@article {pmid41803086,
year = {2026},
author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L},
title = {Water mass specific genes dominate the Southern Ocean microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41803086},
issn = {2041-1723},
support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; },
abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.},
}

*Microbiota/genetics
*Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Antarctic Regions
*Bacteria/genetics/classification
Sulfonium Compounds/metabolism
Arctic Regions
Plankton/genetics
Phylogeny

@article {pmid41801404,
year = {2026},
author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH},
title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {4},
pages = {},
pmid = {41801404},
issn = {1432-0851},
support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; },
abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Middle Aged
Aged
*Immunotherapy/methods
Retrospective Studies
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Prospective Studies
*Neoplasms/drug therapy/immunology/mortality
Melanoma/drug therapy/immunology
Carcinoma, Non-Small-Cell Lung/drug therapy/immunology

@article {pmid41798955,
year = {2026},
author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J},
title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761558},
pmid = {41798955},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Purines/metabolism ; Disease Models, Animal ; *Gout/drug therapy/metabolism ; Inflammation/drug therapy/metabolism ; Signal Transduction/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Hyperuricemia/drug therapy ; Rats, Sprague-Dawley ; Metabolomics/methods ; Arthritis, Gouty/drug therapy/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.

OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.

METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.

RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1β) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.

CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats
Male
*Purines/metabolism
Disease Models, Animal
*Gout/drug therapy/metabolism
Inflammation/drug therapy/metabolism
Signal Transduction/drug effects
*Anti-Inflammatory Agents/pharmacology
Hyperuricemia/drug therapy
Rats, Sprague-Dawley
Metabolomics/methods
Arthritis, Gouty/drug therapy/metabolism
Multiomics

@article {pmid41797508,
year = {2026},
author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W},
title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71656},
pmid = {41797508},
issn = {1530-6860},
support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; },
abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bile Acids and Salts/metabolism
*Dysbiosis/microbiology/metabolism/complications
*Gallstones/microbiology/metabolism/etiology
Male
Female
Middle Aged
Feces/microbiology
Adult
Aged
Multiomics
Amidohydrolases

@article {pmid41673107,
year = {2026},
author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG},
title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41673107},
issn = {2045-2322},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology ; *Inflammation/pathology/genetics ; Mice, Knockout ; Disease Models, Animal ; Dysbiosis ; Autoimmunity ; Mice, Inbred C57BL ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology
*Inflammation/pathology/genetics
Mice, Knockout
Disease Models, Animal
Dysbiosis
Autoimmunity
Mice, Inbred C57BL

@article {pmid41645054,
year = {2026},
author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H},
title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41645054},
issn = {1471-2164},
support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Enterocytozoon/physiology ; *Vitamin K 2 ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; Biosynthetic Pathways ; },
abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Enterocytozoon/physiology
*Vitamin K 2
*Rodentia/microbiology
*Microsporidiosis/microbiology/veterinary/metabolism
Biosynthetic Pathways

@article {pmid41448605,
year = {2026},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Johnson, S and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary Nitrate Intake and 16S rRNA-Inferred Nitrite-Generating Capacity of the Subgingival Microbiome May Influence Glucose Metabolism: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {Journal of clinical periodontology},
volume = {53},
number = {4},
pages = {508-519},
doi = {10.1111/jcpe.70084},
pmid = {41448605},
issn = {1600-051X},
support = {R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; DK-63608//Vagelos College of Physicians and Surgeons, Columbia University/ ; UL1TR001873/TR/NCATS NIH HHS/United States ; R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; UL1TR001873/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *RNA, Ribosomal, 16S/genetics ; Male ; *Insulin Resistance ; *Nitrates/administration & dosage/metabolism ; *Gingiva/microbiology ; *Microbiota/genetics ; *Nitrites/metabolism ; *Diet ; Blood Glucose/metabolism ; *Glucose/metabolism ; Biomarkers ; Cardiometabolic Risk Factors ; *Glucose Intolerance/metabolism/microbiology ; },
abstract = {AIMS: To investigate whether the association between the nitrite-generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake.

MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31 ± 9 years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome-Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA-IR), blood pressure) on nitrate intake and MINES together with a MINES × nitrate intake interaction term.

RESULTS: Mean nitrate intake was 190 ± 171 mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p < 0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA-IR (1.2 [1.1-1.4] vs. 1.5 [1.3-1.6]; p = 0.002), but levels were similar in those with high MINES (p = 0.84).

CONCLUSIONS: A biomarker of higher microbial NO-generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate-rich diets should incorporate measures of the entire oral microbiome.},
}

Humans
Female
Cross-Sectional Studies
Adult
*RNA, Ribosomal, 16S/genetics
Male
*Insulin Resistance
*Nitrates/administration & dosage/metabolism
*Gingiva/microbiology
*Microbiota/genetics
*Nitrites/metabolism
*Diet
Blood Glucose/metabolism
*Glucose/metabolism
Biomarkers
Cardiometabolic Risk Factors
*Glucose Intolerance/metabolism/microbiology

@article {pmid37762509,
year = {2023},
author = {Zabolotneva, AA and Gaponov, AM and Roumiantsev, SA and Vasiliev, IY and Grigoryeva, TV and Kit, OI and Zlatnik, EY and Maksimov, AY and Goncharova, AS and Novikova, IA and Appolonova, SA and Markin, PA and Shestopalov, AV},
title = {Alkylresorcinols as New Modulators of the Metabolic Activity of the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {24},
number = {18},
pages = {},
pmid = {37762509},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Resorcinols/pharmacology/metabolism ; Humans ; Mice ; Feces/microbiology/chemistry ; Mice, Inbred C57BL ; Male ; Fecal Microbiota Transplantation ; Receptors, LDL/genetics ; Female ; },
abstract = {Alkylresorcinols (ARs) are polyphenolic compounds with a wide spectrum of biological activities and are potentially involved in the regulation of host metabolism. The present study aims to establish whether ARs can be produced by the human gut microbiota and to evaluate alterations in content in stool samples as well as metabolic activity of the gut microbiota of C57BL, db/db, and LDLR (-/-) mice according to diet specifications and olivetol (5-n-pentylresorcinol) supplementation to estimate the regulatory potential of ARs. Gas chromatography with mass spectrometric detection was used to quantitatively analyse AR levels in mouse stool samples; faecal microbiota transplantation (FMT) from human donors to germ-free mice was performed to determine whether the intestinal microbiota could produce AR molecules; metagenome sequencing analysis of the mouse gut microbiota followed by reconstruction of its metabolic activity was performed to investigate olivetol's regulatory potential. A significant increase in the amounts of individual members of AR homologues in stool samples was revealed 14 days after FMT. Supplementation of 5-n-Pentylresorcinol to a regular diet influences the amounts of several ARs in the stool of C57BL/6 and LDLR (-/-) but not db/db mice, and caused a significant change in the predicted metabolic activity of the intestinal microbiota of C57BL/6 and LDLR (-/-) but not db/db mice. For the first time, we have shown that several ARs can be produced by the intestinal microbiota. Taking into account the dependence of AR levels in the gut on olivetol supplementation and microbiota metabolic activity, AR can be assumed to be potential quorum-sensing molecules, which also influence gut microbiota composition and host metabolism.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Resorcinols/pharmacology/metabolism
Humans
Mice
Feces/microbiology/chemistry
Mice, Inbred C57BL
Male
Fecal Microbiota Transplantation
Receptors, LDL/genetics
Female

@article {pmid37648194,
year = {2023},
author = {Kakakhel, MA and Narwal, N and Kataria, N and Johari, SA and Zaheer Ud Din, S and Jiang, Z and Khoo, KS and Xiaotao, S},
title = {Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {117002},
doi = {10.1016/j.envres.2023.117002},
pmid = {37648194},
issn = {1096-0953},
mesh = {Animals ; *Dysbiosis/chemically induced/veterinary/microbiology ; *Fishes/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Fish Diseases/microbiology/chemically induced ; },
abstract = {The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.},
}

Animals
*Dysbiosis/chemically induced/veterinary/microbiology
*Fishes/microbiology
*Gastrointestinal Microbiome/drug effects
*Water Pollutants, Chemical/toxicity
*Fish Diseases/microbiology/chemically induced

@article {pmid37634690,
year = {2023},
author = {Liu, L and Xin, Y and Guang, SB and Lin, GF and Liu, CX and Zeng, LQ and He, SQ and Zheng, YM and Chen, GY and Zhao, QB},
title = {Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {116999},
doi = {10.1016/j.envres.2023.116999},
pmid = {37634690},
issn = {1096-0953},
mesh = {*Rivers/microbiology ; *Drinking Water/microbiology ; *Microbiota ; China ; *Plankton ; Bacteria/metabolism/classification ; *Water Microbiology ; Environmental Monitoring ; },
abstract = {To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10[-2]), amino acid metabolism (5.78-7.21 × 10[-2]) and energy metabolism (4.07-5.17 × 10[-2]) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R[2] of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.},
}

*Rivers/microbiology
*Drinking Water/microbiology
*Microbiota
China
*Plankton
Bacteria/metabolism/classification
*Water Microbiology
Environmental Monitoring

@article {pmid37541958,
year = {2023},
author = {Patil, PK and Nagaraju, VT and Baskaran, V and Avunje, S and Rameshbabu, R and Ghate, SD and Solanki, HG},
title = {Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture.},
journal = {Journal of applied microbiology},
volume = {134},
number = {8},
pages = {},
doi = {10.1093/jambio/lxad173},
pmid = {37541958},
issn = {1365-2672},
mesh = {*Aquaculture/methods ; *Sulfur/metabolism ; Ammonia/metabolism ; *Saline Waters ; *Nitrogen/metabolism ; Nitrites/metabolism ; *Bacteria/metabolism/genetics ; *Microbial Consortia ; Nitrates/metabolism ; Nitrification ; Sulfides/metabolism ; Animals ; Water Purification/methods ; Salinity ; },
abstract = {AIM: The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.

