@article {pmid41542635,
year = {2026},
author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA},
title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41542635},
issn = {2692-8205},
support = {F31 DK138748/DK/NIDDK NIH HHS/United States ; R21 AI173448/AI/NIAID NIH HHS/United States ; F31 HD117458/HD/NICHD NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI055449/AI/NIAID NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; },
abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS carriage in the vaginal tract is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D paired with vaginal GBS colonization to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokine profiles at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to an array of eight pro-inflammatory cytokines post-GBS infection. Pairing cytokine observations with GBS colonization outcomes revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS vaginal colonization. Supplementation with intravaginal rIL-1α was sufficient to resolve GBS burden differences between diabetic mice and non-diabetic controls, confirming that deficient vaginal cytokine responses contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention in the susceptible diabetic population.},
}

@article {pmid41663924,
year = {2026},
author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y},
title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.},
journal = {BMC microbiology},
volume = {26},
number = {},
pages = {},
pmid = {41663924},
issn = {1471-2180},
support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; },
abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling.

RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI.

CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04788-0.},
}

@article {pmid41666437,
year = {2026},
author = {Kohsar, M and Haar, M and Schmidt-Chanasit, J and Ramharter, M and Buchholz, BM and Krasemann, S and Bernreuther, C and Cadar, D and Omansen, TF and Wichmann, D and Ko, LM and Jordan, S},
title = {Fatal Dengue Fever in a Traveler Returning from Togo to Germany.},
journal = {The American journal of tropical medicine and hygiene},
volume = {114},
number = {4},
pages = {720-723},
pmid = {41666437},
issn = {1476-1645},
mesh = {Humans ; *Travel ; *Dengue/complications/diagnosis ; Fatal Outcome ; Germany ; Togo ; Male ; *Liver Failure, Acute/virology ; Adult ; },
abstract = {A previously healthy traveler of Togolese origin visiting friends and relatives presented with severe dengue complicated by acute liver failure. Despite intensive care management and listing for high-urgency liver transplantation, the patient succumbed to the disease. This case highlights the risk for life-threatening travel-related complications of dengue.},
}

Humans
*Travel
*Dengue/complications/diagnosis
Fatal Outcome
Germany
Togo
Male
*Liver Failure, Acute/virology
Adult

@article {pmid41736110,
year = {2026},
author = {Pirolo, M and Sherwani, MK and Espinosa-Gongora, C and Eriksen, EØ and Tassinato, C and Alberdi, A and Guardabassi, L},
title = {Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41736110},
issn = {2524-4671},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a major health and economic concern in intensive pig production. In this study, we hypothesized that the faecal microbiome, sampled before disease onset, could provide early prognostic markers of PWD risk and applied a machine-learning framework to identify biomarkers predictive of piglet susceptibility or resilience to PWD. At two Danish commercial farms experiencing PWD outbreaks, four pens per farm were monitored for 14 days post-weaning, with daily clinical assessments and rectal swabs collected every other day. In a nested case–control design, we profiled 140 samples from 41 piglets that developed PWD and 82 samples from 16 piglets that remained healthy by 16S rRNA sequencing. Additionally, we performed shotgun metagenomics on 56 pre-diarrhoeic samples from susceptible piglets and 47 from resilient piglets. A random-forest classifier with recursive feature elimination identified metagenome-assembled genomes (MAGs) predictive of resilience or susceptibility, trained and cross-validated independently within each farm. Negative binomial zero-inflated mixed (NBZIM) models assessed associations with known PWD risk factors (e.g. birth/weaning weights, weaning age and dam parity).

RESULTS: Prior to diarrhoea onset, microbial community structures differed significantly between resilient and susceptible piglets at both farms (PERMANOVA, p < 0.05). Feature-reduced models achieved high accuracy (AUC = 0.94 and 0.82 in Farm A and Farm B, respectively) and identified 10 and 13 MAGs enriched in resilient piglets, and one and two MAGs enriched in susceptible piglets from the two farms, respectively. All MAGs were farm-specific, highlighting the multifactorial aetiology of PWD. NBZIM models indicated that most predictive MAGs were independent of established PWD risk factors. Temporally, these MAGs peaked in relative abundance early after weaning (day 4 in Farm A; day 0 in Farm B). In the farm with unclear aetiology, functional analysis showed that susceptibility-associated MAGs were depleted for arginine/ornithine and vitamin (cobalamin, thiamine) biosynthesis and lactate production traits, suggesting metabolic dysbiosis.

