@article {pmid40957978,
year = {2026},
author = {Ocampo-Chih, C and Hendricks, H and Weitkamp, S and Gowda, NS and Singh, H and Banerjee, R and Rajagopala, SV and Weitkamp, JH},
title = {Impact of donor human milk pasteurization methods on the gut microbiome of preterm infants.},
journal = {Pediatric research},
volume = {100},
number = {3},
pages = {1414-1420},
pmid = {40957978},
issn = {1530-0447},
mesh = {Humans ; *Pasteurization/methods ; *Milk, Human/microbiology ; *Infant, Premature ; Infant, Newborn ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Gestational Age ; },
abstract = {BACKGROUND: Preterm infants are often fed donor human milk (DHM) when the mother's own milk is insufficient or not available. Holder or Retort pasteurization is used to inactivate potential pathogens in DHM. The effects of DHM pasteurization methods on the infant gut microbiome are unknown.

METHODS: To compare the gut microbiome and clinical outcomes between preterm infants fed Holder- versus Retort-pasteurized DHM, we performed weekly collections of stool samples from infants born <34 weeks' gestation and/or <1500 g birth weight. We analyzed stool samples from 150 patients exclusively fed DHM [Retort (n = 80), Holder (n = 54)] or exclusively fed mother's own milk (n = 16). Whole-metagenome sequencing was performed to assess microbiome composition, diversity, and functional enrichment.

RESULTS: Compared to infants fed Retort-pasteurized DHM, infants fed Holder-pasteurized DHM showed higher alpha-diversity (Chao-1 p = 0.007) and a higher abundance of beneficial anaerobes, such as Bacteroides thetaiotaomicron, Clostridium spp., and Bifidobacterium spp. Functional enrichment analysis revealed significant differences in carbohydrate metabolism, transport systems, and regulatory pathways between feeding groups. There were no statistically significant differences in short-term clinical outcomes, such as necrotizing enterocolitis, length of hospitalization or death.

CONCLUSION: Differences in pasteurization methods for DHM resulted in measurable gut microbiome changes in preterm infants.

IMPACT: It is known that the preterm infant gut microbiota is different in infants fed pasteurized donor milk compared to mother's own milk. However, the impact of different pasteurization methods for donor milk on the infant gut microbiome is unknown. We show that the type of pasteurization of donor human milk influences the gut microbiome and its function in preterm infants. In contrast to feeding Retort-pasteurized donor human milk, feeding Holder-pasteurized donor human milk generates an infant gut microbiome similar to feeding mother's own milk.},
}

Humans
*Pasteurization/methods
*Milk, Human/microbiology
*Infant, Premature
Infant, Newborn
Female
Feces/microbiology
*Gastrointestinal Microbiome
Male
Gestational Age

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {100},
number = {3},
pages = {1301-1312},
pmid = {41519950},
issn = {1530-0447},
mesh = {Humans ; *Constipation/microbiology/blood/metabolism ; Child ; *Gastrointestinal Microbiome ; Bile Acids and Salts/metabolism ; Female ; Male ; Child, Preschool ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Bacteria/genetics ; },
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

Humans
*Constipation/microbiology/blood/metabolism
Child
*Gastrointestinal Microbiome
Bile Acids and Salts/metabolism
Female
Male
Child, Preschool
Metabolomics
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Bacteria/genetics