METHODS AND RESULTS: Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.

CONCLUSIONS: The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.},
}

*Aquaculture/methods
*Sulfur/metabolism
Ammonia/metabolism
*Saline Waters
*Nitrogen/metabolism
Nitrites/metabolism
*Bacteria/metabolism/genetics
*Microbial Consortia
Nitrates/metabolism
Nitrification
Sulfides/metabolism
Animals
Water Purification/methods
Salinity

@article {pmid37470119,
year = {2023},
author = {Chen, Q and Ren, R and Sun, Y and Xu, J and Yang, H and Li, X and Xiao, Y and Li, J and Lyu, W},
title = {The combination of metagenome and metabolome to compare the differential effects and mechanisms of fructose and sucrose on the metabolic disorders and gut microbiota in vitro and in vivo.},
journal = {Food & function},
volume = {14},
number = {15},
pages = {7284-7298},
doi = {10.1039/d3fo02246c},
pmid = {37470119},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fructose/metabolism/adverse effects ; Mice ; *Sucrose/metabolism/adverse effects ; Male ; *Metabolome/drug effects ; *Metagenome/drug effects ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; *Metabolic Diseases/metabolism/microbiology ; },
abstract = {Sucrose and fructose are the most commonly used sweeteners in the modern food industry, but there are few comparative studies on the mechanisms by which fructose and sucrose affect host health. The aim of the present study was to explain the different effects of fructose and sucrose on host metabolism from the perspective of gut microbiota. Mice were fed for 16 weeks with normal drinking water (CON), 30% fructose drinking water (CF) and 30% sucrose drinking water (SUC). Compared with fructose treatment, sucrose caused significantly higher weight gain, epididymal fat deposition, hepatic steatosis, and jejunum histological injury. Sucrose increased the abundance of LPS-producing bacteria which was positively correlated with obesity traits, while fructose increased the abundance of Lactobacillus. An in vitro fermentation experiment also showed that fructose increased the abundance of Lactobacillus, while sucrose increased the abundance of Klebsiella and Escherichia. In addition, combined with microbial functional analysis and metabolomics data, fructose led to the enhancement of carbohydrate metabolism and TCA cycle capacity, and increased the production of glutamate. The cross-cooperation network greatly influenced the microbiota (Klebsiella, Lactobacillus), metabolites (glutamate, fructose 1,6-biosphosphate, citric acid), and genes encoding enzymes (pyruvate kinase, 6-phosphofructokinase 1, fructokinase, lactate dehydrogenase, aconitate hydratase, isocitrate dehydrogenase 3), suggesting that they may be the key differential factors in the process of fructose and sucrose catabolism. Therefore, the changes in gut microbiome mediated by fructose and sucrose are important reasons for their differential effects on host health and metabolism.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Fructose/metabolism/adverse effects
Mice
*Sucrose/metabolism/adverse effects
Male
*Metabolome/drug effects
*Metagenome/drug effects
Bacteria/classification/genetics/isolation & purification/metabolism
Mice, Inbred C57BL
*Metabolic Diseases/metabolism/microbiology

@article {pmid37385587,
year = {2023},
author = {Taniguchi, M and Okumura, R and Matsuzaki, T and Nakatani, A and Sakaki, K and Okamoto, S and Ishibashi, A and Tani, H and Horikiri, M and Kobayashi, N and Yoshikawa, HY and Motooka, D and Okuzaki, D and Nakamura, S and Kida, T and Kameyama, A and Takeda, K},
title = {Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon.},
journal = {Mucosal immunology},
volume = {16},
number = {5},
pages = {624-641},
doi = {10.1016/j.mucimm.2023.06.004},
pmid = {37385587},
issn = {1935-3456},
mesh = {Animals ; Mice ; *Mucin-2/metabolism ; *Sialyltransferases/genetics/metabolism ; *Colon/microbiology/metabolism/immunology ; *Mucus/metabolism ; *Galactosyltransferases/genetics/metabolism ; Mice, Knockout ; Humans ; *Intestinal Mucosa/metabolism/microbiology ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Inflammatory Bowel Diseases/immunology/metabolism ; Polysaccharides/metabolism ; Disease Models, Animal ; N-Acetylneuraminic Acid/metabolism ; Glycosylation ; },
abstract = {In the intestine, mucin 2 (Muc2) forms a network structure and prevents bacterial invasion. Glycans are indispensable for Muc2 barrier function. Among various glycosylation patterns of Muc2, sialylation inhibits bacteria-dependent Muc2 degradation. However, the mechanisms by which Muc2 creates the network structure and sialylation prevents mucin degradation remain unknown. Here, by focusing on two glycosyltransferases, St6 N-acetylgalactosaminide α-2,6-sialyltransferase 6 (St6galnac6) and β-1,3-galactosyltransferase 5 (B3galt5), mediating the generation of desialylated glycans, we show that sialylation forms the network structure of Muc2 by providing negative charge and hydrophilicity. The colonic mucus of mice lacking St6galnac6 and B3galt5 was less sialylated, thinner, and more permeable to microbiota, resulting in high susceptibility to intestinal inflammation. Mice with a B3galt5 mutation associated with inflammatory bowel disease (IBD) also showed the loss of desialylated glycans of mucus and the high susceptibility to intestinal inflammation, suggesting that the reduced sialylation of Muc2 is associated with the pathogenesis of IBD. In mucins of mice with reduced sialylation, negative charge was reduced, the network structure was disturbed, and many bacteria invaded. Thus, sialylation mediates the negative charging of Muc2 and facilitates the formation of the mucin network structure, thereby inhibiting bacterial invasion in the colon to maintain gut homeostasis.},
}

Animals
Mice
*Mucin-2/metabolism
*Sialyltransferases/genetics/metabolism
*Colon/microbiology/metabolism/immunology
*Mucus/metabolism
*Galactosyltransferases/genetics/metabolism
Mice, Knockout
Humans
*Intestinal Mucosa/metabolism/microbiology
Gastrointestinal Microbiome
Mice, Inbred C57BL
*Inflammatory Bowel Diseases/immunology/metabolism
Polysaccharides/metabolism
Disease Models, Animal
N-Acetylneuraminic Acid/metabolism
Glycosylation

@article {pmid37382438,
year = {2023},
author = {Goffredi, SK and Panossian, B and Brzechffa, C and Field, N and King, C and Moggioli, G and Rouse, GW and Martín-Durán, JM and Henry, LM},
title = {A dynamic epibiont community associated with the bone-eating polychaete genus Osedax.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0314022},
pmid = {37382438},
issn = {2150-7511},
support = {IOS-0923775//National Science Foundation (NSF)/ ; NE/M018016/1//UKRI | Natural Environment Research Council (NERC)/ ; 213981/Z/18/Z//Wellcome Trust (WT)/ ; },
mesh = {Animals ; Symbiosis ; *Polychaeta/microbiology ; Phylogeny ; *Microbiota ; Metagenome ; Bone and Bones ; },
abstract = {Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.},
}

Animals
Symbiosis
*Polychaeta/microbiology
Phylogeny
*Microbiota
Metagenome
Bone and Bones

@article {pmid37209219,
year = {2023},
author = {Ma, W and Yu, J and Yang, F and Zhang, X and Zhang, F and Jin, W and Sun, Z and Zhao, Z and Jia, S and Zhong, C and Xue, J},
title = {Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China.},
journal = {Journal of the science of food and agriculture},
volume = {103},
number = {13},
pages = {6429-6439},
doi = {10.1002/jsfa.12718},
pmid = {37209219},
issn = {1097-0010},
support = {2022A02002-2//the Xinjiang Autonomous Region Key Project of Science and Technology/ ; 2019YFD1002500//the National Key Research and Development Project/ ; },
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; China ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Taste ; Metagenomics ; *Fungi/metabolism/genetics/classification/isolation & purification ; *Vitis/microbiology/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Odorants/analysis ; },
abstract = {BACKGROUND: The natural fermentation of multispecies microbial communities is responsible for unique flavors of winery regions of the eastern foothills of the Ningxia Helan Mountains in China. However, the participation of different microorganisms in the metabolic network for the development of important flavor substances is not clearly defined. Microbial population and diversity on different fermentation phases of Ningxia wine were analyzed by metagenomic sequencing approach.

RESULTS: Gas chromatography-mass spectrometry and ion chromatography were used to identify flavor components, and 13 esters, 13 alcohols, nine aldehydes and seven ketones were detected in volatile substances with odor activity values > 1, and eight organic acids were detected as important flavor components in young wine. Thus, 52 238 predicted protein-coding genes from 24 genera were identified in the Kyoto Encyclopedia of Genes and Genomes level 2 pathways of global and overview maps, and the genes were primarily involved in amino acid metabolism and carbohydrate metabolism. Major microbial genera (Saccharomyces, Tatumella, Hanseniaspora, Lactobacillus, and Lachancea) were closely related to self-characteristic compound metabolism and further contributed to wine flavor.