CONCLUSIONS: Our findings indicate that pre-diarrhoeic faecal microbiome signatures predict PWD risk and provide a foundation for early prognostic tools and targeted interventions, including probiotic development, to mitigate PWD and reduce reliance on antimicrobials in pig production.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00522-3.},
}

@article {pmid41742048,
year = {2026},
author = {Zhang, Y and Wangjia, P and Yang, S and Liu, P and Xu, X and Han, H},
title = {Bartonella quintana endocarditis presenting with severe coombs-positive anemia: a case report.},
journal = {BMC cardiovascular disorders},
volume = {26},
number = {1},
pages = {},
pmid = {41742048},
issn = {1471-2261},
support = {XZ202501ZR0145//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402030(W)//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402105(W)//Natural Science Foundation of Tibet Autonomous Region/ ; },
abstract = {BACKGROUND: Bartonella quintana is a recognized cause of blood culture-negative endocarditis, often associated with predisposing social factors or pre-existing valvulopathy. Diagnosis is challenging and relies on advanced microbiological techniques.

CASE PRESENTATION: A 17-year-old Tibetan herdsman from a high-altitude region presented with a two-week history of fever, dyspnea, and lower limb edema. He had no history of homelessness or alcoholism but lived in poor sanitary conditions. Laboratory investigations revealed severe Coombs-positive hemolytic anemia and serological markers suggestive of systemic lupus erythematosus (SLE). Transthoracic echocardiography showed vegetations on both aortic (bicuspid) and mitral valves with severe regurgitation and rapid hemodynamic progression. All blood cultures were negative. Metagenomics Next-Generation Sequencing (mNGS) of peripheral blood identified B. quintana as the causative pathogen. Antibiotic therapy was adjusted to doxycycline (9 weeks) and gentamicin (3 weeks). Concurrently, immunomodulatory therapy with methylprednisolone and intravenous immunoglobulin was administered for the hemolytic anemia. Given the severe valvular insufficiency, the patient successfully underwent urgent aortic and mitral valve replacement. His clinical condition improved significantly post-operatively.

CONCLUSION: This case highlights the diagnostic utility of mNGS in confirming B. quintana endocarditis in a culture-negative scenario, especially when clinical presentation is complicated by concomitant autoimmune features mimicking Libman-Sacks endocarditis. A treatment strategy combining targeted antibiotics for the infection and immunomodulation for the hematologic complication, followed by definitive surgery, led to a successful outcome. It underscores that B. quintana infection should be considered in patients from disadvantaged backgrounds with endocarditis, even in the absence of classic risk factors.},
}

@article {pmid41749306,
year = {2026},
author = {Liu, Z and Liu, M and Chen, H and Li, S and Zheng, N and Xing, G and Zhang, Y and Xu, J and Li, M and Xiao, C and Lu, T and Yan, Q and Lei, Z and Feng, M and Li, Y},
title = {Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41749306},
issn = {1479-5876},
abstract = {BACKGROUND: The gut microbiota is a key modulator of immune checkpoint inhibitor (ICI) efficacy, yet the contribution of the gut virome remains poorly defined, particularly in advanced non–small cell lung cancer (NSCLC). Here, we characterized the gut virome and explored its potential role in shaping response to PD-1 blockade.

METHODS: We performed metagenomic virome profiling of fecal samples from 338 advanced NSCLC patients treated with PD-1 inhibitors and evaluated model generalizability in an independent external cohort (n = 30). Viral diversity, taxonomic composition, and functional potential were analyzed. Virus–bacteria co-occurrence networks were constructed, and random forest classifiers were developed to predict treatment response.

