota composition to boost indole production and subsequently activate AHR signaling. This activation inhibits endotoxin translocation and induces hepatic DNMT3B-mediated epigenetic reprogramming to reverse hepatic steatosis. These results offer scientific evidence supporting the potential of ECD as an effective therapeutic strategy for MASLD.},
}

@article {pmid41918743,
year = {2026},
author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F},
title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745166},
pmid = {41918743},
issn = {1664-3224},
mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; },
abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.

METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.

RESULTS AND DISCUSSION: On average, 23.29% ± 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% ± 17.88%), pyelonephritis (22.75% ± 12.91%), asymptomatic bacteriuria (18.17% ± 17.14%)] and 30.63% ± 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% ± 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.},
}

Humans
*Extracellular Traps/immunology/metabolism
Female
Pilot Projects
Male
*Urinary Tract Infections/immunology/microbiology/urine
Middle Aged
Adult
*Neutrophils/immunology/metabolism
Aged
Biomarkers
Pyelonephritis/immunology/urine
Bacteriuria/immunology

@article {pmid41918857,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M},
title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20990},
pmid = {41918857},
issn = {2167-8359},
mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; },
abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.

METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.

RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.},
}

*Peptides/genetics/pharmacology
*Antineoplastic Agents/pharmacology
*Metagenome
Humans
*Genome, Microbial
*Software
High-Throughput Nucleotide Sequencing
Algorithms
Computational Biology/methods

@article {pmid41918874,
year = {2026},
author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D},
title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1782744},
pmid = {41918874},
issn = {2235-2988},
mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; },
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.

METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.

RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-α and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.

DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.},
}

Humans
Female
*Probiotics/administration & dosage
*Diabetes, Gestational/microbiology
Pregnancy
*Gastrointestinal Microbiome/drug effects
Adult
Metabolomics/methods
Metagenomics
Multiomics

@article {pmid41918946,
year = {2026},
author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG},
title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41918946},
issn = {2312-0541},
abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.

METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32 weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and α-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).

CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.},
}

@article {pmid41919078,
year = {2026},
author = {Fan, Y and Qin, H and Liu, J and Abbas, M and Yang, C and Cheng, H and Dong, X},
title = {Lactobacillus acidophilus alleviates slow transit constipation by modulating 5-HT pathway and gut microbial composition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1775405},
pmid = {41919078},
issn = {2296-861X},
abstract = {INTRODUCTION: Slow transit constipation (STC) is a chronic disease characterized by delayed intestinal transit and weakened spontaneous contractions of colonic smooth muscle. Current pharmacological treatments are often associated with adverse effects, highlighting the need for safe and more effective therapeutic strategies. This study investigated the potential role of Lactobacillus acidophilus (L. acidophilus) in regulating intestinal motility and alleviating STC, as well as the underlying mechanism.

METHODS: A humanized mouse model was established by intragastric administration of fecal bacterial suspension from STC patients on alternate days, in order to evaluate the effect of L. acidophilus on constipation. The regulatory effect of L. acidophilus on intestinal motility was evaluated using defecation parameters. Colon histopathology was assessed by hematoxylin-eosin (H&E) staining. Immunohistochemistry (IHC), RT-qPCR, ELISA, and in vitro cell experiments were performed to examine the inflammatory cytokine levels and changes in the 5-hydroxytryptamine (5-HT) signaling pathway. In addition, metagenomic sequencing was used to analyze changes in the intestinal microbial community.

RESULTS: The results showed L. acidophilus treatment significantly enhanced intestinal peristalsis and maintained the intestinal barrier by up-regulating Occludin expression and down-regulating inflammatory cytokines, including TNF-α and IL-1β, thereby suppressing inflammatory responses. Both in vivo and in vitro experiments showed that L. acidophilus affected the synthesis and release of 5-HT by regulating the expression of TPH1 and the mechanosensitive ion channel Piezo1. Additionally, L. acidophilus reshaped the intestinal microbial community structure and altered the inter-bacterial interaction network, which was closely associated with improved intestinal motility.

CONCLUSION: Our current research reveals that constipation symptoms by L. acidophilus through the gut microbiota composition, intestinal barrier, and the 5-HT signaling pathway. These findings provide a strong theoretical basis for the development of L. acidophilus as a potential therapeutic strategy for the treatment of STC.},
}

@article {pmid41919237,
year = {2026},
author = {Zheng, D and Li, L and Qi, H and Jiao, XF and Wang, K},
title = {Successful azithromycin treatment of Chlamydia psittaci pneumonia in second-trimester pregnancy resulting in term delivery: a case report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1780706},
pmid = {41919237},
issn = {1663-9812},
abstract = {Psittacosis pneumonia is a zoonotic infection caused by Chlamydia psittaci (C. psittaci), primarily transmitted via contact with infected avian species. Diagnostic challenges arise from the inherent difficulties of pathogen culture and serological testing, frequently resulting in misdiagnosis or underdiagnosis. Gestational psittacosis, in particular, is a rare but life-threatening condition, with delayed diagnosis conferring risk of severe maternal and fetal complications. We present a case of C. psittaci pneumonia in a 24-week pregnant woman, with the diagnosis confirmed by metagenomic next-generation sequencing (mNGS). Empirical intravenous azithromycin (0.5 g daily) was promptly initiated for 3 days, leading to rapid symptomatic resolution. After a 2-day interruption, targeted oral azithromycin (0.5 g daily) was restarted for an additional 3 days following pathogen confirmation via mNGS. The patient was successfully discharged after a 10-day hospital stay under multidisciplinary management. She finally gave birth to a healthy baby girl at 40 weeks and 3 days of gestation, with favorable maternal and neonatal outcomes. To our knowledge, this represents one of the few reported cases of full-term delivery following azithromycin monotherapy for gestational psittacosis. It provides valuable insights into the diagnosis and management of gestational psittacosis, emphasising the importance of multidisciplinary involvement in preserving maternal and fetal safety.},
}

@article {pmid41919563,
year = {2026},
author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W},
title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70091},
pmid = {41919563},
issn = {1522-7278},
abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.},
}

@article {pmid41919955,
year = {2026},
author = {Pan, W and Tang, S and Wanek, W and Liu, X and Zhou, J and Gregory, AS and Marsden, KA and Chadwick, DR and Liang, Y and Wu, L and Jones, DL and Ma, Q},
title = {Organic Fertilization Promotes the Microbial Formation of Moderately Active Soil Phosphorus Pools to Sustain Phosphorus Availability: Insights from 180 years of Fertilization.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12810},
pmid = {41919955},
issn = {1520-5851},
abstract = {Phosphorus (P) fertilization is essential for crop production, but most applied P is rapidly fixed into mineral-associated forms. Although fertilization regulates P distribution in soils, its effects on microbe-mediated processes that regulate P availability and stabilization remain unclear. Here, we investigated P transformations under organic fertilization (FYM), inorganic fertilization (NPK), and no fertilization (NIL) using the 180 year Broadbalk experiment. Through [33]P isotopic tracing, metagenomics, and enzymatic profiling, we found that FYM and NPK stimulate distinct P transformation pathways. FYM, through sustained organic carbon inputs, enhanced microbial immobilization and phosphatase activity, causing a 41% reduction in stable P formation and 47% increase in moderately active P levels and shifting P dynamics toward more bioavailable forms. NPK fertilization reduced pH and limited microbial carbon availability; 33% of [33]P was recovered in the stable P fraction, indicating abiotic immobilization into inorganic P pools. The microbial community under NPK adapted to P fixation by enriching P-cycling-related genes and acid-tolerant taxa, enhancing P turnover relative to NIL but preventing long-term immobilization less effectively than FYM. Thus, organic fertilization maintains P in more biologically available forms and mitigates abiotic P fixation; our research provides a mechanistic foundation for more efficient and resilient P management in agroecosystems.},
}

@article {pmid41919968,
year = {2026},
author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C},
title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0039226},
doi = {10.1128/aem.00392-26},
pmid = {41919968},
issn = {1098-5336},
abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.},
}

@article {pmid41920399,
year = {2026},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Rahman, MS and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41920399},
issn = {1573-2959},
support = {Grant ID: Proc-451-05//This work was conducted as part of the CGIAR Research Initiative on Resilient Cities Through Sustainable Urban and Peri-urban Agri-food Systems and is supported by contributors to the CGIAR Trust Fund (https://www.cgiar.org/funders)./ ; },
mesh = {*Soil Microbiology ; Bangladesh ; Soil/chemistry ; *Environmental Monitoring ; *Drug Resistance, Microbial/genetics ; Gardens ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Despite the growing expansion of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (i.e., resistome) of microbial communities in rooftop and surface garden soils in Bangladesh remain insufficiently characterized, limiting our understanding of their potential role as reservoirs and disseminators of AMR. In this study, shotgun metagenome sequencing was applied to 27 soil samples, including 7 from Dhaka rooftop gardens (DRG), 6 from Dhaka surface gardens (DSG), 8 from Gazipur rooftop gardens (GRG), and 6 from Gazipur surface gardens (GSG) to comprehensively characterize their resistome profiles. We identified 88 antibiotic resistance genes (ARGs), of which 19 (21.6%) were shared across all sites, and found significant differences in resistome composition by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG, 50; GRG, 48) than surface soils (DSG, 40; GSG, 41) and were dominated by glycopeptide resistance genes, collectively representing 62.43-74.07% of ARGs. Rooftop garden soils were also enriched in efflux pumps (adeF, 45.21% of rooftop ARGs) and ribosomal-protection-related oxazolidinone resistance gene O23S (62.13% in GRG). Conversely, surface soils featured a higher abundance of genes mediating antibiotic inactivation, such as CATA (11.64% in DSG) and fosBx1 (5.94% of surface ARGs), as well as those conferring co-resistance to biocides (qacG) and metals. The efflux pump gene adeF also remained a significant component of the surface resistome (24.33% of surface ARGs). Geographic location also modulated resistome composition. Garden soils from Gazipur emerged as notable hotspots, characterized by extremely high abundances of tetracycline efflux pumps (TET45) and multiple copper resistance genes and regulators (e.g., COPA, YCNJ, CSOR). Key ARG carriers included Bacillus licheniformis, B. paralicheniformis, Pseudomonas sabulinigri, and Paenibacillus spp. Spearman correlation analyses revealed strong positive associations (r = 1.0) between specific taxa and resistance mechanisms, as well as co-occurrence patterns among antibiotic, biocide, and metal resistance genes. Collectively, these results indicate that garden soils represent important reservoirs of ARGs, with resistome architecture influenced by both garden type and location, highlighting the necessity for sustainable management practices and a One Health approach to environmental resistome surveillance.},
}

*Soil Microbiology
Bangladesh
Soil/chemistry
*Environmental Monitoring
*Drug Resistance, Microbial/genetics
Gardens
Anti-Bacterial Agents
*Drug Resistance, Bacterial/genetics