CONCLUSION: This study clarifies the different metabolic roles of microorganisms in flavor formation during Ningxia wine spontaneous fermentation. Saccharomyces, dominant fungi involved in glycolysis and pyruvate metabolism, produces not only ethanol but also two important precursors, pyruvate and acetyl-CoA, which are necessary for the tricarboxylic acid cycle, fatty acid metabolism, amino acid metabolism, and flavor formation. Lactobacillus and Lachancea, dominant bacteria involved in lactic acid metabolism. Tatumella, dominant bacteria involved in amino acid metabolism, fatty acid metabolism, and acetic acid metabolism to produce esters in the Shizuishan City region samples. These findings provide insights into the use of local functional strains to generate unique flavor formation, as well as improved stability and quality, in wine production. © 2023 Society of Chemical Industry.},
}

Fermentation
*Wine/microbiology/analysis
*Volatile Organic Compounds/metabolism/chemistry/analysis
China
*Flavoring Agents/metabolism/chemistry
*Bacteria/genetics/metabolism/classification/isolation & purification
Taste
Metagenomics
*Fungi/metabolism/genetics/classification/isolation & purification
*Vitis/microbiology/metabolism/chemistry
Gas Chromatography-Mass Spectrometry
Microbiota
Odorants/analysis

@article {pmid37189250,
year = {2023},
author = {Tong, CCL and Lin, X and Seckar, T and Koptyra, M and Kohanski, MA and Cohen, NA and Kennedy, DW and Adappa, ND and Papagiannopoulos, P and Kuan, EC and Baranov, E and Jalaly, JB and Feldman, MD and Storm, PB and Resnick, AC and Palmer, JN and Wei, Z and Robertson, ES},
title = {A metagenomic analysis of the virome of inverted papilloma and squamous cell carcinoma.},
journal = {International forum of allergy & rhinology},
volume = {13},
number = {11},
pages = {2055-2062},
doi = {10.1002/alr.23182},
pmid = {37189250},
issn = {2042-6984},
mesh = {Humans ; *Papilloma, Inverted/virology/pathology ; *Carcinoma, Squamous Cell/virology ; *Papillomavirus Infections/virology/epidemiology ; Male ; Female ; Middle Aged ; *Virome/genetics ; Metagenomics ; Aged ; Human papillomavirus 16/genetics ; *Paranasal Sinus Neoplasms/virology ; *Papillomaviridae/genetics ; Human papillomavirus 18/genetics ; Adult ; },
abstract = {INTRODUCTION: Inverted papilloma (IP) is a sinonasal tumor with a well-known potential for malignant transformation. The role of human papillomavirus (HPV) in its pathogenesis has been controversial. The purpose of this study was to determine the virome associated with IP, with progression to carcinoma in situ (CIS), and invasive carcinoma.

METHODS: To determine the HPV-specific types, a metagenomics assay that contains 62,886 probes targeting viral genomes in a microarray format was used. The platform screens DNA and RNA from fixed tissues from eight controls, 16 IP without dysplasia, five IP with CIS, and 13 IP-associated squamous cell carcinoma (IPSCC). Paired with next-generation sequencing, 48 types of HPV with 857 region-specific probes were interrogated against the tumors.

RESULTS: The prevalence of HPV-16 was 14%, 42%, 70%, and 73% in control tissue, IP without dysplasia, IP with CIS, and IPSCC, respectively. The prevalence of HPV-18 had a similar progressive increase in prevalence, with 14%, 27%, 67%, and 74%, respectively. The assay allowed region-specific analysis, which identified the only oncogenic HPV-18 E6 to be statistically significant when compared with control tissue. The prevalence of HPV-18 E6 was 0% in control tissue, 25% in IP without dysplasia, 60% in IP with CIS, and 77% in IPSCC.

CONCLUSIONS: There are over 200 HPV types that infect human epithelial cells, of which only a few are known to be high-risk. Our study demonstrated a trend of increasing prevalence of HPV-18 E6 that correlated with histologic severity, which is novel and supports a potential role for HPV in the pathogenesis of IP.},
}

Humans
*Papilloma, Inverted/virology/pathology
*Carcinoma, Squamous Cell/virology
*Papillomavirus Infections/virology/epidemiology
Male
Female
Middle Aged
*Virome/genetics
Metagenomics
Aged
Human papillomavirus 16/genetics
*Paranasal Sinus Neoplasms/virology
*Papillomaviridae/genetics
Human papillomavirus 18/genetics
Adult

@article {pmid41794462,
year = {2026},
author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V},
title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118577},
doi = {10.1016/j.foodres.2026.118577},
pmid = {41794462},
issn = {1873-7145},
mesh = {*Fermentation ; *Vitis/microbiology ; *Wine/microbiology/analysis ; *Mycobiome ; Italy ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metagenomics/methods ; Food Microbiology ; Metabolome ; Kluyveromyces/metabolism ; Multiomics ; },
abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.},
}

*Fermentation
*Vitis/microbiology
*Wine/microbiology/analysis
*Mycobiome
Italy
Metabolomics/methods
Greece
Saccharomyces cerevisiae/metabolism
Metagenomics/methods
Food Microbiology
Metabolome
Kluyveromyces/metabolism
Multiomics

@article {pmid41794459,
year = {2026},
author = {Cai, J and Huang, A and You, L and Wang, Z and Huang, C and Huang, R and Li, Y and Liang, T and Zhang, F and Wu, Q and Wang, J and Zhu, Z and Ding, Y},
title = {Neomycin-sensitive gut bacteria-derived brassicasterol mediates the anti-obesity effects of Cordyceps militaris polysaccharide.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118574},
doi = {10.1016/j.foodres.2026.118574},
pmid = {41794459},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Obesity/prevention & control/drug therapy ; Diet, High-Fat/adverse effects ; Mice ; *Neomycin/pharmacology ; Mice, Inbred C57BL ; *Cordyceps/chemistry ; Male ; *Anti-Obesity Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; Liver/metabolism ; *Fungal Polysaccharides/pharmacology ; Lipid Metabolism/drug effects ; },
abstract = {Diet-based modulation of the gut microbiota has emerged as a promising strategy to alleviate obesity and its related complications. Our previous study demonstrated that polysaccharide derived from Cordyceps militaris (CMP) exerts anti-obesity effects, yet the specific mechanism linking gut microbiota to its metabolic impact remains unclear. Herein, we utilized murine models with distinct gut microbial profiles created via antibiotic cocktails to investigate these mechanisms. The protective effects of CMP against high-fat diet (HFD)-induced obesity and associated metabolic disturbances were substantially impaired in mice depleted of neomycin-sensitive gut bacteria. Metagenomic analyses further established that CMP required these bacteria to restore gut microbial homeostasis. Notably, we observed that CMP elevated hepatic levels of brassicasterol in a manner dependent on neomycin-sensitive gut bacteria. Brassicasterol treatment alone replicated the anti-obesity effects of CMP, as indicated by reduced body weight gain, improved lipid and glucose metabolism, and decreased inflammation. Through transcriptomic and functional analyses, we identified hepatic Apoa4 as a key downstream effector of brassicasterol. Our results indicated that brassicasterol upregulated Apoa4, facilitating lipid transport and suppressing inflammation both in vitro and in vivo. Collectively, our findings indicate that CMP exerts its anti-obesity effects through a neomycin-sensitive gut bacteria-brassicasterol-Apoa4 pathway. This work expands the mechanistic understanding of CMP and highlights a novel microbiota-metabolite-host regulatory axis for dietary intervention in metabolic disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Obesity/prevention & control/drug therapy
Diet, High-Fat/adverse effects
Mice
*Neomycin/pharmacology
Mice, Inbred C57BL
*Cordyceps/chemistry
Male
*Anti-Obesity Agents/pharmacology
Anti-Bacterial Agents/pharmacology
Liver/metabolism
*Fungal Polysaccharides/pharmacology
Lipid Metabolism/drug effects

@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}

*Naphthalenes/metabolism
Biodegradation, Environmental
*Bacteria/metabolism/genetics
Systems Biology
Computer Simulation
*Environmental Pollutants/metabolism
Microbial Consortia

@article {pmid41775000,
year = {2026},
author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, Š and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT},
title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.},
journal = {Veterinary parasitology},
volume = {343},
number = {},
pages = {110729},
doi = {10.1016/j.vetpar.2026.110729},
pmid = {41775000},
issn = {1873-2550},
mesh = {Animals ; Goats ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Cryptosporidiosis/parasitology/prevention & control ; Male ; *Goat Diseases/parasitology/prevention & control/microbiology ; *Saccharomyces cerevisiae ; Cryptosporidium parvum/physiology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/veterinary/prevention & control ; },
abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.},
}

Animals
Goats
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
*Cryptosporidiosis/parasitology/prevention & control
Male
*Goat Diseases/parasitology/prevention & control/microbiology
*Saccharomyces cerevisiae
Cryptosporidium parvum/physiology
RNA, Ribosomal, 16S/genetics
Dysbiosis/veterinary/prevention & control

@article {pmid41747516,
year = {2026},
author = {Hu, X and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and Yan, Z and Li, Y and Zhang, L and Wang, C and Lei, X and Chen, B and He, L},
title = {Polyethylene microplastics specifically drive the dissemination of ARGs: Mechanisms involving microbial community restructuring and horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181587},
doi = {10.1016/j.scitotenv.2026.181587},
pmid = {41747516},
issn = {1879-1026},
mesh = {*Microplastics/toxicity ; *Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity/analysis ; *Polyethylene ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Lakes/microbiology ; },
abstract = {As emerging contaminants, the impact of microplastics (MPs) on antibiotic resistance genes (ARGs), virulence factors (VFs), and host microbial communities in lakes remains unclear. To address this, we conducted a 28-day incubation experiment using water from Yiquan Lake, employing metagenomic sequencing to investigate the effects of different types of microplastics-polyethylene (PE), polystyrene (PS), polypropylene (PP), and a mixture (Mix), each at a concentration of 1 item/L-compared to a raw water control (RAW). Results showed significant enrichment of Proteobacteria and Bacteroidetes in PE and Mix groups. Genera such as Agrobacterium and Microbacterium increased in PE and PS groups, serving as major hosts of ARGs and VFs. Network analysis revealed positive correlations between Agrobacterium, Escherichia, and ARGs, suggesting horizontal gene transfer may facilitate the spread of resistance and virulence. Two-factor PS formed highly connected yet competitive networks, whereas Mix constructed modular and stable networks. Single-factor PE enhanced microbial connectivity but reduced ARGs connectivity, while Mix increased the modularity of both microbes and ARGs. PE elevated the abundance of ARGs, VFs, and mobile genetic elements, with multidrug resistance and efflux pumps as dominant mechanisms. Additionally, PE downregulated quorum sensing transporter genes while upregulating regulatory factors, significantly promoting RND efflux systems (AcrAB-TolC) to maintain resistome homeostasis. This study highlights the distinct environmental effects of different MPs, underscoring the need to prioritize PE-related risks in aquatic ecosystems. Improved management of plastic waste in and around lakes is recommended to mitigate MP-mediated ARG dissemination and preserve freshwater ecosystem services.},
}