RESULTS: Viral Shannon diversity decreased progressively with poorer clinical response, and β-diversity analyses revealed distinct virome community structures between responders (R) and non-responders (NR). Differential abundance analysis identified 194 NR-enriched vOTUs, predominantly assigned to Peduoviridae and Inoviridae, and 594 R-enriched vOTUs, mainly from Herelleviridae and Microviridae. Host prediction indicated that NR-enriched vOTUs frequently targeted bacterial genera such as Clostridium_M, Bacteroides, and Escherichia, whereas R-enriched vOTUs targeted beneficial genera such as Faecalibacterium and Roseburia. Network analyses further revealed response-specific virus–bacteria interaction modules. Functional profiling showed that NR-enriched vOTUs were associated with metabolic functions, including K01689 (eno; enolase). A virus-only random forest model outperformed a bacterium-only model in predicting response (area under the curve [AUC] = 0.768 vs. 0.664) and maintained superior performance in the external cohort (AUC = 0.742). In addition, Akkermansia muciniphila positivity was associated with a higher-diversity, responder-favorable virome configuration.

CONCLUSIONS: The gut virome undergoes marked remodeling during anti–PD-1 therapy in advanced NSCLC and displays distinct taxonomic, ecological, and functional signatures associated with clinical outcome. These findings support the gut virome as a strong predictor of ICI response and highlight its potential as both a biomarker and a therapeutic target.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07900-0.},
}

@article {pmid41761072,
year = {2026},
author = {Costa, J and Pascoal, F and Baptista, MS and Hop, H and Assmy, P and Wold, A and Magalhães, C and Duarte, P},
title = {Comparative analysis of prokaryotic communities, hydrography, and biogeochemistry in Atlantic vs non-Atlantic influenced Svalbard fjords.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41761072},
issn = {1471-2180},
abstract = {BACKGROUND: Fjords in Svalbard are undergoing significant changes due to climate warming. Those along the west coast of Spitsbergen are particularly affected by the increasing influence of “warm” Atlantic Water (AW), a process known as Atlantification. We compared Kongsfjorden, a relatively “warm” fjord on the west coast, with Rijpfjorden, a typical cold Arctic fjord on the north coast of Nordaustlandet, combining physical and biogeochemical data with 16S rRNA gene amplicon and shotgun metagenomic sequencing. We hypothesize that differences in fjords’ water masses and prokaryotic communities provide insight into the effects of Atlantification as it expands eastwards along the shelf north of Svalbard.

RESULTS: We found that warm AW dominated in Kongsfjorden, whereas Rijpfjorden was dominated by cold Arctic Water and Winter Cooled Water. Our results suggest that the Atlantic-influenced Kongsfjorden is a nutrient sink, whereas Rijpfjorden showed similar behavior only in 2016, a particularly warm year, otherwise no clear sink/source role could be identified. Analysis of 16S rRNA gene sequences revealed that Proteobacteria had higher relative abundances in Kongsfjorden while Bacteroidota dominated in Rijpfjorden. Ammonium and nitrite-oxidizing prokaryotes were most prevalent in deeper water masses of both fjords. The archaeal taxa of the ammonia-oxidizing community, mainly Nitrosopumilus and Nitrosopelagicus, were consistently more dominant than ammonium and nitrite-oxidizing bacteria. Denitrification and nitrogen fixation genes differed between the fjords, with Kongsfjorden having a higher coverage of diazotroph genes.

CONCLUSIONS: Kongsfjorden and Rijpfjorden displayed distinct hydrographic conditions, with Kongsfjorden being under a stronger influence of Atlantification. Our results suggest that warmer water masses are linked to higher nutrient uptake. The clear association between microbial communities and water masses offers insight into changes driven by Atlantification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04821-2.},
}

@article {pmid41862737,
year = {2026},
author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY},
title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41862737},
issn = {1420-9071},
support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; },
abstract = {UNLABELLED: Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06176-3.},
}

@article {pmid41923365,
year = {2026},
author = {Merritt, B and Ratcliff, JD and Ta, S and Osis, G and Mauldin, MR and Thielen, PM},
title = {TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag119},
pmid = {41923365},
issn = {1367-4811},
abstract = {MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score.

RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest.

Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

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

@article {pmid41923466,
year = {2026},
author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC},
title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70324},
pmid = {41923466},
issn = {1758-2229},
support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; },
mesh = {*Phytophthora/genetics/isolation & purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; },
abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.},
}

*Phytophthora/genetics/isolation & purification
*Soil Microbiology
New Zealand
RNA, Ribosomal, 16S/genetics
*Metagenome
Forests
*Microbiota
Plant Diseases/microbiology/parasitology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Nucleic Acid Amplification Techniques
Phylogeny

@article {pmid41923582,
year = {2026},
author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A},
title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e9317962},
pmid = {41923582},
issn = {2314-6753},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; },
abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/microbiology/complications/blood
Pilot Projects
Middle Aged
*Dyslipidemias/microbiology/blood
Male
*RNA, Ribosomal, 16S/genetics
Female
Aged
Adult
Bacteria/genetics/classification

@article {pmid41923636,
year = {2026},
author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK},
title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.011},
pmid = {41923636},
issn = {1934-6069},
abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.},
}

@article {pmid41923798,
year = {2026},
author = {Ibisanmi, TA and Jiang, X and Willcox, M and Kumar, N},
title = {Recent advances in computational antimicrobial peptide discovery through big data, modeling, and artificial intelligence and their interplay in ushering the next golden era of drug development.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1749404},
pmid = {41923798},
issn = {2673-7647},
abstract = {The accelerating antimicrobial resistance (AMR) crisis continues to render more and more conventional antibiotics ineffective. Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics due to their broad-spectrum activity, diverse mechanisms of action, and lower propensity for resistance. Traditional discovery approaches face limitations arising from the vast sequence space and the challenge of balancing efficacy with low toxicity. Addressing these challenges is critical for developing next-generation antimicrobial agents, and computational methods are increasingly driving progress. Public repositories, and techniques such as molecular docking enable in silico evaluation of peptide target interactions, identifying candidates with strong binding potential. Molecular dynamics (MD) simulations offer deeper insights into how AMPs disrupt membranes, form pores, or act synergistically, while Steered MD extends this to probing membrane penetration. Artificial intelligence (AI) methods, including machine learning and deep learning, capture complex sequence activity relationships, predict novel AMPs from genomic and metagenomic data, and design new peptides de novo using generative models. Despite rapid advances, most existing reviews treat these approaches in isolation, leaving a fragmented understanding of their interplay. This paper addresses that gap by unifying computational strategies, highlighting synergies, and critiquing limitations. Ultimately, integrating these methodologies offers a path toward more efficient AMP discovery to fight AMR.},
}

@article {pmid41923934,
year = {2026},
author = {Dhawi, F and Alsanie, SI},
title = {Contrasting leaf transcriptomic responses to drought and heat stress in the desert CAM species Mesembryanthemum forsskalii.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1805066},
pmid = {41923934},
issn = {1664-462X},
abstract = {INTRODUCTION: Dryland ecosystems are increasingly exposed to extreme heat and prolonged water limitation. Facultative crassulacean acid metabolism (CAM) enables certain desert plants to enhance water-use efficiency and adjust carbon assimilation under stress conditions. Mesembryanthemum forsskalii Hochst. ex Boiss. (Aizoaceae; locally known as Samh) is a hyper-arid adapted species native to Saudi Arabia, yet genomic and transcriptomic resources for this plant remain scarce. This study aimed to generate foundational genomic resources and characterize transcriptional responses to drought and heat stress.

METHODS: We integrated rhizosphere metagenomics and leaf transcriptomics. A genome-resolved rhizosphere metagenome was generated from mature field-grown plants. In parallel, micropropagated plants were exposed under controlled conditions to progressive drought (17 days without irrigation) or acute heat shock (55 °C for 120 min), each compared with well-watered controls. RNA sequencing generated 123.77 Gb raw data and 121.96 Gb clean reads after quality filtering. Differential gene expression was identified using thresholds of |log2FC| ≥ 2 and FDR ≤ 0.05, followed by transcription factor profiling and KEGG pathway annotation.

RESULTS: Heat stress induced substantially broader transcriptional reprogramming than drought. A total of 1,348 genes were differentially expressed under heat stress, compared with 84 genes under drought. Heat exposure strongly increased the expression of transcription factor families including B3 (20.00-fold relative to drought), bHLH (22.65-fold), and bZIP (8.94-fold). KEGG pathway analysis revealed expanded representation of metabolic pathways under heat, including secondary metabolite biosynthesis, ribosome function, carbon metabolism, and endoplasmic reticulum protein processing. Rhizosphere binning recovered archaeal and bacterial genomes affiliated with stress-tolerant lineages, providing the first microbial genomic framework associated with M. forsskalii.