@article {pmid42631930,
year = {2026},
author = {Choi, W and Mangal, U and Cha, JK and Cho, H and Ryu, JH and Kim, JY and Koh, WG and Lee, KJ and Kim, KW and Choi, SH and Traverso, G and Hong, J},
title = {A Mucosa-Inspired Dynamic Biointerface Engineering a Biofilm-Preventive Niche Against Pathogenic Microbiome Dysbiosis.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {38},
number = {58},
pages = {e74745},
doi = {10.1002/adma.74745},
pmid = {42631930},
issn = {1521-4095},
support = {//Korea-US Collaborative Research Fund/ ; RS-2024-00468036//Ministry of Science and ICT and Ministry of Health & Welfare/ ; 2025-RISE-10-101//Regional Innovation System & Education/ ; //Regional Anchor company-Academia Partnership Innovation Development/ ; //Institute for Project-Y Seed/ ; RS-2024-00438634//Korea Health Technology R&D Project through the Korea Health Industry Development Institute/ ; //Nano & Material Technology Development Program through the National Research Foundation of Korea/ ; RS-2024-00449435//Ministry of Science and ICT/ ; RS-2021-NR059601//National Research Foundation of Korea/ ; RS-2023-00217709//National Research Foundation of Korea/ ; RS-2025-00522998//National Research Foundation of Korea/ ; },
mesh = {*Biofilms/drug effects ; *Dysbiosis/prevention & control/microbiology ; *Microbiota ; Humans ; *Mucous Membrane ; Biocompatible Materials/chemistry/pharmacology ; },
abstract = {A stable symbiosis within the microbiome-host axis is essential for human health. However, preventing microbiome dysbiosis using biomaterials remains challenging due to their unpredictable influence on microbiome evolution. Inspired by the defensive niche of symbiotic mucosa, we have developed a biointerface that forms an engineered mucosa-inspired dynamic niche to prevent pathogenic dysbiosis. This biointerface features a dynamic zwitterionic network that emulates the mucosa's biophysical defensive functions. Notably, by leveraging its dynamic niche, the biointerface restricts microbial attachment and aggregation, thereby preventing biofilm formation. Comprehensive metagenomic analyses reveal that microbial communities adapt to this biofilm-preventive dynamic biointerface compositionally and functionally. In particular, Gram-negative bacteria were relatively reduced, along with decreased abundance of pathways associated with virulence and biofilm formation. Consequently, the mucosa-inspired biointerface intrinsically prevents the development of pathogenic dysbiosis. This study demonstrates the groundbreaking potential of material-based niche engineering to guide the ecological shifts of microbial communities from the material scale.},
}

*Biofilms/drug effects
*Dysbiosis/prevention & control/microbiology
*Microbiota
Humans
*Mucous Membrane
Biocompatible Materials/chemistry/pharmacology

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42880064,
year = {2026},
author = {Sun, P and Tan, Y and Jia, R and Lian, J and Yang, T and Li, H and Zhu, Z and Xi, C},
title = {Impacts and mechanisms of oyster farming on denitrification and anammox in coastal sediments from Tieshan Bay, China.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108453},
doi = {10.1016/j.marenvres.2026.108453},
pmid = {42880064},
issn = {1879-0291},
abstract = {Oyster aquaculture is widely recognized as an effective way to mitigate coastal eutrophication, but critical knowledge gaps remain regarding how it modulates nitrogen removal processes, which requires further investigation. In this study, sediments from oyster farming (OY) and non-oyster farming (NOY) areas in Tieshan Bay, China, were analyzed to explore the impacts of oyster farming on denitrification and anammox in coastal sediments. OY sediments exhibited significantly higher sediment oxygen demand (SOD), total organic carbon (TOC), ammonium (NH4[+]), ferrous iron (Fe[2+]), and sulfide than NOY sediments (P < 0.05), collectively creating hypoxic conditions favorable for nitrogen removal. Denitrification dominated nitrogen removal in both areas (OY: 91.84%; NOY: 90.19%). Potential denitrification and anammox rates in OY areas were 2.25 and 1.80 times higher than those in NOY areas, respectively (P < 0.01). Redundancy analysis (RDA) identified TOC, SOD, sulfide, Fe[2+], Fe[3+], and NH4[+] as key drivers of these processes. Metagenomic analysis revealed that OY sediments were enriched in Bacillota and Bacteroidota at the phylum level, and key functional genes (nirS, nosZ, hzsB) were significantly more abundant in OY areas (P < 0.05), suggesting enhanced genetic potential for nitrogen removal. The stronger promotion of denitrification over anammox was attributed to the combined effects of TOC (electron donors), Fe[2+] (electron carrier), and sulfide (alternative electron donor for denitrification but inhibitor for anammox). These findings demonstrate that oyster aquaculture enhances the functional capacity for sedimentary nitrogen removal through physicochemical modification, microbial community selection, and enrichment of key functional genes.},
}