*Microplastics/toxicity
*Gene Transfer, Horizontal
*Water Pollutants, Chemical/toxicity/analysis
*Polyethylene
*Drug Resistance, Microbial/genetics
*Microbiota/drug effects
Lakes/microbiology

@article {pmid41740355,
year = {2026},
author = {Lee, J and Hong, S and Choi, J and Song, H and Han, JH and Suh, YD and Yeon, SC and Cho, S},
title = {Whole-genome shotgun metagenomics reveals environmental perturbations in the gut microbiome and resistome of wild raccoon dogs rescued at a wildlife center.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181588},
doi = {10.1016/j.scitotenv.2026.181588},
pmid = {41740355},
issn = {1879-1026},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Raccoon Dogs/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Raccoon dogs are potential vectors for the transmission of zoonotic pathogens and antimicrobial resistance, with their gut microbiome carrying genetic determinants of virulence and resistance. However, previous studies have primarily relied on traditional culture-based approaches, limiting our understanding of the entire dynamics and genetic potential of the gut microbiome in raccoon dogs. In this study, we employed both culture-dependent approach and whole-genome shotgun sequencing in raccoon dogs undergoing rehabilitation for eight weeks. We integratively assessed how rehabilitation-related environmental shifts influence the gut microbiome and resistome. Rehabilitation induced shifts in gut microbiome composition. Notably, within-group diversity decreased at week eight, indicating increased compositional similarity. Throughout rehabilitation, a total of 18 genera (e.g., Paeniclostridium, Psychrobacter) significantly increased, and 40 genera (e.g., Intestinimonas, Erysipelatoclostridium) decreased in abundance. Rehabilitation also induced shifts in the gut resistome, with reduced within-group diversity at weeks four and eight, indicating increased compositional similarity over time. Overall, 253 antimicrobial resistance genes (ARGs) present at week 0 disappeared, whereas 273 ARGs were acquired during rehabilitation. Additionally, the abundance of 15 ARGs significantly decreased and that of 33 increased, with beta-lactamases being the most common among the latter. Culture-dependent methods revealed a marked increase in bacteria resistant to third-generation cephalosporins, monobactams, and sulfonamides. Changes in microbiome composition during rehabilitation indirectly influenced the resistome and virulome through mobile genetic elements. Our findings suggest that rehabilitation-induced perturbations in the gut microbiome and resistome of raccoon dogs are likely driven by environmental shifts such as diet and habitat. These changes may affect their post-release fitness and raise concerns owing to the potential dissemination of zoonotic pathogens and antimicrobial resistance.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Raccoon Dogs/microbiology
Metagenomics
*Drug Resistance, Bacterial/genetics

@article {pmid41736367,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS},
title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {2},
pages = {e2511012},
doi = {10.71150/jm.2511012},
pmid = {41736367},
issn = {1976-3794},
support = {//Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; //National Research Foundation of Korea/ ; 2023R1A2C1007759//Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; },
mesh = {Humans ; *Basal Cell Carcinoma/microbiology ; Pilot Projects ; *Skin/microbiology ; *Microbiota/genetics ; *Skin Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Middle Aged ; Female ; Republic of Korea ; Aged ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Aged, 80 and over ; Skin Microbiome ; },
abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.},
}

Humans
*Basal Cell Carcinoma/microbiology
Pilot Projects
*Skin/microbiology
*Microbiota/genetics
*Skin Neoplasms/microbiology
RNA, Ribosomal, 16S/genetics
Male
Middle Aged
Female
Republic of Korea
Aged
*Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics
Aged, 80 and over
Skin Microbiome

@article {pmid41689511,
year = {2026},
author = {Xu, R and Mayer, MJ and Philo, M and Gall, GL and Mulaw, G and Ponsero, A and Narbad, A},
title = {Combining Lactiplantibacillus plantarum and Bifidobacterium adolescentis can improve GABA production in faecal fermentations.},
journal = {Journal of applied microbiology},
volume = {137},
number = {3},
pages = {},
doi = {10.1093/jambio/lxag047},
pmid = {41689511},
issn = {1365-2672},
support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/QU/230001D/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //China Scholarship Council/ ; },
mesh = {Fermentation ; *Feces/microbiology ; *gamma-Aminobutyric Acid/biosynthesis/metabolism ; *Probiotics/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Bifidobacterium adolescentis/metabolism/growth & development ; Humans ; Coculture Techniques ; Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Lactic Acid/metabolism ; },
abstract = {AIMS: This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro.

METHODS AND RESULTS: Strains of intestinally derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions. Isolates synthesized varying amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid, or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 h and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. Bifidobacterium adolescentis supplementation increased short-chain fatty acids acetate and propionate, and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls.

CONCLUSIONS: GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.},
}

Fermentation
*Feces/microbiology
*gamma-Aminobutyric Acid/biosynthesis/metabolism
*Probiotics/metabolism
*Lactiplantibacillus plantarum/metabolism
*Bifidobacterium adolescentis/metabolism/growth & development
Humans
Coculture Techniques
Gastrointestinal Microbiome
Fatty Acids, Volatile/metabolism
Hydrogen-Ion Concentration
Lactic Acid/metabolism

@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.},
journal = {Acta neuropsychiatrica},
volume = {38},
number = {},
pages = {e16},
doi = {10.1017/neu.2026.10056},
pmid = {41572438},
issn = {1601-5215},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology ; Metagenomics ; Male ; Female ; Adult ; *Suicidal Ideation ; Middle Aged ; Dysbiosis/microbiology ; Cognition/physiology ; Affect/physiology ; },
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune–metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Major Depressive Disorder/microbiology/metabolism/psychology
Metagenomics
Male
Female
Adult
*Suicidal Ideation
Middle Aged
Dysbiosis/microbiology
Cognition/physiology
Affect/physiology

@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
mesh = {*Water Purification ; Biofilms/drug effects ; Bioreactors/microbiology ; *Amoxicillin/pharmacology ; *Bacterial Proteins/biosynthesis ; *Drug Resistance, Bacterial/genetics ; Water Pollutants/isolation & purification ; *Microbial Consortia/drug effects ; Cyanobacteria/drug effects ; *Metagenome/drug effects ; Gene Transfer, Horizontal ; },
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}

*Water Purification
Biofilms/drug effects
Bioreactors/microbiology
*Amoxicillin/pharmacology
*Bacterial Proteins/biosynthesis
*Drug Resistance, Bacterial/genetics
Water Pollutants/isolation & purification
*Microbial Consortia/drug effects
Cyanobacteria/drug effects
*Metagenome/drug effects
Gene Transfer, Horizontal

@article {pmid41790792,
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 Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344114},
pmid = {41790792},
issn = {1932-6203},
mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; },
abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.},
}

*Soil Microbiology
Bangladesh
*Bacillus/genetics/classification/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
Gardens
Soil/chemistry
Biodiversity

@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0191025},
pmid = {41609371},
issn = {2165-0497},
support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; *Swine Diseases/microbiology/virology ; *Coinfection/microbiology/veterinary/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Porcine respiratory and reproductive syndrome virus/isolation & purification/genetics ; Influenza A virus/isolation & purification/genetics ; *Bacterial Infections/veterinary/microbiology ; Respiratory System/microbiology/virology ; Metagenomics ; },
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}

Animals
Swine
*Virulence Factors/genetics
*Bacteria/genetics/classification/isolation & purification/pathogenicity
*Swine Diseases/microbiology/virology
*Coinfection/microbiology/veterinary/virology
*Respiratory Tract Infections/veterinary/microbiology/virology
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Porcine respiratory and reproductive syndrome virus/isolation & purification/genetics
Influenza A virus/isolation & purification/genetics
*Bacterial Infections/veterinary/microbiology
Respiratory System/microbiology/virology
Metagenomics

@article {pmid41570402,
year = {2026},
author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL},
title = {Gut microbiota is different before the development of preeclampsia.},
journal = {Pregnancy hypertension},
volume = {43},
number = {},
pages = {101415},
doi = {10.1016/j.preghy.2026.101415},
pmid = {41570402},
issn = {2210-7797},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology/diagnosis ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; },
abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.

STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.

MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.

RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.

CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.},
}

Humans
Female
Pregnancy
*Pre-Eclampsia/microbiology/physiopathology/diagnosis
*Gastrointestinal Microbiome
Adult
Feces/microbiology
Blood Pressure
Case-Control Studies

@article {pmid41312680,
year = {2026},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {53},
number = {3},
pages = {430-436},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/immunology ; *Cyclosporine/therapeutic use/pharmacology ; Male ; Female ; Adult ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Skin/microbiology/drug effects/immunology ; Middle Aged ; *Mycobiome/drug effects ; Malassezia/isolation & purification ; Young Adult ; Calcineurin Inhibitors/therapeutic use/pharmacology ; DNA, Fungal/isolation & purification ; Treatment Outcome ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}

Humans
*Dermatitis, Atopic/drug therapy/microbiology/immunology
*Cyclosporine/therapeutic use/pharmacology
Male
Female
Adult
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Skin/microbiology/drug effects/immunology
Middle Aged
*Mycobiome/drug effects
Malassezia/isolation & purification
Young Adult
Calcineurin Inhibitors/therapeutic use/pharmacology
DNA, Fungal/isolation & purification
Treatment Outcome

@article {pmid41025937,
year = {2026},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {45},
number = {3},
pages = {250-265},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; *Bacillus ; Middle Aged ; Adult ; *Dietary Supplements ; Feces/microbiology ; Flatulence ; },
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).

METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.