DISCUSSION: These results demonstrate a heat-dominant transcriptional response in M. forsskalii and provide the first integrated transcriptomic and rhizosphere metagenomic resources for this desert facultative CAM species. Heat-inducible transcription factors, particularly B3 and NAC families, emerge as promising targets for improving thermotolerance and water-use efficiency in crops.},
}

@article {pmid41924127,
year = {2026},
author = {Booker, AE and Fei, C and Amin, SA and Custer, J and Watkins, K and Yaeger, W and Ahn, SH and Vidyarathna, NK and Burns, A and Klass, S and Glibert, PM and Heil, CA and Schulz, F and Martínez Martínez, J},
title = {Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag051},
pmid = {41924127},
issn = {2730-6151},
abstract = {Karenia brevis regularly forms harmful blooms along the West Florida Shelf that negatively affect marine and terrestrial organisms through toxin production. These blooms impose economic and environmental hardship, driving the need for research to understand the factors influencing their dynamics and to mitigate their impacts. A mostly unresolved issue is the potential role of viruses in bloom termination. We conducted an experiment incubating K. brevis cultures with size-fractionated bloom water samples. Flow cytometry revealed giant virus-like populations (VLPs) in replicate cultures with <1 μm-filtered and <0.2 μm-filtered bloom water. The VLPs' abundance was paralleled by declines in photoefficiency and culture lysis. Metagenomic analyses of the lysates revealed 11 giant virus genomes (35%-100% complete) representing 7 viral operational taxonomic units (vOTUs) within the order Imitervirales (Nucleocytoviricota). Ten of these vOTUs were more abundant in the incubations with <0.2 μm-filtered bloom water, coinciding with the absence or low abundance of algicidal bacteria. The vOTUs and K. brevis cell abundances showed a positive correlation at a coastal site during bloom and nonbloom periods. The most apparent association was to vOTU6, which may owe its competitive advantage to the presence of the auxiliary metabolic genes bacteriorhodopsin, carbonic anhydrase, and dinoflagellate viral nucleoprotein. The metagenomes also contained polinton-like virus (PLV) genomes. Since many PLVs are hypothesized to depend on co-infection with Nucleocytoviricota viruses for their propagation, our results suggest complex viral interactions within K. brevis blooms. Future research to elucidate virus-bacteria-K. brevis interaction mechanisms may be key to understanding bloom dynamics and developing management tools.},
}

@article {pmid41924306,
year = {2026},
author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D},
title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2622259},
pmid = {41924306},
issn = {2993-3935},
abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.},
}

@article {pmid41924310,
year = {2026},
author = {Chen, X and Wang, N and Jiang, C and Luo, S and Cheng, M and Chu, D and Hu, C and Zhang, P and Chen, K and Yang, F and Xiong, J and Ning, K and Miao, W},
title = {Data Mining of Sediment Microbiomes of the Tibetan Plateau Revealed a Genomic Repository of Ancient Lineages and Adaptive Evolution of Asgardarchaeota.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1213},
pmid = {41924310},
issn = {2639-5274},
abstract = {The extreme climatic conditions of the Tibetan Plateau foster unique microbial communities, especially in the sediment ecosystem. A thorough understanding of these communities could facilitate revealing their microbial diversity, biological resources, and response to climate change. Here, we have constructed the Tibetan Plateau Microbial Catalog of Sediment (TPMC-S) based on 248 metagenomic sediment samples from the Tibetan Plateau. We identified 511,056,752 nonredundant genes and recovered 13,696 metagenome-assembled genomes with enormous phylogenetic novelty (over 90% novel species), far exceeding other contemporary Tibetan microbial catalogs and expanding the microbial functional diversity. We also revealed that similarities of sediment microbial communities followed the distance-decay relationship. Furthermore, sediments contained a high proportion of evolutionarily "possible ancient species (PAS)" compared with paired aquatic samples, especially ancient archaeal lineages, suggesting a microbial "sedimentary archive" in sediment. Finally and most importantly, Asgardarchaeota, including 2 potentially novel genera, were identified from the sediments, and their latest divergence predated the uplift of the Tibetan Plateau, while they still gained functions to adapt to extreme environments. Our findings positioned the Tibetan Plateau as both a genomic repository of microbial antiquity, especially Asgardarchaeota, and an active arena for modern extremophile innovation, providing insights for deciphering microbial resilience strategies in climate-sensitive ecosystems and informing novel bioprospecting efforts.},
}