@article {pmid41921236,
year = {2026},
author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X},
title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.},
journal = {Pathology, research and practice},
volume = {282},
number = {},
pages = {156456},
doi = {10.1016/j.prp.2026.156456},
pmid = {41921236},
issn = {1618-0631},
abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.},
}

@article {pmid41921318,
year = {2026},
author = {Wang, F and Shi, C and Zhang, W and Chen, Y and Chen, Z and Yang, S and Zhang, J and Liu, W and Cao, W},
title = {Fresh-seawater interface shapes nitrogen fate in a subtropical estuary: Insights from multi-isotopic and metagenomic analyses.},
journal = {Water research},
volume = {298},
number = {},
pages = {125836},
doi = {10.1016/j.watres.2026.125836},
pmid = {41921318},
issn = {1879-2448},
abstract = {Estuaries, the key transitional interface between freshwater rivers and saline seas, are hotspots of nitrogen (N) cycling processes. In this study, we integrated multi-isotope and metagenomic sequencing techniques to characterize nitrate (NO3[-]) sources, mixing and transformation processes, and the regulatory roles of microbial functional genes in different seasons and subzones in the Jiulong River estuary, a typical subtropical estuary. NO3[-]-N was the dominant form of dissolved inorganic N (70.31-91.70 %), with significantly lower concentrations in the seaward subzone than those in other subzones. Hydrochemical parameters, dual-isotope (δ[15]N-NO3[-] and δ[18]O-NO3[-]) signatures, and MixSIAR model indicated that soil N was the largest contributor to NO3[-] (44.7 %), followed by M&S and groundwater in the riverward subzone. The upstream inflow from the riverward subzone accounted for 64.6 % of NO3[-] sources in the mixing subzone. Extensive aquaculture activities in the estuary were the dominant NO3[-] source (44.8 %), followed by M&S and the upstream inflow from the mixing subzone in the seaward subzone. Nitrate reduction genes dominated the N-cycling functional genes and mediated the primary NO3[-] transformation pathways. The PLS-PM model indicated dissimilatory nitrate reduction to nitrite (DNRN) genes had a significant positive effect (0.892) on NO3[-] concentrations and influenced competition between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification for substrates through the C/N ratios. The lower nosZ/narG ratios and higher nitrous oxide concentrations in the riverward and mixing subzones led to more susceptibility to incomplete denitrification, whereas the higher DNRA/DNRN ratios and the significant positive correlation between DNRA and the C/N ratios favored DNRA in the seaward subzone. The lower temperatures and river flows in winter were significantly lower than those in other seasons, which constrained N transforming capacity and resulted in the lowest dissolved nitrous oxide concentration. Therefore, salinity and temperature regulated the primary N-cycling processes by reshaping the composition of functional genes. Overall, this study clarifies the N sources and transformation pathways and provides a systematic theoretical foundation for the development of subzone-based management strategies for estuarine ecosystems.},
}

@article {pmid41921321,
year = {2026},
author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ},
title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.},
journal = {Water research},
volume = {298},
number = {},
pages = {125784},
doi = {10.1016/j.watres.2026.125784},
pmid = {41921321},
issn = {1879-2448},
abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.},
}

@article {pmid41921326,
year = {2026},
author = {Liu, X and Li, C and Zhao, Y and Li, X and Zhang, Q and Zhang, L and Peng, Y},
title = {A novel approach for achieving high enrichment of anammox and nitrogen removal rate in municipal wastewater treatment: A pure biofilm process.},
journal = {Water research},
volume = {298},
number = {},
pages = {125838},
doi = {10.1016/j.watres.2026.125838},
pmid = {41921326},
issn = {1879-2448},
abstract = {Against the backdrop of global carbon neutrality goals and increasingly stringent pollutant discharge standards, the anammox nitrogen removal process has gained significant attention due to its high efficiency, energy-saving, and environmentally friendly characteristics. The current mainstream wastewater treatment technologies still encounter challenges in enriching anaerobic ammonium-oxidizing bacteria (AnAOB) and managing the disposal of substantial amounts of residual sludge. The pure biofilm process has garnered significant attention as the primary focus for autotrophic nitrogen removal transformation in wastewater treatment plants (WWTPs), owing to its ability to efficiently enrich AnAOB and produce low amounts of sludge. This study innovatively proposed a novel pure biofilm process and explored the self-enrichment mechanism of AnAOB in this system. Over 200 days of municipal wastewater treatment under a low C/N ratio (average of 3), the effluent ammonia nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (NRE) achieved 97.72 ± 1.50 % and 94.27 ± 2.92 %, respectively. Long-term operation and batch experiments revealed that carbon source regulation is crucial for the performance of pure biofilm systems. Furthermore, the pure biofilm system demonstrates greater resilience to organic loading shocks compared to floc sludge and hybrid systems. QPCR and 16S rRNA sequencing confirmed the successful enrichment of AnAOB (pre-anoxic:8.94 %, post-anoxic:8.61 %), with anammox contributing to an impressive 81.10 % of nitrogen removal. Additionally, fluorescence in situ hybridization combined with confocal laser scanning microscopy (FISH-CLAM) technology demonstrated a spatially uniform distribution of AnAOB within the system, in contrast to hybrid systems. Metagenomic sequencing revealed the carbon and nitrogen metabolic pathways of functional bacteria in the pure biofilm system, showing that AnAOB's metabolic diversity and ecological niche adaptation within the biofilm structure drove their self-enrichment. Finally, microelectrode measurements of N2O production in the pure biofilm system confirmed its substantial potential for emission reduction. This work offers a practical solution for WWTPs aiming to reduce energy consumption and transition from heterotrophic to autotrophic nitrogen removal processes.},
}

@article {pmid41921531,
year = {2026},
author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, QL},
title = {Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/ae5a51},
pmid = {41921531},
issn = {1752-7163},
abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated by Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.},
}

@article {pmid41921761,
year = {2026},
author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S},
title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113232},
doi = {10.1016/j.diabres.2026.113232},
pmid = {41921761},
issn = {1872-8227},
abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.},
}

@article {pmid41921901,
year = {2026},
author = {Möller, T and Kreft, A and Dennebaum, M and Hess, G and Michel, C and Kriege, O},
title = {Disseminated Strongyloides stercoralis Infection Diagnosed by Metagenomic Next-Generation Sequencing of a Cell-Free DNA blood sample in a Patient with Hematologic Malignancy in Germany: A Case Report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108668},
doi = {10.1016/j.ijid.2026.108668},
pmid = {41921901},
issn = {1878-3511},
abstract = {BACKGROUND: Rare infections that are atypical for Central Europe are increasingly relevant due to global migration, climate change, and the widespread use of immunosuppressive therapies. Diagnosing such infections is often delayed or missed entirely because conventional testing relies on prior clinical suspicion and region-specific test panels. Hypothesis-free metagenomic next-generation sequencing (mNGS) offers a promising diagnostic strategy in these cases.

CASE PRESENTATION: We report a case of disseminated Strongyloides stercoralis (S. stercoralis) infection with hyperinfection syndrome in a man undergoing B-cell-depleting lymphoma therapy. The patient presented with gastrointestinal and pulmonary symptoms, weight loss, and eosinophilia. Conventional microbiological and serological testing failed to identify a cause. Diagnosis and relevant bacterial and fungal coinfection was established using mNGS (DISQVER®) from blood-derived cell-free DNA. Treatment with ivermectin and albendazole led to rapid clinical improvement, and the patient recovered completely.

CONCLUSION: This case illustrates the diagnostic challenges posed by rare infections in immunocompromised patients in non-endemic regions. It highlights the growing need for broad, rapid, and hypothesis-independent diagnostic tools such as mNGS, which can play a key role in identifying unexpected pathogens and guiding early targeted therapy in high-risk populations.},
}

@article {pmid41921920,
year = {2026},
author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB},
title = {Virulence and Antimicrobial Resistance Profiling of Klebsiella pneumoniae Isolated from Foxes in Northern China.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108476},
doi = {10.1016/j.micpath.2026.108476},
pmid = {41921920},
issn = {1096-1208},
abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.},
}

@article {pmid41922261,
year = {2026},
author = {Adebayo, AA and Babalola, OO},
title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70325},
doi = {10.1111/1758-2229.70325},
pmid = {41922261},
issn = {1758-2229},
support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; },
mesh = {*Daucus carota/microbiology/growth & development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.},
}

*Daucus carota/microbiology/growth & development
*Rhizosphere
*Plant Roots/microbiology
*Microbiota
*Soil Microbiology
Agriculture
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid41922337,
year = {2026},
author = {Doni, L and Trinanes, J and Bosi, E and Vezzulli, L and Martinez-Urtaza, J},
title = {Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71231-3},
pmid = {41922337},
issn = {2041-1723},
abstract = {Long-range dispersals of marine bacteria in the oceans have remained largely indecipherable, which is particularly relevant for Vibrio, responsible for global epidemics in humans and animals. Here, we combine the analysis of 40 terabases of metagenomic data and satellite-tracked surface drifter data, from across the globe revealing that Vibrio are abundant members of the ocean surface and show a strong association with microplankton, which appears to govern their distribution and connectivity at a global scale. We identify long-distance biological corridors connecting Vibrio communities, including potentially pathogenic Vibrio. These corridors allow movement over thousands of kilometres in a fairly short time, with estimates of less than 1.5 years to cross an ocean basin. These findings have deep implications for the demography and community dynamics of Vibrio species and the epidemiology of associated diseases.},
}

@article {pmid41922358,
year = {2026},
author = {Korchagina, MV and Mullin, CE and Soufi, HH and Lambert, S and Moran, IG and Porch, R and Albright, SE and Doran, AS and Jones, LM and Malamud, N and Jin, Q and Wood, AM and Louca, S},
title = {Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07139-w},
pmid = {41922358},
issn = {2052-4463},
abstract = {Hot springs are natural laboratories for studying microbial diversity, evolution, and adaptation to extreme environments. Despite their abundance across the Western US, information about the functional and genomic structure of inhabiting microbial communities is restricted to a handful of locations. Here we present a dataset of 500 deep metagenomes, totaling 3.38 terabasepairs and collected from 56 remote hot springs across the US Great Basin and Yellowstone, with 25 of the hot springs surveyed annually over 4 consecutive years. Additionally, we present 780 bacterial and archaeal metagenome-assembled genomes (MAGs) binned from these metagenomes, with completeness ≥80% and contamination ≤5%, of which 149 are considered "high quality". Many of the MAGs likely represent entirely novel genera and even families, relative to the Genome Taxonomy Database. Our spatiotemporally extensive dataset yields insight into the microbial functional structure at dozens of previously unstudied locations, substantially expands our repertoire of extremophile microbial genomes, provides a new resource for high-temperature biotechnology, and enables future phylogenomic studies of these communities through space and time.},
}

@article {pmid41913289,
year = {2026},
author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P},
title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00828-2},
pmid = {41913289},
issn = {1757-4749},
abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.},
}

@article {pmid41913691,
year = {2026},
author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A},
title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70122},
doi = {10.1111/1755-0998.70122},
pmid = {41913691},
issn = {1755-0998},
support = {//Ministerium für Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft für Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; *Amphibians/classification/genetics ; *DNA, Environmental/genetics ; Workflow ; *Metagenomics/methods ; },
abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Biodiversity
*Amphibians/classification/genetics
*DNA, Environmental/genetics
Workflow
*Metagenomics/methods

@article {pmid41913730,
year = {2026},
author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A},
title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {65},
pmid = {41913730},
issn = {2732-5121},
abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.},
}

@article {pmid41913758,
year = {2026},
author = {Chin, D and Campbell, B and Petersen, J and Lim, SJ and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {131},
pmid = {41913758},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Anodontia alba (buttercup lucine; Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1 862.85 megabases. Most of the assembly (99.28%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Gene annotation of this assembly by Ensembl identified 12 083 protein-coding genes. From the metagenome data, we recovered four bins, of which three were high-quality MAGs.},
}

@article {pmid41913906,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y},
title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {590621},
pmid = {41913906},
issn = {1178-7074},
abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.},
}

@article {pmid41914171,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN},
title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39439},
doi = {10.31083/FBE39439},
pmid = {41914171},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.

METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.

RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).

CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.},
}

Animals
Female
Cattle/microbiology
*Endometrium/microbiology/metabolism
*Microbiota
High-Throughput Nucleotide Sequencing
*Metagenomics

@article {pmid41914631,
year = {2026},
author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS},
title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219825},
doi = {10.1128/spectrum.02198-25},
pmid = {41914631},
issn = {2165-0497},
abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.},
}

@article {pmid41914733,
year = {2026},
author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D},
title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0235725},
doi = {10.1128/aem.02357-25},
pmid = {41914733},
issn = {1098-5336},
abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.},
}

@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}

@article {pmid41915015,
year = {2026},
author = {Sun, Y and Wu, X and Zanina, OG and Rivkina, EM and Lloyd, KG and Löffler, FE and Vishnivetskaya, TA},
title = {Incomplete Denitrifying Bacteria Drive N2O Fluxes in Ancient Siberian Permafrost Microcosms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag034},
pmid = {41915015},
issn = {1574-6941},
abstract = {Nitrous oxide (N2O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N2O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO3-- and N2O to assess denitrification and N2O consumption at 4 and 20°C. Rapid N2O formation was observed in NO3--supplemented microcosms, but N2O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO3- and/or N2O reduction were recovered from both NO3-- and N2O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO3-- and N2O-supplemented microcosms, contained nosZ genes indicating N2O consumption potential, however the complete denitrification (i.e., NO3-→N2) gene sets were not detected in these MAGs. Though, N2O production exceeded N2O consumption in NO3--supplemented microcosms at 4°C. Our microcosm experiments suggest N2O formation surpasses its consumption in newly-thawed ~120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.},
}

@article {pmid41915265,
year = {2026},
author = {Volk, A and Mills, M and Chae, S and Lee, J},
title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41915265},
issn = {1614-7499},
abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.},
}

@article {pmid41915324,
year = {2026},
author = {Varshney, A and Sarethy, IP},
title = {Metagenome-based insights into bacteriophage diversity of an urban river ecosystem.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41915324},
issn = {1573-4978},
}

@article {pmid41915473,
year = {2026},
author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C},
title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117166},
doi = {10.1016/j.celrep.2026.117166},
pmid = {41915473},
issn = {2211-1247},
abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.},
}

@article {pmid41915526,
year = {2026},
author = {Xiao, Z and Wei, A and Jia, Y and Zhao, W and Jiang, X},
title = {Semantic fusion of dual perspectives on genomic sequences and quorum sensing for bacteriophage lifestyle prediction.},
journal = {IEEE journal of biomedical and health informatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/JBHI.2026.3679001},
pmid = {41915526},
issn = {2168-2208},
abstract = {As the most ubiquitous and abundant viral community, bacteriophages (phages for short) play a vital role in regulating the ecological balance by infecting bacteria and archaea. Phages can be classified into two types based on their lifestyles: virulent phages and temperate phages, which are closely related to their functional characteristics and influence their interaction patterns with hosts. Therefore, identifying phage lifestyle is critical for understanding the mechanisms by which phages infect bacteria and represents a key step in mastering their functions and potential applications. In this paper, we propose a novel method for phage lifestyle identification by considering two perspectives. One perspective is based on the genomic sequences of phages, in which both local and global semantic features are integrated. The other perspective focuses on the host quorum sensing phenomena that influence phage lysogen-lysis decisions. Specifically, we first capture local sequence variation patterns by extracting the relative positional information of nucleotide fragments at different intervals, which enables robust representation of local genomic semantics. Secondly, the pretrained nucleotide language model DNABERT is applied to capture the semantics of genome sequences by considering the global contextual information. Finally, combined with quorum sensing signals from the bacterial host, a final fusion representation is obtained, which is fed into a predictive model to identify the phage's lifestyle. Experimental results show that our method has excellent and stable performance in both phage complete genome and short contigs from metagenomic data. We also investigate early-life viral colonization in the human gut metagenome, further validating the model's generalizability and real-world applicability.},
}

@article {pmid41915541,
year = {2026},
author = {Yue, Y and Kang, YJ and Wang, H and Jiang, H and Zhou, H and Jiang, W and Li, K},
title = {Diagnosis of Cat-Scratch Disease by Metagenomic Next-Generation Sequencing.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {15303667261435870},
doi = {10.1177/15303667261435870},
pmid = {41915541},
issn = {1557-7759},
abstract = {Cat-scratch disease caused by Bartonella henselae is a worldwide distributed zoonotic disease. Cats are the major reservoirs of B. henselae, and human infection cases are usually resulted from contact with pet cats. In this study, a 49-year-old woman presented to the hospital after 10 days of fever. She also complaint lymph node enlargement and pain. Laboratory tests indicated liver dysfunction and inflammation. Pathological examination of the lymph node suggested the possibility of cat-scratch disease, and then doxycycline was used. Metagenomic next-generation sequencing showed that 59496 sequences of B. henselae were identified, confirming the diagnosis of cat-scratch disease. Meanwhile, Acinetobacter towneri and Epstein-Barr virus were also identified. Doxycycline therapy was continued, and the enlargement of lymph node was apparently alleviated. Epidemiological investigation showed that she had a pet cat, and she was possibly infected through direct contact with the cat. Cat-scratch disease in China may be an underestimated disease. Although multiple methods for detecting B. henselae have been established, low bacteremia is still a key challenge to molecular diagnosis. mNGS is a preferable choice for the diagnosis of cat-scratch disease due to its feasibility, sensitivity, and timeliness.},
}

@article {pmid41916285,
year = {2026},
author = {Makumbi, JP and Leareng, SK and Bezuidt, OK and Coelho, LP and Makhalanyane, TP},
title = {Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum.},
journal = {Cell reports},
volume = {},
number = {},
pages = {117128},
doi = {10.1016/j.celrep.2026.117128},
pmid = {41916285},
issn = {2211-1247},
abstract = {Inadequate wastewater treatment can drive the spread of antimicrobial resistance (AMR), threatening ecosystems and human health. Extracellular DNA (exDNA) stabilizes antimicrobial resistance genes (ARGs) in the environment and facilitates horizontal gene transfer, yet its taxonomic structure and influence on AMR ecology remain poorly understood, especially in African aquatic systems. We profile exDNA-associated resistomes across nine South African wastewater treatment plants and receiving rivers, comparing single-stage activated sludge process (ASP-only) and combined ASP-biofilter systems. exDNA harbors high-risk mobile ARGs conferring resistance to last-resort antibiotics, with enrichment in effluents and downstream rivers. Surprisingly, upstream river samples also carry abundant ARGs, indicating cumulative inputs from multiple environmental reservoirs. ARGs are mainly associated with Pseudomonadota and Bacteroidota, suggesting that exDNA constitutes an ecologically distinct AMR reservoir dominated by key taxa. These findings underscore the need to integrate exDNA into AMR surveillance and highlight its broader role in microbial adaptation within freshwater environments.},
}

@article {pmid41917109,
year = {2026},
author = {Foresto, L and Radaelli, E and Leuzzi, D and Palladino, G and Scicchitano, D and Bejaoui, S and Turroni, S and Rampelli, S and Santolini, C and Pari, A and Marcellini, F and Danovaro, R and Corinaldesi, C and Candela, M},
title = {Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45229-2},
pmid = {41917109},
issn = {2045-2322},
}

@article {pmid41917329,
year = {2026},
author = {Sun, Y and Hu, X and Han, J and Wang, Y and Luo, J and Yu, J and Duan, Y and Wang, X and Liu, J},
title = {Rapid and noninvasive artificial intelligence-assisted diagnostic method for oral squamous cell carcinoma.},
journal = {NPJ digital medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41746-026-02527-3},
pmid = {41917329},
issn = {2398-6352},
support = {Grant No. 82272815//The National Natural Science Foundation of China/ ; Grant No. 62322114//The National Natural Science Foundation of China Outstanding Youth Fund/ ; Grant No. YG2023LC06//The Medical Engineering Cross Foundation of Shanghai Jiao Tong University/ ; },
abstract = {Oral squamous cell carcinoma (OSCC) remains the most common head and neck malignancy, for which early detection is critical yet challenging with current invasive methods. This study aimed to establish a comprehensive diagnostic framework for OSCC by integrating proton transfer reaction-time-of-flight mass spectrometry (PTR-TOF-MS) breath analysis and metagenomic sequencing with artificial intelligence (AI). Exhaled breath and saliva samples were collected from participants in a discovery cohort (n = 222) and an external validation cohort (n = 83). Samples were analyzed using PTR-TOF-MS and metagenomic sequencing, and multimodal diagnostic models were constructed and trained on the discovery cohort data. We identified OSCC-specific biomarkers, including methanethiol and Fusobacterium nucleatum, and developed an interactive online platform (https://bio.futurecnn.com/) enabling real-time predictions and biomarker interpretability. The AI-driven diagnostic model achieved excellent accuracy (ROC-AUC: 0.92) in distinguishing OSCC patients from healthy controls in the external set. This approach offers a practical, noninvasive solution for OSCC screening and establishes an adaptable framework for other breath-based diagnostics.},
}

@article {pmid41907005,
year = {2026},
author = {Jeunen, GJ and Mills, S and Bailie, M and Mauvisseau, Q and Lamare, M and Mariani, S and Pearman, W and Zavodna, M and Treece, J and Ferreira, S and Gemmell, NJ},
title = {Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70132},
doi = {10.1111/1755-0998.70132},
pmid = {41907005},
issn = {1755-0998},
support = {MFP-UOO2116//Royal Society of New Zealand Marsden Fast-Start Fund/ ; ANTA1801//Ministry of Business, Innovation, and Employment/ ; //University of Otago Research Grant (UORG)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *Metagenomics/methods ; *Specimen Handling/methods ; RNA, Ribosomal, 16S/genetics ; *Preservation, Biological/methods ; Fishes/genetics ; },
abstract = {Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.},
}