RESULTS: Eighty participants (54% female; age: 50.3 ± 10.1 years) were randomized to BV379 (n = 39) or placebo (n = 41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p = 0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p = 0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.

CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Double-Blind Method
Female
*Gastrointestinal Microbiome/drug effects
Male
*Bacillus
Middle Aged
Adult
*Dietary Supplements
Feces/microbiology
Flatulence

@article {pmid40175821,
year = {2026},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {71},
number = {1},
pages = {143-154},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA　2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
mesh = {Humans ; *Dyslipidemias/microbiology/epidemiology ; Japan/epidemiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}

Humans
*Dyslipidemias/microbiology/epidemiology
Japan/epidemiology
Male
Female
Middle Aged
*Mouth/microbiology
*Microbiota
Aged
RNA, Ribosomal, 16S/genetics
Adult
Bacteria/classification/genetics/isolation & purification
Metagenomics

@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth & development ; Metagenomics/methods ; *Microbial Interactions ; Microbial Consortia/genetics ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}

*Vitamin B 12/metabolism/biosynthesis/genetics
*Mesorhizobium/genetics/metabolism
*Synechococcus/genetics/metabolism/growth & development
Metagenomics/methods
*Microbial Interactions
Microbial Consortia/genetics
Transcriptome
Gene Expression Profiling
Multiomics

@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {41785052},
issn = {1477-4054},
mesh = {Humans ; *Lung Diseases/microbiology ; *Microbiota ; *Databases, Factual ; Bacteria/classification/genetics ; Machine Learning ; },
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}

Humans
*Lung Diseases/microbiology
*Microbiota
*Databases, Factual
Bacteria/classification/genetics
Machine Learning

@article {pmid41783570,
year = {2026},
author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW},
title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.},
journal = {Marine life science & technology},
volume = {8},
number = {1},
pages = {206-220},
pmid = {41783570},
issn = {2662-1746},
abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
pmid = {41778780},
issn = {1949-0984},
mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; },
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

Humans
*Tuberculosis/microbiology/diagnosis/therapy
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Animals
Antitubercular Agents/therapeutic use
Metabolomics
Lung/microbiology

@article {pmid41761979,
year = {2026},
author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X},
title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {48584},
doi = {10.31083/FBL48584},
pmid = {41761979},
issn = {2768-6698},
support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; },
mesh = {*Arsenic Trioxide/pharmacology/therapeutic use ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy ; Homeostasis/drug effects ; Humans ; *Bifidobacterium ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; *Tumor Microenvironment/drug effects/immunology ; *Antineoplastic Agents/therapeutic use/pharmacology ; Dysbiosis ; *Intestines/drug effects/microbiology/immunology ; *Probiotics/administration & dosage ; Disease Models, Animal ; },
abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.

METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.

RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.

CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.},
}

*Arsenic Trioxide/pharmacology/therapeutic use
Animals
Gastrointestinal Microbiome/drug effects
Mice
*Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy
Homeostasis/drug effects
Humans
*Bifidobacterium
RNA, Ribosomal, 16S/genetics
Male
Female
*Tumor Microenvironment/drug effects/immunology
*Antineoplastic Agents/therapeutic use/pharmacology
Dysbiosis
*Intestines/drug effects/microbiology/immunology
*Probiotics/administration & dosage
Disease Models, Animal

@article {pmid41747903,
year = {2026},
author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X},
title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134276},
doi = {10.1016/j.biortech.2026.134276},
pmid = {41747903},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Microbial Consortia/physiology ; Anaerobiosis ; Acetates/metabolism ; *Autotrophic Processes ; *Carbon Cycle ; *Bioelectric Energy Sources/microbiology ; Pressure ; Electrodes ; Carbon/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study presents a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.},
}

*Sewage/microbiology
*Microbial Consortia/physiology
Anaerobiosis
Acetates/metabolism
*Autotrophic Processes
*Carbon Cycle
*Bioelectric Energy Sources/microbiology
Pressure
Electrodes
Carbon/metabolism
Carbon Dioxide/metabolism

@article {pmid41707528,
year = {2026},
author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y},
title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119865},
doi = {10.1016/j.ecoenv.2026.119865},
pmid = {41707528},
issn = {1090-2414},
mesh = {China ; *Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Mining ; *Environmental Monitoring ; Manganese/analysis ; Agriculture ; Soil/chemistry ; Bacteria/genetics/classification ; *Microbiota ; Genes, Bacterial ; },
abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.},
}

China
*Soil Microbiology
*Metals, Heavy/analysis
*Soil Pollutants/analysis
Mining
*Environmental Monitoring
Manganese/analysis
Agriculture
Soil/chemistry
Bacteria/genetics/classification
*Microbiota
Genes, Bacterial

@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {690-703},
pmid = {41699270},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Dysbiosis/microbiology/immunology ; Mice ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Ethiopia ; Male ; *HIV Infections/immunology/microbiology/complications ; Israel ; *Opportunistic Infections/immunology/microbiology ; Cryptosporidiosis/immunology/microbiology ; Adult ; CD4-Positive T-Lymphocytes/immunology ; Metagenomics ; Middle Aged ; Disease Susceptibility ; Cryptosporidium parvum ; Intestinal Mucosa/immunology ; },
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
Dysbiosis/microbiology/immunology
Mice
Fecal Microbiota Transplantation
Feces/microbiology
Female
Ethiopia
Male
*HIV Infections/immunology/microbiology/complications
Israel
*Opportunistic Infections/immunology/microbiology
Cryptosporidiosis/immunology/microbiology
Adult
CD4-Positive T-Lymphocytes/immunology
Metagenomics
Middle Aged
Disease Susceptibility
Cryptosporidium parvum
Intestinal Mucosa/immunology

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
mesh = {*Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; Microbiota/genetics ; Biodiversity ; DNA, Bacterial/genetics ; *Alphaproteobacteria/classification/genetics ; Lichens/microbiology ; Bacteria/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

*Phylogeny
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Plant Leaves/microbiology
Microbiota/genetics
Biodiversity
DNA, Bacterial/genetics
*Alphaproteobacteria/classification/genetics
Lichens/microbiology
Bacteria/classification/genetics
Sequence Analysis, DNA

@article {pmid41668418,
year = {2026},
author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S},
title = {Recent Microbial Evolutionary Insights From Metagenomics.},
journal = {Genome biology and evolution},
volume = {18},
number = {3},
pages = {},
pmid = {41668418},
issn = {1759-6653},
support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; },
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Evolution, Molecular ; Humans ; *Biological Evolution ; Phylogeny ; },
abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.},
}

*Metagenomics/methods
*Microbiota/genetics
*Evolution, Molecular
Humans
*Biological Evolution
Phylogeny

@article {pmid41655417,
year = {2026},
author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P},
title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.},
journal = {Water research},
volume = {294},
number = {},
pages = {125493},
doi = {10.1016/j.watres.2026.125493},
pmid = {41655417},
issn = {1879-2448},
mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Humans ; Human Activities ; Microbiota ; China ; Nitrogen ; Bacteria/genetics ; },
abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.},
}

*Groundwater/microbiology/chemistry
Metagenomics
Humans
Human Activities
Microbiota
China
Nitrogen
Bacteria/genetics

@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {664-677},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Humans ; Glomerular Filtration Rate ; Male ; Female ; Feces/microbiology ; Middle Aged ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; Cresols/metabolism ; Biomarkers ; Disease Progression ; Adult ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}

*Renal Insufficiency, Chronic/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Humans
Glomerular Filtration Rate
Male
Female
Feces/microbiology
Middle Aged
Dysbiosis/microbiology
*Kidney/physiopathology
Bacteria/classification/genetics/isolation & purification
Metagenomics
Aged
Cresols/metabolism
Biomarkers
Disease Progression
Adult

@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Humans ; Ethiopia/epidemiology ; *Gastrointestinal Microbiome ; Child, Preschool ; Female ; Male ; Feces/microbiology ; *Urban Population ; *Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Life Style ; *Bacteria/classification/genetics ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}

Humans
Ethiopia/epidemiology
*Gastrointestinal Microbiome
Child, Preschool
Female
Male
Feces/microbiology
*Urban Population
*Diet, Western/adverse effects
RNA, Ribosomal, 16S/genetics
Metagenomics
*Life Style
*Bacteria/classification/genetics

@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617724},
issn = {2052-4463},
mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/genetics ; *Microbiota ; *Genome, Fungal ; Metagenome ; },
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}

*Symbiosis
*Lichens/microbiology
*Ascomycota/genetics
*Microbiota
*Genome, Fungal
Metagenome

@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
mesh = {*Biosensing Techniques/methods ; *Microbiota ; Synthetic Biology ; },
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}

*Biosensing Techniques/methods
*Microbiota
Synthetic Biology

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Thailand ; *Prebiotics/administration & dosage ; Adult ; *Diet ; Fatty Acids, Volatile/metabolism ; Male ; Female ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Models, Biological ; Young Adult ; Middle Aged ; Systems Biology ; Southeast Asian People ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

Humans
*Gastrointestinal Microbiome
Thailand
*Prebiotics/administration & dosage
Adult
*Diet
Fatty Acids, Volatile/metabolism
Male
Female
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics
Models, Biological
Young Adult
Middle Aged
Systems Biology
Southeast Asian People

@article {pmid41579975,
year = {2026},
author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A},
title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.},
journal = {Free radical biology & medicine},
volume = {246},
number = {},
pages = {518-530},
doi = {10.1016/j.freeradbiomed.2026.01.034},
pmid = {41579975},
issn = {1873-4596},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *Pyruvaldehyde/metabolism/blood ; *Glycation End Products, Advanced/metabolism/blood ; *Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology ; Male ; Female ; Feces/chemistry/microbiology ; Middle Aged ; Glyoxal/metabolism ; Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Gastrointestinal Microbiome ; Deoxyglucose/analogs & derivatives/metabolism ; Metabolomics ; Receptor for Advanced Glycation End Products/genetics/metabolism ; },
abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.},
}