@article {pmid41924424,
year = {2026},
author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T},
title = {Correction: Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1817909},
doi = {10.3389/fcimb.2026.1817909},
pmid = {41924424},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1751074.].},
}

@article {pmid41924426,
year = {2026},
author = {Pan, Y and Du, N and Liu, Y and Wu, M and Hao, S and He, Y and Jiang, Y},
title = {Clinical features of Tropheryma Whipplei in pediatric pneumonia: an mNGS and tNGS-based case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1753963},
pmid = {41924426},
issn = {2235-2988},
mesh = {Humans ; Case-Control Studies ; Male ; Female ; *Tropheryma/genetics/isolation & purification ; Child, Preschool ; Child ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; *Whipple Disease/microbiology/pathology ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/isolation & purification ; Coinfection/microbiology ; Adolescent ; },
abstract = {INTRODUCTION: Tropheryma whipplei (TW), which causes Whipple disease, has recently been associated with respiratory diseases, particularly pneumonia. To understand its role in pediatric pneumonia, this study analyzed the clinical and pathogenetic characteristics of TW in pediatric pneumonia patients.

METHODS: We utilized metagenomic and targeted next-generation sequencing (mNGS/tNGS) data from 3,759 pediatric bronchoalveolar lavage fluid (BALF) samples (2023-2024). This case-control study included 103 TW-positive pediatric pneumonia patients (59 with severe pneumonia, SPTW+; 44 with mild pneumonia, MPTW+), along with 206 TW-negative pneumonia patients as controls (118 with severe pneumonia, SPTW-; 88 with mild pneumonia, MPTW-).

RESULTS: Through inter-group comparisons, the results showed that TW-positive patients were younger and had lower BMIs than controls, with shorter hospital stays and milder inflammation. Severe TW-positive cases showed more localized right-lung lesions, less pleural effusion, and more bronchial involvement. Mycoplasma pneumoniae co-detection was frequent (86.4%), along with Moraxella catarrhalis, human bocavirus type 1, and rhinovirus A.

DISCUSSION: TW-positive pediatric pneumonia presents with milder symptoms, suggesting that TW may act as a colonizer rather than a primary pathogen. Consequently, antimicrobial treatment specifically targeting TW may not be immediately warranted at detection. These results provide important insight for the individualized treatment of pediatric pneumonia with TW positive.},
}

Humans
Case-Control Studies
Male
Female
*Tropheryma/genetics/isolation & purification
Child, Preschool
Child
Infant
Bronchoalveolar Lavage Fluid/microbiology
Metagenomics
High-Throughput Nucleotide Sequencing
*Whipple Disease/microbiology/pathology
*Pneumonia/microbiology
Mycoplasma pneumoniae/isolation & purification
Coinfection/microbiology
Adolescent

@article {pmid41925105,
year = {2026},
author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H},
title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71752},
doi = {10.1002/cam4.71752},
pmid = {41925105},
issn = {2045-7634},
support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; },
mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; Rats ; Middle Aged ; *Ovarian Neoplasms/drug therapy ; Rats, Sprague-Dawley ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cisplatin/adverse effects/administration & dosage ; Metabolomics ; Fecal Microbiota Transplantation ; Aged ; Carboplatin/adverse effects/administration & dosage ; Feces/microbiology ; Paclitaxel/adverse effects/administration & dosage ; Metabolome ; Adult ; },
abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).

METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n = 25) and non-CINV (n = 25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.

RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p < 0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p < 0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p < 0.05) and partially reversed by non-CINV FMT (p < 0.05).

CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.},
}

Female
*Gastrointestinal Microbiome
Animals
Humans
Rats
Middle Aged
*Ovarian Neoplasms/drug therapy
Rats, Sprague-Dawley
*Vomiting/chemically induced/microbiology/metabolism
*Nausea/chemically induced/microbiology/metabolism
Dysbiosis/microbiology
*Antineoplastic Combined Chemotherapy Protocols/adverse effects
Cisplatin/adverse effects/administration & dosage
Metabolomics
Fecal Microbiota Transplantation
Aged
Carboplatin/adverse effects/administration & dosage
Feces/microbiology
Paclitaxel/adverse effects/administration & dosage
Metabolome
Adult

@article {pmid41925202,
year = {2026},
author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Cohen, NA and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N},
title = {Phage-display immunoprecipitation sequencing reveals distinct antibody signatures against bacterial flagellins associated with treatment response in Crohn's disease.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000001030},
pmid = {41925202},
issn = {2155-384X},
abstract = {OBJECTIVES: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.

METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index [HBI]>4 or fecal calprotectin [FCP]>150μg/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22 and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.

RESULTS: Using PhIP-Seq analysis, only the anti-flagellin antibodies library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (HBI≤4 and FCP≤150) versus non-remission at all time points (p<0.05). Of the 55 anti-flagellin antibodies analyzed, 15 showed consistent >1.5-fold over-representation in non-remission samples, with high conservation of amino-acid sequences and targeting of Clostridiales, Lachnospiraceae, or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while non-remission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semi-essential amino acids biosynthesis (q<0.05).

CONCLUSIONS: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.},
}

@article {pmid41925227,
year = {2026},
author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y},
title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag068},
pmid = {41925227},
issn = {1751-7370},
abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.},
}

@article {pmid41926886,
year = {2026},
author = {Hoang, HG and Chacha, WE and Binh, QA and Mukherjee, S and Jiang, Y and Zhang, T and Van Tung, T and Tran, HT and Naidu, R},
title = {Biotechnologies for removal of per- and polyfluoroalkyl substances (PFAS) in biosolids: Current status and challenges.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129237},
doi = {10.1016/j.jenvman.2026.129237},
pmid = {41926886},
issn = {1095-8630},
abstract = {Per- and polyfluoroalkyl substances (PFAS), widely recognized as "forever chemicals," pose significant environmental management challenges due to their persistence, mobility, and bioaccumulative behavior. Biosolids derived from wastewater treatment plants represent an important pathway for PFAS redistribution into terrestrial environments, particularly through land application. This review provides a comprehensive assessment of the global distribution, environmental behavior, toxicity, and biodegradation potential of PFAS in biosolids. A bibliometric analysis was conducted using the Web of Science database, and keyword co-occurrence mapping with VOSviewer was applied to evaluate research trends from 2018 to 2024. The findings indicate that research activity is concentrated in China (31%), Europe (30%), and North America (16%), with limited data available from South America, Oceania, and Africa, highlighting regional knowledge gaps. The environmental fate of PFAS in biosolids is governed by pH, temperature, redox conditions, and organic matter content, which influence sorption-desorption processes, mobility, and long-term persistence in soils. Biodegradation pathways include anaerobic reductive defluorination and aerobic oxidative transformation. Certain bacterial genera, such as Dehalobacter spp. and Gordonia spp., have demonstrated degradation efficiencies approaching 80-90% under optimized laboratory conditions. Fungal-mediated oxidative processes may further promote partial mineralization through enzymatic defluorination. In phytoremediation systems, long-chain PFAS preferentially accumulate in plant roots, whereas short-chain compounds exhibit greater mobility and translocation potential. Emerging remediation strategies integrating metagenomics, functional gene characterization, and enzyme-based treatments show promise for enhancing PFAS attenuation. However, substantial uncertainties remain regarding long-term bioaccumulation, biomagnification, and regulatory risk thresholds. Addressing these gaps is essential for developing science-based management strategies for PFAS-contaminated biosolids and protecting environmental and human health.},
}

@article {pmid41926891,
year = {2026},
author = {Duan, P and Guan, Y and Zhang, J and Han, Z and Li, H and Wang, S and Kong, F and Cui, Y},
title = {Enhanced performance and mechanism of nano-iron-nickel modified substrate in the treatment of compound antibiotic wastewater in constructed wetland.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129455},
doi = {10.1016/j.jenvman.2026.129455},
pmid = {41926891},
issn = {1095-8630},
abstract = {Nano zero-valent iron nickel (nZVI/Ni) was loaded on the walnut shell activated carbon (AC) and its spheres (ACS) to prepare nZVI/Ni-ACS and nZVI/Ni/AC-SAS composites. These were applied in constructed wetlands (CWs) to construct a "substrate-microorganism" synergistic system for treating tetracycline (TC) and sulfamethoxazole (SMX) in livestock and poultry wastewater. Adsorption experiments determined the optimal mass ratios were ACS:Fe:Ni = 2:1:0.05; AC:Fe:Ni = 1:1:0.05; nZVI/Ni/AC:SA = 6:1. At 500 μg/L influent concentrations, TC and SMX removal efficiencies in CWs with modified substrates (CW-LA: 86.96%/87.79%; CW-LB: 89.88%/86.94%) significantly exceeded gravel (CW-G: 26.07%/55.28%) and ACS (CW-Z: 39.90%/67.56%) systems. Mechanistically, the modified substrates strongly adsorbed TC and SMX, while Fe and Ni acted as electron donors and catalysts to drive their chemical reduction and stimulate biological co-metabolism. Metagenomic analysis revealed that the TC/SMX removal mechanisms were associated with an increased abundance of antibiotic-resistant microorganisms (Methanothrix, Desulfobacter, Thauera, Geobacter, Pseudomonas), which benefited efficient antibiotic degradation, while their immobilization within the tightly bound EPS (TB-EPS) matrix effectively minimized ecological risks. This study provided critical data for the enhanced CW treatment of TC and SMX in livestock and poultry wastewater by modified substrates.},
}