*DNA Barcoding, Taxonomic/methods
Museums
Animals
*Metagenomics/methods
*Specimen Handling/methods
RNA, Ribosomal, 16S/genetics
*Preservation, Biological/methods
Fishes/genetics

@article {pmid41907295,
year = {2026},
author = {Liu, J and Zhou, Y and Xu, F and Liu, W and Chen, H and Yan, Q and Guo, J and Lai, L},
title = {Case Report: Cavitary Legionella pneumophila pneumonia in a kidney transplant recipient: mNGS-guided diagnosis and prolonged combination therapy.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1697062},
pmid = {41907295},
issn = {2296-858X},
abstract = {Legionella pneumophila is an uncommon but potentially life-threatening cause of pneumonia in solid organ transplant (SOT) recipients. Diagnosis is challenging due to nonspecific features and the limited sensitivity of conventional assays. Metagenomic next-generation sequencing (mNGS) offers unbiased detection and may be particularly valuable in immunocompromised hosts with refractory pneumonia. We report the first documented case in Asia of cavitary Legionella pneumonia in a kidney transplant recipient. A 60-year-old man presented with fever and bilateral pulmonary nodules 5 months post-transplant. Despite empirical antifungal and antibacterial therapy, his condition progressed radiologically to cavitary disease. Bronchoalveolar lavage fluid mNGS identified abundant L. pneumophila reads, confirming the diagnosis. Initial azithromycin monotherapy achieved transient improvement but failed to prevent radiological progression. Escalation to prolonged dual therapy with azithromycin and levofloxacin resulted in rapid symptomatic relief, progressive cavity regression on serial computed tomography, and preserved allograft function. Sequential blood-based mNGS demonstrated declining pathogen reads paralleling recovery. This brief research report emphasizes three practice points for SOT recipients with refractory pneumonia: (1) early mNGS can shorten time-to-diagnosis when routine tests are inconclusive; (2) Legionella infection may manifest with atypical cavitary lesions in immunocompromised hosts, warranting scheduled imaging even when symptoms improve; and (3) prolonged macrolide-fluoroquinolone combination therapy may be required for severe or non-resolving cases. Together with our literature review, this case expands understanding of the radiological spectrum, diagnostic strategies, and therapeutic considerations of Legionella pneumonia in transplant populations.},
}

@article {pmid41907709,
year = {2024},
author = {Nirmalkar, K and Patel, J and Kang, DW and Bellinghiere, A and Bowes, DA and Qureshi, F and Adams, JB and Krajmalnik-Brown, R},
title = {Bimodal distribution of intestinal Candida in children with autism and its potential link with worse ASD symptoms.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2358324},
pmid = {41907709},
issn = {2993-3935},
abstract = {The gastrointestinal (GI) tract harbors a complex and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e. mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. This work aimed to elucidate the gut mycobiota in a cohort of 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants, autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We performed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in the ASD fecal samples compared to TD children. Candida and C. albicans demonstrated a bimodal distribution among children with ASD. The small subset of children with elevated C. albicans or decreased S. cerevisiae had increased Autism Treatment Evaluation Checklist (ATEC) scores. Our findings suggest that a deficit of S. cerevisiae, and an overgrowth of C. albicans in a subset of children is associated with worse autism severity. Future work employing shotgun metagenomics with a larger cohort is encouraged to advance understanding of the functional role of fungi, and their possible interplay with GI symptoms and autism severity in children with ASD.},
}

@article {pmid41907719,
year = {2024},
author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G},
title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {2438621},
pmid = {41907719},
issn = {2993-3935},
abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.},
}

@article {pmid41908157,
year = {2024},
author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F},
title = {Diversity and composition of gut protist in young rural Zimbabwean children.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1399160},
pmid = {41908157},
issn = {2813-4338},
abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.

METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.

RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).

SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.},
}

@article {pmid41908294,
year = {2026},
author = {Schulz, S and Börner, S and Bitter, K and Gheit, H and Partsakhashvili, J and Ukkat, J and Misiak, D and Reichert, S},
title = {Possible association between the microbiota in subgingival and atherosclerotic plaque in a cohort of patients with carotid stenosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2648325},
pmid = {41908294},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontal pathogens have been implicated in systemic diseases, including atherosclerosis. This study investigates the relationship between subgingival and microbial colonization of carotid plaque in patients undergoing carotid endarterectomy (DRKS00021598).

METHODS: Microbial samples from both subgingival and carotid plaques were collected from 25 hospitalized patients. Preoperative all patients underwent periodontal examination. The microbial composition was assessed using metagenomics sequencing of 16S rRNA gene (V3/V4 regions).

RESULTS: Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between both communities. Alpha diversity was significantly higher in subgingival samples than in carotid plaques (p = 0.039). Beta diversity analysis, (including unweighted UniFrac (p < 0.001), linear discriminant analysis, principal component analysis) confirmed significant differences between subgingival and carotid plaque microbiota. The study revealed overlaps in a few individual cases.

CONCLUSIONS: These findings show that carotid plaque microbiota differ from subgingival communities and are not exclusively of oral origin, suggesting additional systemic sources.},
}

@article {pmid41908297,
year = {2026},
author = {Shantha, JG and Chen, C and Hinterwirth, A and Gonzales, JA and Acharya, NR and Lietman, TM and Doan, T},
title = {Integrated metagenomic sequencing and phage display-based immunoprecipitation sequencing for presumptive viral infection: a case report.},
journal = {American journal of ophthalmology case reports},
volume = {42},
number = {},
pages = {102561},
pmid = {41908297},
issn = {2451-9936},
abstract = {PURPOSE: To report a case of uveitis in which unbiased metagenomic sequencing (MDS) and phage immunoprecipitation sequencing (PhIP-Seq) were performed on intraocular fluid.

OBSERVATIONS: A female patient with a past medical history of human immunodeficiency virus (HIV-1) who presented with chronic active anterior and intermediate uveitis with cystoid macular edema in the left eye. She had a previous ocular history of viral retinitis presumed to be secondary to cytomegalovirus (CMV). An anterior chamber tap was performed for viral polymerase chain reactions (PCRs), MDS, and pathogen PhIP-Seq. PCR testing and MDS were negative for pathogen genetic materials. PhIP-Seq detected antibody enrichment of CMV, as well as HIV-1 andSARS-CoV-2.

CONCLUSIONS: The combination of MDS and PhIP-Seq has the potential to provide additional insights into the pathogenesis and the ocular microenvironment of uveitis patients.},
}

@article {pmid41908958,
year = {2026},
author = {Song, Y and Pu, X and Liu, Q and Hou, S and Zou, D and Xiang, Y and Gu, S and Chu, M},
title = {Dietary energy alters jejunal microbial function without changing its structure in small-tailed Han sheep.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1730873},
pmid = {41908958},
issn = {2297-1769},
abstract = {Dietary energy levels typically influence the structure and functional profile of the gastrointestinal microbial community. In this study, thirty 6-month-old Small-tailed Han (STH) sheep were randomly divided into three groups and fed corn-based diets with different energy levels for 150 days. Jejunal contents were then collected and analyzed using metagenomic sequencing to assess microbial alpha diversity and taxonomic composition. Functional annotation and enrichment analysis were performed using the KEGG database. Principal coordinate analysis (PCoA) and alpha diversity indices (Chao1, Shannon, Simpson and good coverage) revealed no significant changes in the overall structure or macro-ecological characteristics of the jejunal microbial community in response to dietary energy levels. At the phylum level, Bacillota was the absolutely dominant phylum, while at the genus level, Methanobrevibacter was the most abundant genus. The abundances of these core microbial taxa did not differ significantly among groups. However, KEGG functional enrichment analysis revealed significant differences in microbial functions between groups. The low-energy group exhibited enrichment in pathways related to energy deficiency and stress adaptation, whereas the high-energy group showed significant enrichment in pathways associated with active growth and anabolic metabolism. In conclusion, although dietary energy levels did not significantly alter the microbial community structure in the jejunum of STH sheep, they profoundly influenced its functional potential. These findings suggest that dietary energy may modulate host nutrient acquisition and health status by regulating the functional characteristics of the jejunal microbiota.},
}

@article {pmid41909054,
year = {2025},
author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M},
title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.},
journal = {Applied microbiology (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {},
pmid = {41909054},
issn = {2673-8007},
abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.},
}

@article {pmid41909251,
year = {2026},
author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y},
title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1735540},
pmid = {41909251},
issn = {1664-302X},
abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.

METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.

RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).

DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.},
}

@article {pmid41909254,
year = {2026},
author = {Pan, K and Zhang, Z and Feng, L and Wu, X and Yang, X and He, X and Xiao, Y and Yang, D and Duan, C and Wang, Q},
title = {Biochar regulates putative keystone microbial taxa to drive phosphorus cycling and increase availability in urban greenspace soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786258},
pmid = {41909254},
issn = {1664-302X},
abstract = {The quality of soil in urban green spaces often deteriorates due to poor design practices, insufficient maintenance, and environmental pressures associated with urbanization. Although biochar, as an effective soil additive, can significantly improve the soil quality in greenspace, it significantly influences the phosphorus (P) cycling processes through functional regulation of microbial community; however, further analysis is essential to validate this mechanism. Therefore, this study reported pot experiments using Euonymus kiautschovicus, a typical urban greenspace plant, followed by metagenomic analysis for investigating microbial-driven P cycle mechanisms. Four treatment groups were established according to the dosage of biochar, including 0% (CK), 4% (BC4), 8% (BC8), and 12% (BC12). Biochar application significantly increased soil available P (AP) and total P (TP) content, with BC12 demonstrating maximum AP and TP content of 21.79 mg kg[-1] and 0.62 g kg[-1], respectively. On the one hand, biochar serves as a direct source of P. On the other hand, it enhances AP by regulating P-cycling functional microorganisms. Random forest model identified phnP, phoA, relA, ppnK, pstA, phnD, and pstS as the putative keystone genes regulating soil P cycling. Microbial co-occurrence network analysis and partial least squares path modeling (PLS-PM) demonstrated that the biochar application improved soil AP by regulating putative keystone microbial taxa (Modules 1 and 2) involved in P cycling. This study elucidates the microbial mechanisms underlying biochar-mediated P cycling in greenspace soils, providing a scientific basis for biochar application for improved soil quality in urban greenspace.},
}