Humans
*Pyruvaldehyde/metabolism/blood
*Glycation End Products, Advanced/metabolism/blood
*Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology
Male
Female
Feces/chemistry/microbiology
Middle Aged
Glyoxal/metabolism
Aged
Lactoylglutathione Lyase/genetics/metabolism
Gastrointestinal Microbiome
Deoxyglucose/analogs & derivatives/metabolism
Metabolomics
Receptor for Advanced Glycation End Products/genetics/metabolism

@article {pmid41570514,
year = {2026},
author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T},
title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119288},
doi = {10.1016/j.marpolbul.2026.119288},
pmid = {41570514},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Microbiota ; *Nitrogen Cycle ; Metagenomics ; *Metagenome ; Nitrogen/metabolism ; Denitrification ; Bacteria ; Ecosystem ; },
abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.},
}

*Lakes/microbiology
*Microbiota
*Nitrogen Cycle
Metagenomics
*Metagenome
Nitrogen/metabolism
Denitrification
Bacteria
Ecosystem

@article {pmid41565819,
year = {2026},
author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N},
title = {Baby-to-baby strain transmission shapes the developing gut microbiome.},
journal = {Nature},
volume = {651},
number = {8104},
pages = {191-200},
pmid = {41565819},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation & purification/drug effects ; Metagenomics ; },
abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics/physiology
Infant
Female
Feces/microbiology
Male
Infant, Newborn
Longitudinal Studies
Anti-Bacterial Agents/pharmacology
Siblings
Adult
Bacteria/classification/genetics/isolation & purification/drug effects
Metagenomics

@article {pmid41558447,
year = {2026},
author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K},
title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119293},
doi = {10.1016/j.marpolbul.2026.119293},
pmid = {41558447},
issn = {1879-3363},
mesh = {*Archaea ; *Oxygen/analysis ; China ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Eutrophication ; Microbiota ; Bacteria ; Proteomics ; Multiomics ; },
abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed ‌integrated multi-omics‌ approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.},
}

*Archaea
*Oxygen/analysis
China
Seawater/microbiology/chemistry
Nitrogen/metabolism
Eutrophication
Microbiota
Bacteria
Proteomics
Multiomics

@article {pmid41387308,
year = {2026},
author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R},
title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {12},
pages = {e17747},
pmid = {41387308},
issn = {2198-3844},
support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; },
mesh = {*Aspirin/adverse effects/toxicity/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Mice ; Male ; Intestines/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; *Carboxylesterase/metabolism ; *Carboxylic Ester Hydrolases/metabolism ; *Intestinal Diseases/chemically induced/microbiology ; },
abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.},
}

*Aspirin/adverse effects/toxicity/metabolism
Animals
*Gastrointestinal Microbiome/physiology/drug effects
Mice
Male
Intestines/drug effects
Disease Models, Animal
Mice, Inbred C57BL
*Carboxylesterase/metabolism
*Carboxylic Ester Hydrolases/metabolism
*Intestinal Diseases/chemically induced/microbiology

@article {pmid41350118,
year = {2026},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {55},
number = {3},
pages = {368-380},
pmid = {41350118},
issn = {1600-0714},
mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; Male ; *Microbiota/genetics ; *Mouth Neoplasms/microbiology/pathology ; Female ; Middle Aged ; Aged ; Saliva/microbiology ; Case-Control Studies ; Adult ; *Mouth/microbiology ; DNA, Bacterial ; },
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.

METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.

RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.

CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}

Humans
*Carcinoma, Squamous Cell/microbiology/pathology
Male
*Microbiota/genetics
*Mouth Neoplasms/microbiology/pathology
Female
Middle Aged
Aged
Saliva/microbiology
Case-Control Studies
Adult
*Mouth/microbiology
DNA, Bacterial

@article {pmid41078118,
year = {2026},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {24},
number = {3},
pages = {1189-1203},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Microbiota/genetics ; *Plants/microbiology/genetics ; *Metagenomics/methods ; *DNA, Plant/genetics/isolation & purification ; CRISPR-Cas Systems ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}

*Microbiota/genetics
*Plants/microbiology/genetics
*Metagenomics/methods
*DNA, Plant/genetics/isolation & purification
CRISPR-Cas Systems

@article {pmid41078079,
year = {2026},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {81},
number = {3},
pages = {764-780},
pmid = {41078079},
issn = {1398-9995},
support = {//the Harvard University William F. Milton Fund/ ; R01 AI127507/AI/NIAID NIH HHS/United States ; R01 ES036966/ES/NIEHS NIH HHS/United States ; R01 AI148338/AI/NIAID NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //American Lung Association Innovation Award/ ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; //Massachusetts General Hospital/ ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Bronchiolitis/microbiology/genetics/etiology ; Infant ; *Microbiota ; *Nasopharynx/microbiology ; Female ; Male ; DNA Methylation ; *Epigenome ; Prospective Studies ; Genome-Wide Association Study ; Severity of Illness Index ; Asthma ; Infant, Newborn ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.

METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age < 1 year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24 h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR] < 0.05), regions (mbDMRs, FDR < 0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6 years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR < 0.10).

RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).

CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}

Humans
*Bronchiolitis/microbiology/genetics/etiology
Infant
*Microbiota
*Nasopharynx/microbiology
Female
Male
DNA Methylation
*Epigenome
Prospective Studies
Genome-Wide Association Study
Severity of Illness Index
Asthma
Infant, Newborn

@article {pmid41015495,
year = {2026},
author = {Castells-Nobau, A and Fumagalli, A and Del Castillo-Izquierdo, Á and Rosell-Díaz, M and de la Vega-Correa, L and Samulėnaitė, S and Motger-Albertí, A and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Burokas, A and Coll, C and Zapata-Tona, C and Perez-Brocal, V and Ramio, L and Moya, A and Swann, J and Martín-García, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Gut microbial modulation of 3-hydroxyanthranilic acid and dopaminergic signalling influences attention in obesity.},
journal = {Gut},
volume = {75},
number = {4},
pages = {705-724},
doi = {10.1136/gutjnl-2025-336391},
pmid = {41015495},
issn = {1468-3288},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Obesity/metabolism/microbiology/psychology ; Mice ; *3-Hydroxyanthranilic Acid/metabolism ; Tryptophan/metabolism/blood ; Humans ; Male ; Fecal Microbiota Transplantation ; Drosophila melanogaster ; Female ; *Dopamine/metabolism ; Metagenomics ; Mice, Inbred C57BL ; Signal Transduction ; ortho-Aminobenzoates/metabolism ; Metabolomics ; },
abstract = {BACKGROUND: Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood.

OBJECTIVE: To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention.

DESIGN: We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster.

RESULTS: Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation.

CONCLUSIONS: We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Obesity/metabolism/microbiology/psychology
Mice
*3-Hydroxyanthranilic Acid/metabolism
Tryptophan/metabolism/blood
Humans
Male
Fecal Microbiota Transplantation
Drosophila melanogaster
Female
*Dopamine/metabolism
Metagenomics
Mice, Inbred C57BL
Signal Transduction
ortho-Aminobenzoates/metabolism
Metabolomics

@article {pmid40696533,
year = {2025},
author = {Liu, W and Wang, J and Xue, Y and Li, J and Huang, Y and Zhu, S and Wang, L and Wang, G and Chen, W and Zhao, J},
title = {The impact of Bifidobacterium longum CCFM1112 on chronic constipation: a randomised, double-blind, placebo-controlled study.},
journal = {Beneficial microbes},
volume = {17},
number = {2},
pages = {109-125},
doi = {10.1163/18762891-bja00085},
pmid = {40696533},
issn = {1876-2891},
mesh = {Humans ; *Constipation/therapy/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; Male ; Female ; *Bifidobacterium longum/physiology ; Middle Aged ; Adult ; Gastrointestinal Microbiome ; Quality of Life ; Feces/microbiology/chemistry ; Chronic Disease/therapy ; Treatment Outcome ; },
abstract = {A mounting body of evidence suggests that probiotics may mitigate constipation through their favourable modulation of gut microbiota and its metabolic byproducts. The precise mechanisms underlying this effect remain to be fully elucidated. This randomised, double-blind, placebo-controlled study investigates the clinical efficacy of Bifidobacterium longum (B. longum) CCFM1112 in treating chronic constipation. Fifty-six volunteers diagnosed with chronic constipation according to the Rome IV criteria were randomly assigned to either the B. longum CCFM1112 group or a placebo group for a 4-week intervention. Key outcomes measured included weekly spontaneous bowel movements (SBM), stool consistency (Bristol Stool Form Scale [BSFS]), Patient Assessment of Constipation-Symptoms (PAC-SYM) questionnaire, and Quality of Life (PAC-QOL) questionnaire. In addition, gut microbiota was detected using metagenomic sequencing, and non targeted metabolomics was used to detect fecal and serum metabolites. Results demonstrated that B. longum CCFM1112 significantly reduced PAC-QOL scores and improved BSFS in patients with chronic constipation. Correlation analyses revealed that B. longum CCFM1112 significantly increased the abundance of the genera Blautia, Anaerobutyricum, and Streptococcus. Furthermore, the abundance of species, including Blautia massiliensis, Blautia sp. SC05B48, Anaerobutyricum hallii, and Streptococcus salivarius, was also significantly elevated. Furthermore, it elevated fecal levels of linoleic acid, gamma-aminobutyric acid (GABA), and arachidonic acid, while increasing L-glutamic acid and decreasing adenosine in serum. Our research findings provide evidence that the intake of B. longum CCFM1112 can alleviate constipation.},
}

Humans
*Constipation/therapy/microbiology
*Probiotics/administration & dosage/therapeutic use
Double-Blind Method
Male
Female
*Bifidobacterium longum/physiology
Middle Aged
Adult
Gastrointestinal Microbiome
Quality of Life
Feces/microbiology/chemistry
Chronic Disease/therapy
Treatment Outcome