@article {pmid41927118,
year = {2026},
author = {Huang, H and Liu, Z and Liu, X and Li, Q and Yang, X and Chen, L and Ye, W},
title = {Coinfection of Human Cytomegalovirus and Pneumocystis jirovecii Caused Severe Pneumonia in a Non-HIV Elderly Patient: A Case Report.},
journal = {Annals of clinical and laboratory science},
volume = {56},
number = {1},
pages = {122-129},
pmid = {41927118},
issn = {1550-8080},
mesh = {Humans ; *Pneumocystis carinii/isolation & purification ; *Cytomegalovirus Infections/complications/virology/drug therapy ; *Pneumonia, Pneumocystis/microbiology/complications/drug therapy ; *Coinfection/virology/microbiology ; *Cytomegalovirus/isolation & purification ; Male ; Aged ; *Pneumonia ; },
abstract = {OBJECTIVE: To present a case of a non-human immunodeficiency virus (HIV)-infected patient with human cytomegalovirus (HCMV) viremia and severe Pneumocystis jirovecii (PJ) pneumonia.

CASE REPORT: The patient was admitted in June 2024 for chronic dry cough and dyspnea. Sputum-targeted next-generation sequencing (tNGS) and blood pathogen metagenomic detection were used to identify concurrent infections of sputum HCMV and PJ, along with blood HCMV. The extensive treatment included intravenous ganciclovir, in conjunction with caspofungin and oral sulfamethoxazole, augmented by glucocorticoids and breathing assistance. After three weeks, the patient's oxygenation index markedly improved, accompanied by the significant resolution of imaging lesions, leading to patient discharge in June 2024.

CONCLUSION: This case underscores the diagnostic efficacy of tNGS on several opportunistic infections for older people with several comorbidities.},
}

Humans
*Pneumocystis carinii/isolation & purification
*Cytomegalovirus Infections/complications/virology/drug therapy
*Pneumonia, Pneumocystis/microbiology/complications/drug therapy
*Coinfection/virology/microbiology
*Cytomegalovirus/isolation & purification
Male
Aged
*Pneumonia

@article {pmid41927536,
year = {2026},
author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J},
title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.},
journal = {Nutrition & diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41387-026-00418-w},
pmid = {41927536},
issn = {2044-4052},
abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.

METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.

RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs > 0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.

CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.},
}

@article {pmid41927550,
year = {2026},
author = {Oki, H and Takebe, K and Bonsu, A and Fujii, K and Masuda, R and Henderson, N and Mima, T and Koide, T and Moradi, M and Matsushita, O and Sakon, J and Kawahara, K},
title = {Bacterial collagenase harnesses collagen geometry for processive cleavage.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71099-3},
pmid = {41927550},
issn = {2041-1723},
support = {24K10218//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K14519//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K06545//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2218054//Armenian National Science and Education Fund (Armenian National Science & Education Fund)/ ; GM103429 and GM151696//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
abstract = {Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.},
}

@article {pmid41927589,
year = {2026},
author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, Č and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H},
title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71145-0},
pmid = {41927589},
issn = {2041-1723},
abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.},
}

@article {pmid41927746,
year = {2026},
author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA},
title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46933-9},
pmid = {41927746},
issn = {2045-2322},
support = {SRUG2204254606//National Research Foundation/ ; },
abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.},
}

@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.},
}