@article {pmid41909264,
year = {2026},
author = {Li, L and Zhao, D and Du, R and Tang, K and Zhang, Y},
title = {Niche adaptation of particle-associated ammonia-oxidizing archaea sustains nitrification under marine deoxygenation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1773718},
pmid = {41909264},
issn = {1664-302X},
abstract = {Marine deoxygenation is restructuring coastal microbial niches and metabolic networks, with cascading effects on biogeochemical cycles, a key component of which is the nitrogen cycle. Particles constitute a critical ecological interface that mediates microbial niche partitioning and oxygen-sensitive balance between nitrogen loss and retention in deoxygenating coastal waters. However, the niche-dependent metabolic partitioning of microbial communities and its influence on the nitrogen cycle under deoxygenation remains poorly constrained. We conducted a 22-day field investigation of the deoxygenated water column off the Zhoushan coast, China, combining temporal [15]N-tracer-based nitrification rate measurements with size-fractionated metagenomic sequencing during the day of the most severe bottom-water oxygen depletion. Our data revealed a nitrification hotspot in the low-oxygen waters below the pycnocline, with persistently elevated rates and an enriched abundance of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria. Notably, particle-associated AOA exhibited significantly enriched genomic potential for coupled nitrogen cycling and carbon fixation, while the dominant groups adapted to low-oxygen particles via distinct metabolic strategies. Nitrosomarinus-like AOA exhibited higher gene counts (amoA-normalized) for ammonia (amt) and high-affinity phosphate (pst) transporters, whereas their Water column group A-like counterparts were enriched in low-affinity phosphate transporters (pit). Urease gene enrichment in both major AOA clades implicates urea as an ecologically relevant alternative nitrogen source for ammonia acquisition in coastal waters. Furthermore, particle-associated AOA may couple nitrite production and consumption via co-enriched ammonium monooxygenase (amoA) and nitrite reductase (nirK), potentially increasing nitrogen loss through local nitrite utilization. Collectively, our findings demonstrate that differential adaptation across clades underpins the pivotal role of AOA in nitrogen cycling under deoxygenation.},
}

@article {pmid41909265,
year = {2026},
author = {Nagy, Á and Tóth, GE and Sály, P and Pereszlényi, CI and Babinszky, GC and Makrai, L and Somogyi, BA and Gyuranecz, M},
title = {Development of Nanopore amplicon sequencing method for culture-free genotyping of Bacillus anthracis strains directly from environmental samples.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771578},
pmid = {41909265},
issn = {1664-302X},
abstract = {Fast and accurate genetic subtyping of pathogens is required to respond appropriately to biological events caused by natural outbreaks or bioattacks involving anthrax. In this study, we developed and validated a culture-free genotyping method that combines a multiplex PCR-based amplicon sequencing method on the Nanopore platform with in silico multiple-locus variable-number tandem repeat analysis (MLVA) of 31 loci to identify an unknown Bacillus anthracis strain directly from environmental samples. The novel method accurately identified repeat numbers for all loci in 12 different MLVA genotype Bacillus anthracis strains analyzed in the study, matching 100% with the reference capillary electrophoresis and Sanger sequencing results. The detection limit of the method, at which all 31 variable-number tandem repeat loci were successfully identified, was found to be 10[4] CFU spores/sample for pure spore samples and at 10[6] CFU spores/sample for spiked environmental samples from three matrices (soil, swab, and muddy water). Specificity tests yielded negative results for samples containing only non-Bacillus anthracis members of the Bacillus cereus group, which produced sequencing reads for 15 loci but were non-specific to Bacillus anthracis. To validate the method, we genotyped 11 Bacillus anthracis strains originating from a historical collection of Hungarian isolates. The MLVA31 typing scheme classified the strains into five groups, four of which fell into the A.Br.008/009 Trans-Eurasian (TEA) group within the clade A, and one into the B.Br.CNEVA group within the clade B. The largest group within clade A comprises six strains that are assumed to be members of the dominant Bacillus anthracis population in Hungary. Our results demonstrate that PCR-based amplicon sequencing using the portable MinION device is highly effective for on-site genotyping of pathogens directly from environmental samples. This establishes the NGS-based MLVA genotyping as a valuable tool for biodefense laboratories in preliminary forensic investigations of bioterrorism-related anthrax outbreaks. Furthermore, our results provide new insights into the genetic diversity of Bacillus anthracis in a region (Hungary, Central Europe) that is underrepresented in research and has limited scientific data.},
}

@article {pmid41909643,
year = {2026},
author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O},
title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.},
journal = {Biofilm},
volume = {11},
number = {},
pages = {100357},
pmid = {41909643},
issn = {2590-2075},
abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.},
}

@article {pmid41909838,
year = {2026},
author = {Zhang, B and Wang, L and Wang, J and Qi, D and Zhang, N},
title = {Comparative diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture in spinal infections: a systematic review and meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1689254},
pmid = {41909838},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Spinal Diseases/diagnosis/microbiology ; *Microbiological Techniques/methods ; },
abstract = {BACKGROUND: Spinal infections are relatively uncommon but clinically serious conditions that require timely and accurate diagnosis to prevent severe complications. Traditional microbial culture methods remain the gold standard but suffer from low sensitivity and prolonged turnaround times. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool offering broad-spectrum pathogen detection. However, its diagnostic performance in spinal infections remains unclear.

OBJECTIVE: To systematically evaluate and compare the diagnostic accuracy of mNGS and conventional microbial culture in detecting pathogens in spinal infections.

METHODS: This systematic review and meta-analysis adhered to the 2020 PRISMA guidelines and was registered in PROSPERO. A comprehensive literature search of PubMed, Cochrane Library, Web of Science, and Scopus was performed up to July 2025. Studies involving suspected spinal infection patients tested by both conventional microbiological methods and metagenomic next-generation sequencing (mNGS) were included. Data extraction and quality assessment were independently conducted by two reviewers using standardized tools. Meta-analyses were performed to pool diagnostic accuracy metrics, and publication bias was assessed.

RESULTS: A total of 14 studies involving 1,353 patients were included after screening 4,132 records. All studies originated from China, with sample sizes ranging from 17 to 301. Quality assessment showed generally high methodological rigor with low risk of bias. Conventional meta-analysis demonstrated that mNGS had significantly better positive agreement (OR = 0.46, p < 0.00001), higher sensitivity (OR = 0.45, p < 0.00001), and superior negative predictive value (OR = 0.36, p < 0.00001) compared to traditional methods, while specificity and positive predictive value were comparable. Diagnostic meta-analysis revealed pooled sensitivity and specificity of 0.86 and 0.90, respectively, with an AUC of 0.90, indicating high diagnostic accuracy. Fagan nomogram analysis showed that with a 50% pre-test probability, positive and negative mNGS results corresponded to post-test probabilities of 89% and 13%, respectively. No significant publication bias was detected.

CONCLUSIONS: mNGS exhibits superior sensitivity and overall diagnostic accuracy compared to traditional microbial culture in spinal infections, supporting its use as a valuable complementary diagnostic tool. Further prospective, multicenter studies are warranted to validate these findings and promote standardized clinical implementation.

PROSPERO, identifier CRD420251114975.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
*Spinal Diseases/diagnosis/microbiology
*Microbiological Techniques/methods

@article {pmid41909845,
year = {2026},
author = {Wang, C and Min, M and Dai, Z and Wang, G and Wang, Y and Hu, T and Ma, Y and Zhang, S and Wu, C and Zhou, R},
title = {Diagnostic value of metagenomic next-generation sequencing in patients with febrile lung cancer with negative conventional microbiological tests and without neutropenia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1715563},
pmid = {41909845},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology/diagnosis ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; *Fever/microbiology/diagnosis/etiology ; Aged, 80 and over ; },
abstract = {INTRODUCTION: Fever in nonneutropenic lung cancer often remains microbiologically unresolved because of the limitations of conventional microbiological tests (CMT). We assessed whether plasma metagenomic next-generation sequencing (mNGS) improves diagnostic yield and accelerates defervescence in these patients.

METHODS: We retrospectively analyzed 53 CMT-negative febrile lung cancer patients (August 2023-October 2024). Patients were classified into high-suspicion infectious fever (HSIF) or high-suspicion tumor fever (HSTF) groups based on mNGS results, and clinical management was adjusted accordingly.

RESULTS: mNGS identified pathogens in 69.8% (37/53) of patients, commonly including Epstein-Barr virus, Mycobacterium tuberculosis, and Candida albicans. Patients in the HSIF group showed significantly higher baseline inflammatory markers than those in the HSTF group. Importantly, following mNGS-guided antimicrobial therapy, the HSIF group achieved significantly higher defervescence rates at 48 h (73.0% vs. 37.5%; p = 0.029) and 96 h (89.2% vs. 68.8%; p = 0.027) compared to the HSTF group.

DISCUSSION: In conclusion, in CMT-negative, nonneutropenic febrile lung cancer, plasma mNGS significantly increases pathogen detection and informs antimicrobial decisions associated with earlier defervescence, although interpretation is limited by the retrospective design and lack of an independent gold standard.},
}

Humans
*Lung Neoplasms/complications/microbiology/diagnosis
Retrospective Studies
Female
Male
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
*Metagenomics/methods
Aged
*Fever/microbiology/diagnosis/etiology
Aged, 80 and over

@article {pmid41909847,
year = {2026},
author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L},
title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779296},
pmid = {41909847},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Bacteriophages/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing ; Sputum/virology/microbiology ; Bronchoalveolar Lavage Fluid/virology/microbiology ; *Respiratory Tract Infections/virology/microbiology ; Male ; Female ; Middle Aged ; Bacteria/virology/genetics ; Aged ; Computational Biology ; Adult ; Virome ; },
abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.

METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.

RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.

CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.},
}

Humans
*Metagenomics/methods
*Bacteriophages/genetics/classification/isolation & purification
*High-Throughput Nucleotide Sequencing
Sputum/virology/microbiology
Bronchoalveolar Lavage Fluid/virology/microbiology
*Respiratory Tract Infections/virology/microbiology
Male
Female
Middle Aged
Bacteria/virology/genetics
Aged
Computational Biology
Adult
Virome

@article {pmid41909891,
year = {2025},
author = {Manzoor, H and Kayani, MUR},
title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2483446},
pmid = {41909891},
issn = {2993-3935},
abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.},
}

@article {pmid41909892,
year = {2025},
author = {Montenegro-Borbolla, E and Wakim El-Khoury, J and Bertelli, C and Schoepfer, A and Guery, B and Galperine, T},
title = {Resolution of long-term severe irritable bowel syndrome following fecal microbiota transplantation: A case report and microbiota analysis.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2487905},
pmid = {41909892},
issn = {2993-3935},
abstract = {The diagnosis and management of irritable bowel syndrome (IBS) is challenging due to its complex symptoms and inconsistent treatment responses. Given the important role of gut microbiota in gastrointestinal health, fecal microbiota transplantation (FMT) is a promising intervention. We describe the case of a 55-y-old woman without prior gastrointestinal issues who, following severe depression, developed multiple gastrointestinal symptoms, including abdominal pain, fluctuating bowel habits, and a persistent burning sensation in her mouth and upper gastrointestinal tract. At Lausanne University Hospital, she was diagnosed with IBS resistant to multiple lines of treatment and a multidisciplinary team proposed multiple oral FMTs. One-month post-FMT, her gastrointestinal symptoms significantly improved and remained better after a year, with only the burning sensation persisting. Analysis of pre- and post-FMT samples and donor material, using 16S rRNA amplicon metagenomics, revealed a 90% genus-level taxonomic overlap between the patient and the donor. The observed changes in the relative abundance of these genera, including the enrichment of beneficial gut commensals, as well as the elimination of IBS-associated genera likely supported her recovery. Overall, FMT led to substantial improvement in her long-standing gastrointestinal symptoms.},
}

@article {pmid41909896,
year = {2025},
author = {Yasuda, T and Takagi, T and Naito, Y and Inoue, R and Mizushima, K and Asaeda, K and Hashimoto, H and Kitae, H and Uchiyama, K and Ouchi, N and Adachi, A and Kamitani, T and Matoba, S and Itoh, Y},
title = {Sarcopenia-related gut microbiota in the elderly: Insights from the longevity region of Kyotango and its nutritional associations.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2591561},
pmid = {41909896},
issn = {2993-3935},
abstract = {Sarcopenia is influenced by the gut microbiota and dietary habits; however, the underlying mechanisms remain elusive. This study investigated the gut microbiota composition of elderly individuals in a healthy longevity region and examined its association with sarcopenia and dietary habits. Fecal metagenomic analysis was used to identify gut microbiota taxonomy. Sarcopenia was diagnosed on the basis of grip strength, gait speed, and muscle volume. Japanese dietary habits were assessed using a brief-type self-administered diet history questionnaire. A total of 318 elderly individuals from Kyotango were recruited, 5.7% of whom were diagnosed with sarcopenia. Individuals with sarcopenia exhibited a lower abundance of a genus belonging to the family Lachnospiraceae, and a higher abundance of Megasphera. Several butyrate-producing bacteria, including Lachnospira and Coprococcus showed a positive correlation with sarcopenia related factors, whereas Dorea and Streptococcus were negatively correlated. Hierarchical cluster analysis revealed that these beneficial genera were also positively associated with the frequent intake of traditional Japanese dietary components. These findings suggest that the observed microbial and dietary associations may provide a mechanistic basis for potential protective effects against sarcopenia. Our findings suggest that butyrate-producing bacteria associated with Japanese dietary patterns play a protective role against sarcopenia.},
}

@article {pmid41909897,
year = {2025},
author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M},
title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2527766},
pmid = {41909897},
issn = {2993-3935},
abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.},
}

@article {pmid41909909,
year = {2025},
author = {Wang, H and Yu, S and Zhao, K and Hu, T and Wu, Z and Liang, H and Lin, X and Cui, L and Yao, J and Liu, X and Tong, X and He, N and Xiao, L and Kristiansen, K and Li, S and Zou, Y},
title = {Faecalibacterium longum alleviates high-fat diet-induced obesity and protects the intestinal epithelial barrier in mice.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2459599},
pmid = {41909909},
issn = {2993-3935},
abstract = {Numerous studies have indicated that depletion of Faecalibacterium is related to obesity. Here we show that Faecalibacterium longum CM04-06 out of 29 strains of the Faecalibacterium genus annotated in CGR2 exhibited the strongest inverse correlation with body mass index (BMI) in a cohort of 1120 han Chinese individuals. Administration of F. longum CM04-06 to mice prevented high-fat diet (HFD)-induced obesity, improved glucose tolerance, reduced adipose tissues mass, and liver steatosis. Supplementation with F. longum CM04-06 reduced the level of pro-inflammatory cytokines in liver, colon, and circulation. F. longum CM04-06 protected the intestinal epithelial barrier increasing the expression of tight junction proteins. Metagenomic sequencing indicated that F. longum supplementation did not change the overall composition of the gut microbiota in mice, but selectively increased the relative abundance of Staphylococcus xylosus and Staphylococcus nepalensis. In conclusion, our results point to a potential therapeutic potential of F. longum CM04-06.},
}

@article {pmid41909910,
year = {2025},
author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J},
title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2570502},
pmid = {41909910},
issn = {2993-3935},
abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.},
}

@article {pmid41909911,
year = {2025},
author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO},
title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2589861},
pmid = {41909911},
issn = {2993-3935},
abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.},
}

@article {pmid41910132,
year = {2026},
author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A},
title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019126},
doi = {10.1128/msystems.00191-26},
pmid = {41910132},
issn = {2379-5077},
abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.

IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.},
}

@article {pmid41910137,
year = {2026},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418725},
doi = {10.1128/spectrum.04187-25},
pmid = {41910137},
issn = {2165-0497},
abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.

IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20°C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25°C and 30°C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.},
}

@article {pmid41910214,
year = {2026},
author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J},
title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649440},
doi = {10.1080/19490976.2026.2649440},
pmid = {41910214},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; Rats ; *Prenatal Exposure Delayed Effects/microbiology ; Male ; Social Behavior ; Oxytocin/metabolism ; Fecal Microbiota Transplantation ; *Stress, Psychological/microbiology ; Rats, Sprague-Dawley ; *Probiotics/administration & dosage ; Paraventricular Hypothalamic Nucleus/metabolism ; Behavior, Animal ; },
abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
Pregnancy
*Limosilactobacillus reuteri/physiology
Rats
*Prenatal Exposure Delayed Effects/microbiology
Male
Social Behavior
Oxytocin/metabolism
Fecal Microbiota Transplantation
*Stress, Psychological/microbiology
Rats, Sprague-Dawley
*Probiotics/administration & dosage
Paraventricular Hypothalamic Nucleus/metabolism
Behavior, Animal

@article {pmid41910252,
year = {2026},
author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y},
title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0252325},
doi = {10.1128/aem.02523-25},
pmid = {41910252},
issn = {1098-5336},
abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.},
}

@article {pmid41910273,
year = {2026},
author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P},
title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0179025},
doi = {10.1128/msystems.01790-25},
pmid = {41910273},
issn = {2379-5077},
abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.

IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.},
}

@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/msphere.00856-25},
pmid = {41910342},
issn = {2379-5042},
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}

@article {pmid41910375,
year = {2026},
author = {Sprenger, GA and Gee, JE and Elrod, MG and Weiner, ZP and Gulvik, CA},
title = {Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent Burkholderia pseudomallei for rapid public health response events.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0292625},
doi = {10.1128/spectrum.02926-25},
pmid = {41910375},
issn = {2165-0497},
abstract = {Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with Burkholderia pseudomallei caused an outbreak of melioidosis in the United States. Metagenome-assembled genome binning depends in part on different nucleotide compositions, and the contaminated aromatherapy spray contained other bacteria, including related species (e.g., Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia multivorans, Burkholderia pseudomultivorans, Cupriavidus pauculus, and Pseudomonas aeruginosa with average nucleotide identity (ANI) to B. pseudomallei being 84.2%, 84.4%, 84.7%, 84.8%, 75.7%, and 72.3%, respectively, and AAI being 79.5%, 79.8%, 80.5%, 80.4%, 62.5%, and 52.9%, respectively). We performed metagenomic sequencing on the contaminated aromatherapy spray to determine if a public metagenomic pipeline (https://github.com/nf-core/mag) can form a MAG of B. pseudomallei. Upon completion of the pipeline, inter- and intracontig comparisons revealed few potential contaminants of related taxa. Conservative removal of those contigs was especially valuable, ultimately obtaining an ANI of 99.9% between the B. pseudomallei MAG and the genome of an isolate from the aromatherapy spray. This underscores the importance of quality checking recovered MAGs (e.g., for congeneric chimerism) for high-resolution objectives such as outbreak pathogenomics. Importantly, our analysis revealed that the identical conclusion was made possible with the B. pseudomallei MAG (as with its corresponding isolate genome), which was that the aromatherapy B. pseudomallei originated from South Asia (specifically India). Because rapid read-based (k-mer) taxonomic classification methods often report false positives, this operational framework could be valuable for rapid biothreat radar detection systems in public health surveillance.IMPORTANCEIn 2021, an imported aromatherapy spray caused a U.S. outbreak of melioidosis after contamination with Burkholderia pseudomallei. Using shotgun metagenomics, we reconstructed a near-complete genome of the pathogen directly from the product, despite the presence of other related microbes. The assembled genome showed 99.9% similarity to a cultured isolate. This work demonstrates that metagenomics can recover high-quality pathogen genomes from complex samples, supporting outbreak investigations and enhancing public health surveillance.},
}

@article {pmid41910449,
year = {2026},
author = {Santos, JCE and Go, DJL and Unciano, RD and Yu, PK and Lao, AR and Enriquez, MLD and Espiritu, LM and Shrestha, AMS},
title = {Investigating the resistome, taxonomic composition, and mobilome of bacterial communities in hospital wastewaters of Metro Manila using a shotgun metagenomics approach.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0396325},
doi = {10.1128/spectrum.03963-25},
pmid = {41910449},
issn = {2165-0497},
abstract = {We profiled antibiotic resistance genes, bacterial communities, and mobile genetic elements in untreated hospital wastewater from three tertiary hospitals in Metro Manila using shotgun metagenomic sequencing. The resistome analysis revealed high abundances of genes known to confer resistance against sulfonamides (sul1, sul2), aminoglycosides (aadS), and macrolides/streptogramins (msrE, mphE). High-risk resistance genes were also detected, including those known to confer resistance to β-lactams (blaOXA, blaTEM, blaGES, blaNDM, blaKPC), colistins (mcr-5), and tetracyclines [tet(C), tet(A), tet(L), tet(M)]. Comparisons with hospital wastewater resistome profiles from regional neighbors and other lower-and-middle-income countries indicated broadly similar relative abundances of dominant resistance genes, with differences largely driven by low-abundance resistance genes. The bacterial community was dominated by the phylum Pseudomonadota, with high relative abundances of the genera Stenotrophomonas, Rhodococcus, and Pseudomonas, while ESKAPEE pathogens were detected at lower levels. A diverse array of mobile genetic elements-many known to be associated with resistance to multiple drug classes and disinfectants-was also observed. Overall, this study provides a valuable preliminary evidence base for future antimicrobial resistance and epidemiological surveillance efforts in the Philippines, particularly those employing wastewater-based approaches.IMPORTANCEAntimicrobial resistance (AMR) is a growing public health threat caused by pathogenic bacteria that are no longer controlled by commonly used treatments. Infections caused by these resistant bacteria may lead to prolonged illness, more severe symptoms, or even death. Hospitals are critical hotspots for the emergence and spread of AMR. Their wastewater, which contains antibiotics, medical and human waste, and diverse microbial communities, can support the persistence and dissemination of resistant bacteria. The significance of this research lies in identifying and characterizing these bacterial communities and the resistance genes they carry. Such information can provide an indication of the resistance burden faced by patients and serve as an early warning system to strengthen infection prevention and control measures, support national surveillance efforts, and inform the development of more effective treatment and management strategies in healthcare settings.},
}

@article {pmid41910593,
year = {2026},
author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , },
title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002618},
pmid = {41910593},
issn = {1536-4828},
abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.

OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).

METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.

RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.

CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.},
}

@article {pmid41910796,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D},
title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41910796},
issn = {1573-7446},
}

@article {pmid41910951,
year = {2026},
author = {Dasgupta, S},
title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261419483},
doi = {10.1177/15578100261419483},
pmid = {41910951},
issn = {1557-8100},
abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.},
}

@article {pmid41911008,
year = {2026},
author = {Hosen, ME and Horwood, PF and Sarker, S},
title = {Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology.},
journal = {The Journal of general virology},
volume = {107},
number = {3},
pages = {},
doi = {10.1099/jgv.0.002247},
pmid = {41911008},
issn = {1465-2099},
mesh = {*Metagenomics/methods ; Humans ; *Flaviviridae Infections/diagnosis/virology ; *Flaviviridae/genetics/isolation & purification ; Transcriptome ; *Gene Expression Profiling/methods ; Virology/methods ; },
abstract = {Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are Orthoflavivirus infections, which pose ongoing diagnostic challenges due to antigenic cross-reactivity, overlapping clinical symptoms and the narrow temporal sensitivity of standard tools such as serology and reverse transcription polymerase chain reaction. These constraints have led to widespread misdiagnoses and underreporting, ultimately hampering both effective clinical management and public health response. Recent advances in metagenomic and metatranscriptomic sequencing offer a transformative solution by enabling unbiased, simultaneous pathogen detection and real-time profiling of viral and host transcriptomics. In this review, we assess the diagnostic performance and translational value of these approaches in resolving Orthoflavivirus infections, with case examples from clinical settings in countries like the USA, UK, China and Germany which have already implemented these approaches into routine diagnosis in some settings. We examine key methodological considerations, including optimal sample timing, sample types and processing, sequencing strategy selection and the diagnostic performance of various platforms. We highlight the growing use of metatranscriptomics for detecting active infections, profiling viral and host responses, identifying coinfections and supporting real-time surveillance. We also discuss the key challenges such as technical expertise, lack of standardization, cost, turnaround time and regulatory approval that currently limit global implementation. Finally, we highlight emerging international efforts to integrate sequencing-based diagnostics into routine hospital workflows. Together, these innovations mark a critical shift toward precision diagnostics for Orthoflavivirus infections, with broad implications for clinical settings.},
}

*Metagenomics/methods
Humans
*Flaviviridae Infections/diagnosis/virology
*Flaviviridae/genetics/isolation & purification
Transcriptome
*Gene Expression Profiling/methods
Virology/methods

@article {pmid41911519,
year = {2026},
author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R},
title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/jisesa/ieag027},
pmid = {41911519},
issn = {1536-2442},
support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Male ; *Orthoptera/microbiology ; Bacteria/classification ; },
abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.},
}

Animals
*Gastrointestinal Microbiome
Female
Male
*Orthoptera/microbiology
Bacteria/classification

@article {pmid41912071,
year = {2026},
author = {Zhang, PP and Cui, MY and Shen, Y and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF},
title = {Ophiopogon japonicus Polysaccharide Ameliorates Pulmonary Fibrosis via Gut Microbiota-Metabolite Crosstalk.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108464},
doi = {10.1016/j.micpath.2026.108464},
pmid = {41912071},
issn = {1096-1208},
abstract = {Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log2FC = 2.17) and Duncaniella muricolitica (log2FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log2FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.},
}

@article {pmid41912361,
year = {2026},
author = {Rathwell, C and Fuchsman, CA and Rocap, G},
title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70274},
doi = {10.1111/1462-2920.70274},
pmid = {41912361},
issn = {1462-2920},
support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; },
mesh = {Pacific Ocean ; *Bacteria/virology/genetics/classification/metabolism ; Phylogeny ; *Chlorophyll/metabolism/analysis ; *Microbiota ; *Seawater/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.},
}

Pacific Ocean
*Bacteria/virology/genetics/classification/metabolism
Phylogeny
*Chlorophyll/metabolism/analysis
*Microbiota
*Seawater/microbiology/virology
*Bacteriophages/genetics/classification/isolation & purification
Metagenomics

@article {pmid41912389,
year = {2026},
author = {Wang, YY and Zhang, Q and Zhao, ZF and Zhao, YX and He, Y and Liu, PL and Li, YH},
title = {[Coexistence of lung cancer, brucellosis, and tuberculosis in a single patient: a case report].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {4},
pages = {421-424},
doi = {10.3760/cma.j.cn112147-20260105-00006},
pmid = {41912389},
issn = {1001-0939},
support = {H2024206551//Hebei Natural Science Foundation/ ; 20260411//Hebei Medical Research Project/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Lung Neoplasms/complications/diagnosis ; *Brucellosis/complications/diagnosis ; *Tuberculosis, Pulmonary/complications/diagnosis ; Mycobacterium tuberculosis/isolation & purification ; *Carcinoma, Squamous Cell/complications/diagnosis ; Coinfection ; },
abstract = {Lung cancer, pulmonary tuberculosis, and brucellosis are common clinical diseases. They share overlapping clinical manifestations and pulmonary imaging findings, and all may involve multiple organ systems, making differential diagnosis challenging. We reported a rare case of lung cancer, and co-infection with pulmonary tuberculosis and brucellosis. A 57-year-old male was admitted to our hospital, presenting with intermittent fever for 7 months and cough accompanied by shortness of breath for 1 month. He had previously sought medical care at multiple hospitals, where he was diagnosed with brucellosis and suspected of having pulmonary tuberculosis. Despite receiving anti-tuberculosis and anti-brucellosis treatments, his pulmonary imaging abnormalities and dyspnea progressively worsened. Pathological examination of mucosal biopsies obtained via bronchoscopy and cervical lymph node biopsy at our hospital confirmed squamous cell lung carcinoma. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected Mycobacterium tuberculosis. Although his pulmonary condition temporarily improved following standardized anti-tuberculosis treatment and chemotherapy for lung cancer, the lung cancer subsequently progressed, and the patient ultimately died.},
}

Humans
Male
Middle Aged
*Lung Neoplasms/complications/diagnosis
*Brucellosis/complications/diagnosis
*Tuberculosis, Pulmonary/complications/diagnosis
Mycobacterium tuberculosis/isolation & purification
*Carcinoma, Squamous Cell/complications/diagnosis
Coinfection

@article {pmid41912482,
year = {2026},
author = {Shao, Y and Wang, J and Liu, Y and Ni, Y and Liu, Z and Li, Y and Jia, Q and Li, Q and Wang, X and Li, T and Liu, M and Zhang, S and Guo, Y and Guo, X and Wang, D and Liu, Y and Liu, C and Cai, H and Ning, Y and Zhang, J and Xu, G and Le, W},
title = {Distinct metabolomic and proteomic signatures in Parkinson's disease patients with REM sleep behavior disorder.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {41912482},
issn = {2059-3635},
support = {82271524//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401742//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024RY003//Dalian Science and Technology Bureau/ ; No. 2023-MS-262//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Humans ; *Parkinson Disease/genetics/metabolism/complications/microbiology/pathology/blood ; Female ; Male ; *REM Sleep Behavior Disorder/genetics/metabolism/pathology/blood/complications/microbiology ; *Metabolomics ; Middle Aged ; Aged ; *Proteomics ; Gastrointestinal Microbiome/genetics ; },
abstract = {Rapid eye movement sleep behavior disorder (RBD) is the most specific prodromal marker of Parkinson's disease (PD), affecting 40-50% of PD patients. PD with RBD (RBD-PD) represents a clinically aggressive subtype characterized by more severe motor and nonmotor symptoms, prominent autonomic dysfunction, and accelerated disease progression; however, its underlying pathogenesis remains poorly understood. Here, we integrated multiplatform metabolomics and proteomics with precise clinical phenotyping to delineate molecular signatures in plasma across different PD subtypes. Our analyses demonstrated that PD patients exhibit significant metabolic reprogramming, characterized by a shift in energy metabolism from the tricarboxylic acid cycle toward glycolysis, a dysregulated urea cycle, and lipid remodeling, as well as extensive activation of inflammatory and immune responses involving the PI3K-Akt, IL-17, NF-kappaB, MAPK and TNF signaling pathways. Notably, the RBD-PD subgroup exhibited distinctive metabolic disturbances characterized by the accumulation of gut microbiota-derived toxic aromatic amino acid catabolites. Importantly, these alterations were also observed in idiopathic RBD (iRBD) patients, representing the prodromal stage of PD. By integrating metagenomic profiles, we further revealed that gut microbial dysbiosis in RBD-PD and iRBD drives a functional shift away from dietary fiber fermentation and toward enhanced degradation of protein, aromatic amino acids, glycine, and intestinal mucin glycans. This metabolic reprogramming is associated with exacerbated oxidative stress, neuroinflammation, and accelerated pathological progression. These findings provide multiomic evidence that clarifies the molecular heterogeneity in PD and highlights gut microbiota-driven dysfunction as a key contributor to both the iRBD and RBD-PD subtypes.},
}

Humans
*Parkinson Disease/genetics/metabolism/complications/microbiology/pathology/blood
Female
Male
*REM Sleep Behavior Disorder/genetics/metabolism/pathology/blood/complications/microbiology
*Metabolomics
Middle Aged
Aged
*Proteomics
Gastrointestinal Microbiome/genetics

@article {pmid41912529,
year = {2026},
author = {Achudhan, AB and Narayanan, R and Madhavan, T},
title = {Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07068-8},
pmid = {41912529},
issn = {2052-4463},
abstract = {Plastic pollution is an escalating environmental concern, particularly in coastal regions where sediments serve as long-term sinks for plastic debris. Despite this, the microbial communities inhabiting plastic-contaminated sediments remain poorly characterized in highly polluted hotspots. In this study, we conducted a genome-resolved metagenomic investigation of sediment sample from plastic pollution hotspot in India. Using Illumina short-read sequencing and three high-performing binning tools we reconstructed 52 non-redundant metagenome-assembled genomes (MAGs) from 2,374 initial bins. All MAGs met the MIMAG criteria with 15% reaching near-complete genomes. Taxonomic classification revealed diverse representation of 18 different phyla. Interestingly, 90% of the MAGs could only be classified at intermediate taxonomic levels in the Genome Taxonomy Database (GTDB), suggesting the presence of novel microbial lineages. Taxonomic novelty was further confirmed using the Type Strain Genome Server (TYGS), which identified 3 novel orders, 16 families, and 28 genera. This study provides the first comprehensive genomic insight into microbial communities from plastic-polluted coastal sediments in India and lays the groundwork for exploring their ecological functions.},
}

@article {pmid41913056,
year = {2026},
author = {Marques, LL and Pinho, AJ and Pratas, D},
title = {FALCON2: compression-based metagenomic classification of ancient viruses.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag155},
pmid = {41913056},
issn = {1367-4811},
abstract = {MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples.

RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC = 0.625), Kraken2 (AUPRC = 0.184), and CLARK-S (AUPRC = 0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40 bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses.

AVAILABILITY: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.

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

@article {pmid41704740,
year = {2026},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Integrated metagenomic and metabolomic analysis reveals regional style differences in Maotai-flavour Baijiu.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100558},
pmid = {41704740},
issn = {2666-5174},
abstract = {This research focused on Maotai-flavour Baijiu from three representative production regions in the Chishui River Basin, namely Maotai Town (MT), Jinsha (JS), and Renhuai (RH). By integrating metabolomics and macrogenomics techniques, the study analyzed the differences in volatile flavor compounds and microbial community structures in the fourth-round fermented grains and base liquor. Additionally, it explored the associative mechanism between microorganisms and flavor metabolism. The findings indicate that the microbial community compositions of fermented grains vary significantly across different production areas. The production area of Maotai Town mainly consists of Saccharomyces and Lactobacillus, with the highest content of ester substances. The fungal community in Jinsha is extremely stochastic, abundant in Mucoromycota, and has elevated contents of aldehydes and phenols. The distribution of microorganisms and flavor substances in the Renhuai production area lies between the two. The sensory evaluation of the base liquor indicates that the Jinsha production area features prominent floral and fruity aromas, the Maotai Town exhibits significant sour and sauce aromas, and the Renhuai production area has a well-balanced flavor. The correlation analysis shows that yeasts such as Saccharomyces and Pichia are positively correlated with esters such as ethyl acetate, while bacteria such as Limosilactobacillus are closely associated with short-chain fatty acid metabolism. This research reveals the microbiological basis for the differences in the Maotai style among different production regions and provides a theoretical foundation for regional characteristic production and process optimization.},
}

@article {pmid41704794,
year = {2025},
author = {Basu, U and Ahanger, SA and Gai, X and Hu, X},
title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1749879},
pmid = {41704794},
issn = {1664-462X},
abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.},
}

@article {pmid41704809,
year = {2026},
author = {Zhang, M and Jiao, T and Li, W},
title = {Allergic bronchopulmonary aspergillosis in a patient without history of asthma: a case report.},
journal = {Medical mycology case reports},
volume = {51},
number = {},
pages = {100770},
pmid = {41704809},
issn = {2211-7539},
abstract = {Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary hypersensitivity disease triggered by Aspergillus fumigatus. While the standard first-line therapy per International Society for Human and Animal Mycology (ISHAM) guidelines is glucocorticoids or itraconazole alone, combination therapy may be used briefly for rapid symptom control. We present a 39-year-old man without asthma who presented with cough and sputum. Chest computed tomography (CT) revealed diagnostic findings of central bronchiectasis and high-attenuation mucus, later confirmed as mucus plugs by bronchoscopy. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) detected a high load of A. fumigatus. Markedly elevated total IgE, A. fumigatus-specific IgE, and eosinophils confirmed ABPA. Although initial voriconazole monotherapy failed, adding oral glucocorticoids led to rapid clinical and radiographic improvement. No recurrence was observed on CT 7 months post-treatment, reinforcing that asthma is not a prerequisite for ABPA diagnosis.},
}

@article {pmid41704848,
year = {2025},
author = {Nayak, D and Behera, P and Singh, S and Tripathy, PS and Dash, SS and Dasgupta, M and Mohanty, S and Sahoo, MR and Satapathy, CR and Sasmal, A and Sahu, S},
title = {Sucrose supplementation influences gut microbial diversity and functional shifts in Apis cerana indica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733283},
pmid = {41704848},
issn = {1664-302X},
abstract = {Honeybee colonies are increasingly threatened by nutritional scarcity and biotic stressors, underscoring the need to understand the role of gut microbiota in mitigating these challenges. This study examined the gut microbial composition of Apis cerana indica under two dietary regimes: sucrose-fed and sucrose-unfed, to assess how nutrition influences microbial diversity and metabolic potential following metagenomics. Metagenomic sequencing of gut samples revealed 147,146 contigs, with the longest and shortest contigs measuring 615,154 kb and 200 kb, respectively. Comparative analysis indicated a higher relative abundance of Bacillus spp. in sucrose-fed bees, whereas Enterococcus was more dominant in unfed populations. Sucrose feeding significantly enhanced gut microbial diversity (Shannon index: 2.59; Simpson's index: 0.87) compared to unfed bees (Shannon: 1.91; Simpson: 0.68). Key genera, including Gilliamella, Bacillus, and Lactobacillus, were consistently present but showed varying relative abundances. Functional annotation via KEGG pathway analysis revealed elevated activity of glycolysis and the pentose phosphate pathway in sucrose-fed bees, with exclusive detection of key metabolic enzymes, hexokinase and enolase. Additionally, elevated sucrose metabolism and proteolytic enzyme activity were noted, reflecting enhanced metabolic versatility. Our findings highlight the importance of sucrose dietary supplementation in shaping gut microbial structure and function, their diversity, and metabolic capacity, suggesting its potential as a practical nutritional intervention to sustain honeybee health during a period of floral dearth. The outcome of the study encourages exploring the long-term ecological and physiological impacts of dietary strategies on colony resilience and productivity.},
}

@article {pmid41704904,
year = {2025},
author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y},
title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1722274},
pmid = {41704904},
issn = {2296-861X},
abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.},
}

@article {pmid41704957,
year = {2026},
author = {Zhu, J and Xia, T and Wang, L and Yin, X and Ma, Y and Shen, J},
title = {Investigating the benefits of metagenomic next-generation sequencing for patients experiencing infections after total hip replacement surgery: a retrospective cohort study with a minimum of one year of follow-up.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1735867},
pmid = {41704957},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Arthroplasty, Replacement, Hip/adverse effects ; Female ; Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis/drug therapy ; Aged, 80 and over ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Follow-Up Studies ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {OBJECTIVE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) technology in diagnosing and treating periprosthetic joint infection (PJI) following total hip arthroplasty (THA).

METHODS: From September 2018 to September 2024, 15 patients with periprosthetic infection after total hip arthroplasty were admitted. There were 11 males and 4 females; ages ranged from 28 to 87 years old, with an average of 63 years old. Infection occurred 6 to 42 months after total hip arthroplasty, with an average of 22.7 months. The infection lasted between 15 and 115 days, averaging 37.6 days. After being admitted to the hospital, joint fluid was collected for bacterial culture and mNGS. Following admission, joint fluid was collected for bacterial culture and mNGS, and antibiotics were adjusted based on the results, with surgery used to control the infection if needed.

RESULTS: Bacterial culture method was positive in 10 cases (66.7%), with a total of 12 pathogenic bacteria types detected. MNGS was positive in 15 cases (100.0%), with a total of 19 pathogenic bacteria types detected. There was a statistically significant difference in the positive rate between the two methods (P < 0.05). Out of the 10 patients, 5 who tested positive using both the bacterial culture method and mNGS test showed identical pathogenic bacterial types, resulting in a 50.0% compliance rate. The testing time (from sample delivery to results) was (3.07 ± 0.96) days for bacterial culture method and (1.67 ± 0.49) days for mNGS test, and the difference was statistically significant (t=5.03, P<0.001). The patients were followed up for 13 to 82 months, with a mean of 40.7 months. In one patient, the infection returned three months after undergoing one-stage revision surgery, while the other 14 patients showed no signs of infection, resulting in an infection control rate of 93.3%.

CONCLUSION: MNGS can detect the pathogenic bacteria of postoperative PJI after THA more quickly and accurately than the bacterial culture method, which is crucial for guiding antibiotic and surgical treatment combinations for patients with postoperative PJI after THA.},
}

Humans
Male
Middle Aged
*Arthroplasty, Replacement, Hip/adverse effects
Female
Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Prosthesis-Related Infections/microbiology/diagnosis/drug therapy
Aged, 80 and over
*Metagenomics/methods
Adult
*Bacteria/genetics/classification/isolation & purification
Follow-Up Studies
Anti-Bacterial Agents/therapeutic use

@article {pmid41705163,
year = {2026},
author = {},
title = {Correction to: Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag020},
doi = {10.1093/ismeco/ycag020},
pmid = {41705163},
issn = {2730-6151},
abstract = {[This corrects the article DOI: 10.1093/ismeco/ycaf183.].},
}

@article {pmid41705261,
year = {2026},
author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH},
title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101318},
pmid = {41705261},
issn = {2665-9271},
abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.},
}

@article {pmid41705811,
year = {2026},
author = {Paietta, EN and Kraberger, S and Gordon, M and Ehmke, E and Yoder, AD and Varsani, A},
title = {Metagenome-assembled genomes of anelloviruses in crowned lemur and aye-aye swabs.},
journal = {Microbiology resource announcements},
volume = {15},
number = {3},
pages = {e0147325},
pmid = {41705811},
issn = {2576-098X},
abstract = {Two circular, complete genomes of anelloviruses were identified from a crowned lemur anal swab and an aye-aye skin swab from individuals at the Duke Lemur Center (Durham, NC, USA). The anelloviruses represent two species in the Anelloviridae family and expand a developing lemur-associated anellovirus lineage.},
}

@article {pmid41705822,
year = {2026},
author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K},
title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0242225},
pmid = {41705822},
issn = {1098-5336},
support = {22176133//National Natural Science Foundation of China/ ; },
mesh = {*Metagenome ; *Anti-Bacterial Agents/pharmacology ; Microbiota ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Computational Biology/methods ; },
abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.},
}

*Metagenome
*Anti-Bacterial Agents/pharmacology
Microbiota
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
*Computational Biology/methods

@article {pmid41705858,
year = {2026},
author = {Teixeira Martins, C and Gombert, AK and Venturini, AM},
title = {Lactobacillus and Limosilactobacillus MAGs from alcoholic fermentation in sugarcane biorefineries.},
journal = {Microbiology resource announcements},
volume = {15},
number = {3},
pages = {e0070525},
pmid = {41705858},
issn = {2576-098X},
support = {2022/15256-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/10728-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306190/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {We recovered and characterized four bacterial MAGs from two Brazilian sugarcane biorefineries, with the aim of investigating the microbial environment during fuel ethanol production. MAGs belonged to Lactobacillus amylovorus and Limosilactobacillus fermentum, both known lactic acid bacterial contaminants. Genomic analyses revealed key functional traits but no resistance or virulence genes.},
}

@article {pmid41705859,
year = {2026},
author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM},
title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.},
journal = {Microbiology resource announcements},
volume = {15},
number = {3},
pages = {e0134625},
pmid = {41705859},
issn = {2576-098X},
support = {2020/11534-0, 2022/15112-8, and 2017/03172-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 88887.514375/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.},
}