@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; },
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

Animals
*Lacticaseibacillus rhamnosus/physiology
*Probiotics/pharmacology
Mice
*Lipid Metabolism/drug effects
Male
*Gastrointestinal Microbiome
*Lipopolysaccharides/biosynthesis/metabolism
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
*Non-alcoholic Fatty Liver Disease/metabolism
*Metabolic Diseases/metabolism

@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41775849},
issn = {2045-2322},
abstract = {UNLABELLED: Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41937-x.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/administration & dosage ; Disulfides ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed/analysis ; *Drug Resistance, Microbial/genetics ; Diet/veterinary ; *Fishes/growth & development/microbiology ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}

Animals
*Sulfinic Acids/pharmacology/administration & dosage
Disulfides
*Antioxidants/metabolism
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Animal Feed/analysis
*Drug Resistance, Microbial/genetics
Diet/veterinary
*Fishes/growth & development/microbiology

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/complications ; *HIV Infections/microbiology/complications ; Male ; Female ; *Bacterial Translocation ; *Coinfection/microbiology/virology ; Middle Aged ; Adult ; Lipopolysaccharide Receptors/blood ; Lipopolysaccharides/blood ; Feces/microbiology ; SARS-CoV-2 ; Cohort Studies ; Severity of Illness Index ; Haptoglobins ; Protein Precursors/blood ; },
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

Humans
*Gastrointestinal Microbiome
*COVID-19/microbiology/complications
*HIV Infections/microbiology/complications
Male
Female
*Bacterial Translocation
*Coinfection/microbiology/virology
Middle Aged
Adult
Lipopolysaccharide Receptors/blood
Lipopolysaccharides/blood
Feces/microbiology
SARS-CoV-2
Cohort Studies
Severity of Illness Index
Haptoglobins
Protein Precursors/blood

@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Lactobacillus/physiology ; *Ileum/metabolism/microbiology ; Mice ; *Gallstones/microbiology/prevention & control/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; *Probiotics/administration & dosage ; Disease Models, Animal ; Colon/microbiology ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}

Animals
*Lactobacillus/physiology
*Ileum/metabolism/microbiology
Mice
*Gallstones/microbiology/prevention & control/metabolism
Mice, Inbred C57BL
*Gastrointestinal Microbiome
Male
*Probiotics/administration & dosage
Disease Models, Animal
Colon/microbiology

@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
pmid = {41758194},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/pharmacology/therapeutic use/pharmacokinetics ; Dysbiosis/chemically induced/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; Animals ; Metabolomics ; Neoplasms/drug therapy ; },
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Antimetabolites/pharmacology/therapeutic use/pharmacokinetics
Dysbiosis/chemically induced/microbiology
Bacteria/metabolism/drug effects/genetics/classification
Animals
Metabolomics
Neoplasms/drug therapy

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
mesh = {*Biofilms/growth & development ; Humans ; Pilot Projects ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Biodiversity ; Archaea/genetics/isolation & purification/classification ; Fungi/genetics/classification/isolation & purification ; Male ; Viruses/classification/genetics/isolation & purification ; Female ; Middle Aged ; },
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

*Biofilms/growth & development
Humans
Pilot Projects
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Microbiota
*Biodiversity
Archaea/genetics/isolation & purification/classification
Fungi/genetics/classification/isolation & purification
Male
Viruses/classification/genetics/isolation & purification
Female
Middle Aged

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
mesh = {Humans ; Child, Preschool ; *Choledochal Cyst/microbiology ; Infant ; Male ; Female ; Child ; Age Factors ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; },
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

Humans
Child, Preschool
*Choledochal Cyst/microbiology
Infant
Male
Female
Child
Age Factors
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Biliary Tract/microbiology

@article {pmid41754175,
year = {2026},
author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H},
title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754175},
issn = {2072-6643},
support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Methylamines/metabolism/blood ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Choline/administration & dosage/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism/etiology ; Mice ; *Metagenomics ; *Machine Learning ; Liver/metabolism/pathology ; Feces/microbiology ; },
abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.

METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.

RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.

CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.},
}

Animals
*Methylamines/metabolism/blood
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
*Choline/administration & dosage/metabolism
*Gastrointestinal Microbiome
*Obesity/microbiology/metabolism/etiology
Mice
*Metagenomics
*Machine Learning
Liver/metabolism/pathology
Feces/microbiology

@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Milk ; Animals ; Feces/microbiology/chemistry ; Adult ; Bacteroides ; *Body Weight ; Obesity/microbiology/diet therapy ; Middle Aged ; Streptococcus thermophilus ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
*Milk
Animals
Feces/microbiology/chemistry
Adult
Bacteroides
*Body Weight
Obesity/microbiology/diet therapy
Middle Aged
Streptococcus thermophilus

@article {pmid41752220,
year = {2026},
author = {Kareem, HA and Khan, MF},
title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752220},
issn = {1422-0067},
support = {82930-NP//University College Dublin Internal Fund/ ; },
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Soil Pollutants/metabolism ; *Fluorocarbons/metabolism ; Soil Microbiology ; *Environmental Restoration and Remediation/methods ; },
abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.},
}

Biodegradation, Environmental
*Microbial Consortia
*Soil Pollutants/metabolism
*Fluorocarbons/metabolism
Soil Microbiology
*Environmental Restoration and Remediation/methods

@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
mesh = {*Colorectal Neoplasms/epidemiology/genetics/microbiology ; Humans ; *Fusobacterium nucleatum/genetics ; *Polyketides/metabolism ; *Peptides/metabolism ; *Gastrointestinal Microbiome ; Mutation ; *Bacteriocins/metabolism/genetics ; *Microbiota ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}

*Colorectal Neoplasms/epidemiology/genetics/microbiology
Humans
*Fusobacterium nucleatum/genetics
*Polyketides/metabolism
*Peptides/metabolism
*Gastrointestinal Microbiome
Mutation
*Bacteriocins/metabolism/genetics
*Microbiota

@article {pmid41746975,
year = {2026},
author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C},
title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0343817},
pmid = {41746975},
issn = {1932-6203},
mesh = {Humans ; *Tacrolimus/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Liver Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Adult ; Feces/microbiology ; Aged ; Dysbiosis ; Transplant Recipients ; Tandem Mass Spectrometry ; Metabolome/drug effects ; },
abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.

METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.

RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.

CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.},
}

Humans
*Tacrolimus/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Liver Transplantation/adverse effects
Male
Female
Middle Aged
*Immunosuppressive Agents/therapeutic use/pharmacology
Adult
Feces/microbiology
Aged
Dysbiosis
Transplant Recipients
Tandem Mass Spectrometry
Metabolome/drug effects

@article {pmid41729067,
year = {2026},
author = {Liu, Y and Zhang, T and Liu, J and Dong, X},
title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {8},
pages = {6824-6839},
doi = {10.1021/acs.jafc.5c14510},
pmid = {41729067},
issn = {1520-5118},
mesh = {*Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; *Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics ; Probiotics/metabolism ; Humans ; *Polymers/metabolism/chemistry ; Feces/microbiology ; *Lactobacillaceae/metabolism/genetics/isolation & purification ; Animals ; },
abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.},
}

*Proanthocyanidins/metabolism/chemistry
*Caffeic Acids/metabolism
Fermentation
*Gastrointestinal Microbiome
*Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics
Probiotics/metabolism
Humans
*Polymers/metabolism/chemistry
Feces/microbiology
*Lactobacillaceae/metabolism/genetics/isolation & purification
Animals

@article {pmid41719987,
year = {2026},
author = {Dang, X and Xu, S},
title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119906},
doi = {10.1016/j.ecoenv.2026.119906},
pmid = {41719987},
issn = {1090-2414},
mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects ; *Behavior, Animal/drug effects ; Molecular Docking Simulation ; Diabetes Mellitus, Experimental ; *Alkanesulfonic Acids/toxicity ; Salmonella enterica ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; Molecular Dynamics Simulation ; Colon/microbiology ; Fluorobenzenes ; },
abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.},
}

Animals
Male
Mice
Hippocampus/drug effects
*Behavior, Animal/drug effects
Molecular Docking Simulation
Diabetes Mellitus, Experimental
*Alkanesulfonic Acids/toxicity
Salmonella enterica
Gastrointestinal Microbiome/drug effects
*Environmental Pollutants/toxicity
Molecular Dynamics Simulation
Colon/microbiology
Fluorobenzenes

@article {pmid41715225,
year = {2026},
author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M},
title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41715225},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Sheep/microbiology/physiology/blood ; *Temperament/physiology ; *Vocalization, Animal/physiology ; Rumen/microbiology ; *Metabolome ; Female ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; gamma-Aminobutyric Acid/metabolism ; },
abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.

METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.

RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.

CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Sheep/microbiology/physiology/blood
*Temperament/physiology
*Vocalization, Animal/physiology
Rumen/microbiology
*Metabolome
Female
Metagenomics
Bacteria/classification/genetics/isolation & purification
gamma-Aminobutyric Acid/metabolism

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
mesh = {Methane/metabolism ; Wastewater ; Microbiota ; Acetates/metabolism ; },
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

Methane/metabolism
Wastewater
Microbiota
Acetates/metabolism

@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {44},
number = {4},
pages = {673-681},
pmid = {41669888},
issn = {1473-5598},
mesh = {Humans ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; Cohort Studies ; },
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}

Humans
*Hypertension/epidemiology/microbiology
Middle Aged
Female
Male
*Gastrointestinal Microbiome
Adult
Aged
Prospective Studies
Finland/epidemiology
Incidence
Risk Factors
Cohort Studies

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household environmental characteristics influence the house dust metagenome.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
mesh = {*Dust/analysis ; *Metagenome ; Humans ; *Microbiota ; *Family Characteristics ; Housing ; *Air Pollution, Indoor/analysis ; *Environmental Exposure ; },
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

*Dust/analysis
*Metagenome
Humans
*Microbiota
*Family Characteristics
Housing
*Air Pollution, Indoor/analysis
*Environmental Exposure

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0226425},
pmid = {41636495},
issn = {2165-0497},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
mesh = {Humans ; Female ; *Tears/chemistry/metabolism ; Male ; *Dry Eye Syndromes/microbiology/etiology ; *Proteome/analysis ; *Microbiota ; Adult ; *Contact Lenses/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Middle Aged ; Eye Proteins ; },
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

Humans
Female
*Tears/chemistry/metabolism
Male
*Dry Eye Syndromes/microbiology/etiology
*Proteome/analysis
*Microbiota
Adult
*Contact Lenses/adverse effects
Bacteria/classification/genetics/isolation & purification
Young Adult
Middle Aged
Eye Proteins

@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41634815},
issn = {2049-2618},
mesh = {*Triticum/growth & development/microbiology/physiology ; *Droughts ; *Caragana/microbiology ; *Plant Roots/microbiology ; Biofilms/growth & development ; *Microbiota ; Desert Climate ; Quorum Sensing ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Drought Resistance ; },
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}

*Triticum/growth & development/microbiology/physiology
*Droughts
*Caragana/microbiology
*Plant Roots/microbiology
Biofilms/growth & development
*Microbiota
Desert Climate
Quorum Sensing
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
Drought Resistance

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; Fresh Water ; *Fishes/microbiology/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

Animals
*Skin/microbiology
*Metagenomics/methods
Fresh Water
*Fishes/microbiology/genetics
Phylogeny
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Microbiota/genetics

@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617733},
issn = {2052-4463},
mesh = {Pacific Ocean ; *Metagenomics ; *Metagenome ; *Chlorophyll/analysis ; *Seawater/microbiology ; *Microbiota ; },
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}

Pacific Ocean
*Metagenomics
*Metagenome
*Chlorophyll/analysis
*Seawater/microbiology
*Microbiota

@article {pmid41617710,
year = {2026},
author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F},
title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617710},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Plastids/genetics/classification ; *Metagenomics/methods ; Phylogeny ; Symbiosis/genetics ; Cyanobacteria/genetics/classification ; Biodiversity ; Genetic Variation ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Genome, Plastid ; Alveolata/genetics ; Photosynthesis/genetics ; Evolution, Molecular ; },
abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.},
}

*Plastids/genetics/classification
*Metagenomics/methods
Phylogeny
Symbiosis/genetics
Cyanobacteria/genetics/classification
Biodiversity
Genetic Variation
Haptophyta/genetics/classification
Cryptophyta/genetics/classification
Genome, Plastid
Alveolata/genetics
Photosynthesis/genetics
Evolution, Molecular

@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxalates/metabolism ; *Kidney/metabolism ; Hyperoxaluria/metabolism ; Disease Management ; },
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Oxalates/metabolism
*Kidney/metabolism
Hyperoxaluria/metabolism
Disease Management

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41540332},
issn = {1471-2180},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

Animals
*Gastrointestinal Microbiome/genetics/drug effects
Mice
*Metagenomics/methods
Mice, Inbred C57BL
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
Mice, Inbred BALB C
Specific Pathogen-Free Organisms
Cecum/microbiology
Metagenome
*Drug Resistance, Microbial/genetics

@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; },
mesh = {Humans ; *Parkinson Disease/virology/microbiology ; *Gastrointestinal Microbiome ; *Virome ; Male ; Female ; Aged ; Case-Control Studies ; Middle Aged ; Metagenomics ; },
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}

Humans
*Parkinson Disease/virology/microbiology
*Gastrointestinal Microbiome
*Virome
Male
Female
Aged
Case-Control Studies
Middle Aged
Metagenomics

@article {pmid41468749,
year = {2026},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
pmid = {41468749},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology ; *Particulate Matter/analysis ; *Housing, Animal ; Metagenomics ; *Microbiota ; Risk Assessment ; *Air Microbiology ; Aerosols/analysis ; *Air Pollutants/analysis ; Bacteria/isolation & purification/classification ; Age Factors ; Animal Husbandry ; },
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}

Animals
*Chickens/microbiology/physiology
*Particulate Matter/analysis
*Housing, Animal
Metagenomics
*Microbiota
Risk Assessment
*Air Microbiology
Aerosols/analysis
*Air Pollutants/analysis
Bacteria/isolation & purification/classification
Age Factors
Animal Husbandry

@article {pmid41413233,
year = {2026},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {49},
number = {3},
pages = {958-968},
pmid = {41413233},
issn = {1348-4214},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Blood Pressure/physiology ; *Polyamines/metabolism ; Female ; *Hypertension/microbiology/metabolism/physiopathology ; Aged ; Adult ; Feces/microbiology ; },
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

Humans
*Gastrointestinal Microbiome/physiology
Middle Aged
Male
*Blood Pressure/physiology
*Polyamines/metabolism
Female
*Hypertension/microbiology/metabolism/physiopathology
Aged
Adult
Feces/microbiology

@article {pmid41401693,
year = {2026},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
pmid = {41401693},
issn = {1525-3171},
mesh = {China/epidemiology ; Animals ; *Virome ; Metagenomics ; *Galliformes/virology ; *Metagenome ; },
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}

China/epidemiology
Animals
*Virome
Metagenomics
*Galliformes/virology
*Metagenome

@article {pmid41364878,
year = {2026},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma.},
journal = {Blood advances},
volume = {10},
number = {5},
pages = {1634-1645},
pmid = {41364878},
issn = {2473-9537},
mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Immunotherapy, Adoptive/adverse effects/methods ; Aged ; Biomarkers ; Treatment Outcome ; Adult ; Recurrence ; },
abstract = {CD19 chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (R/R-DLBCL), but challenges such as posttreatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from patients with R/R-DLBCL were analyzed at apheresis (47 samples) and 1 month after infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly-diagnosed DLBCL, R/R-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders had higher levels of Bacteroides fragilis, whereas nonresponders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in R/R-DLBCL.},
}

Humans
*Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Immunotherapy, Adoptive/adverse effects/methods
Aged
Biomarkers
Treatment Outcome
Adult
Recurrence

@article {pmid41093027,
year = {2026},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
mesh = {Serine/analogs & derivatives/analogs & derivatives ; Quorum Sensing ; Microbial Consortia ; Microbiota ; *Photobioreactors/microbiology ; Microalgae/physiology ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Biomass ; Membranes, Artificial ; 4-Butyrolactone/analogs & derivatives/metabolism ; Bacteria/metabolism ; Metagenomics ; Chlorella/physiology ; Water Purification/methods ; },
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}

Serine/analogs & derivatives/analogs & derivatives
Quorum Sensing
Microbial Consortia
Microbiota
*Photobioreactors/microbiology
Microalgae/physiology
Nitrogen/analysis/metabolism
Phosphorus/analysis/metabolism
Biomass
Membranes, Artificial
4-Butyrolactone/analogs & derivatives/metabolism
Bacteria/metabolism
Metagenomics
Chlorella/physiology
Water Purification/methods

@article {pmid40814761,
year = {2026},
author = {Qin, P and Kragsnaes, MS and Holm, DK and Horn, HC and Nilsson, AC and Kjeldsen, J and Kristiansen, K and Ellingsen, T},
title = {Clinical Significance of Gut Microbiota Community Types for Long-Term Response to Fecal Microbiota Transplantation in Patients With Psoriatic Arthritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {78},
number = {2},
pages = {320-331},
pmid = {40814761},
issn = {2326-5205},
support = {Sundhedsdonationer 2022-0026//Sygeforsikringen "danmark"/ ; //Fabrikant Vilhelm Pedersen's Mindelegat (on recommendation by the Novo Nordisk Foundation)/ ; //Medicine Fund of the Danish Regions (Regionernes Medicin- og behandlingspulje)/ ; //University of Southern Denmark Research Fund/ ; //the Danish Rheumatism Association/ ; //the Danish Psoriasis Research Foundation/ ; //Research Fund of Odense University Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; *Arthritis, Psoriatic/therapy/microbiology ; Bacteroides ; Adult ; Prevotella ; Treatment Outcome ; Feces/microbiology ; Clinical Relevance ; },
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) holds promises as a beneficial supplement to methotrexate in patients with psoriatic arthritis (PsA). We therefore investigated how gut bacterial signatures in patients and donor strain engraftment were associated with long-term response to FMT.

METHODS: This exploratory study is based on the FLORA trial cohort, encompassing 31 patients with moderate-to-high PsA disease activity and four FMT donors. Of the 15 patients receiving one single-donor FMT, 13 were included in the per-protocol (PP) population. Stool samples were collected before and after FMT (week 4, 12, and 26). We performed shotgun metagenomics to characterize gut microbiota features.

RESULTS: At baseline, 17 patients (55%) had a gut microbiota community type dominated by the Bacteroides genus (B-type), whereas 14 (45%) had a Prevotella-driven community type (P-type). The B- and P-type patients did not differ in disease activity or demographics, but the B-type had a significantly higher species diversity compared to the P-type (P = 0.005). In the PP population, five of seven B-type patients versus none of six P-type patients (P = 0.021) achieved a long-term clinical beneficial response at week 26. Bacterial strain richness increased significantly from baseline to week 4 and week 26 in B-type (P = 0.016), but not in P-type, patients. Eighteen engrafted strains persisted only in B-type recipients by week 26, including a Bacteroides clarus strain, which demonstrated a negative effect size regarding arthritis pain and the patients' global assessment of disease.

CONCLUSION: Recipients with a Bacteroides-dominated community structure were more likely to achieve long-term beneficial response following one FMT.},
}

Humans
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation
Male
Female
Middle Aged
*Arthritis, Psoriatic/therapy/microbiology
Bacteroides
Adult
Prevotella
Treatment Outcome
Feces/microbiology
Clinical Relevance