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42883692,
year = {2026},
author = {Zhang, W and Zhu, Y and Chu, X and Zhang, X and Pan, Z and Li, A},
title = {Co-Enrichment of Desulfovibrio and Erysipelotrichaceae and Dysregulation of Multiple Amino Acid Pathways in HFpEF: Insights into TXG-Associated Metabolic Changes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198445},
pmid = {42883692},
issn = {1422-0067},
support = {82174080//National Natural Science Foundation of China/ ; H2022423333//Hebei Provincial Department of Science and Technology/ ; },
mesh = {Animals ; *Amino Acids/metabolism/blood ; *Heart Failure/metabolism/microbiology/drug therapy ; *Desulfovibrio/genetics/isolation & purification ; Mice ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Male ; *Eubacteriales/genetics ; Diet, High-Fat/adverse effects ; Metabolome ; Metagenomics ; },
abstract = {Gut enrichment of Desulfovibrio and Erysipelotrichaceae may be associated with systemic amino acid metabolic dysfunction, myocardial injury, and heart failure with preserved ejection fraction (HFpEF). These taxa appear to influence host amino acid metabolism through distinct processes, but the functional implications of their co-enrichment in HFpEF remain unclear. Total xanthones from Gentianella acuta (TXG) have documented cardioprotective effects, although their effects on gut microbiota and systemic metabolism remain unexplored. We established a mouse model of HFpEF using a high-fat diet (HFD) combined with Nω-nitro-L-arginine methyl ester (L-NAME). We integrated 16S rRNA sequencing, fecal metagenomics, and targeted serum amino acid metabolomics to examine microbe-metabolite associations, with echocardiography and histopathology providing complementary phenotypic evidence. Microbial and metabolomic analyses revealed pronounced enrichment of Desulfovibrio and Erysipelotrichaceae (particularly Dubosiella), accompanied by elevated serum isoleucine, tryptophan, and homocysteine levels. TXG treatment was associated with lower abundance of both taxa, altered serum amino acid profiles, preserved colonic barrier integrity, and reduced myocardial inflammation and fibrosis. These changes coincided with improved diastolic function. Together, these findings associate co-enrichment of the two taxa with dysregulation of multiple amino acid pathways in HFpEF. TXG treatment was accompanied by attenuated cardiac and metabolic injury as well as shifts in gut-microbiota profiles, with these correlative observations motivating further investigation of Gentianella acuta for metabolic heart failure.},
}

Animals
*Amino Acids/metabolism/blood
*Heart Failure/metabolism/microbiology/drug therapy
*Desulfovibrio/genetics/isolation & purification
Mice
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Male
*Eubacteriales/genetics
Diet, High-Fat/adverse effects
Metabolome
Metagenomics

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods

@article {pmid42883729,
year = {2026},
author = {Liu, N and Zhang, S and Li, Y},
title = {Molecular Mechanisms of the Gut-Liver-Placenta Axis in Intrahepatic Cholestasis of Pregnancy: Microbiota-Associated Pathogenesis and Next-Generation Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198481},
pmid = {42883729},
issn = {1422-0067},
support = {XLYC2412033//LiaoNing Revitalization Talents Program/ ; },
mesh = {Humans ; Female ; *Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology ; Pregnancy ; *Pregnancy Complications/metabolism/microbiology/therapy/etiology ; *Placenta/metabolism ; Bile Acids and Salts/metabolism ; Animals ; *Liver/metabolism/pathology ; *Gastrointestinal Microbiome ; Dysbiosis ; },
abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder characterized by elevated maternal bile acid concentrations and an increased risk of adverse perinatal outcomes. Genetic susceptibility, hormonal changes, and impaired bile acid transport contribute to its development but do not fully explain the variability in disease severity and fetal outcomes. Increasing evidence suggests that gut microbiota dysbiosis and altered bile acid metabolism are associated with ICP and may participate in disease development through the gut-liver-placenta axis. In this review, we integrate evidence on bile acid-microbiota interactions during pregnancy, ICP-associated microbial and metabolic alterations, and their possible links to placental and fetal outcomes. Human studies primarily support associations among microbial alterations, bile acid profiles, and disease severity, whereas the microbiota-mediated effects on placental function and fetal injury proposed to date are supported largely by experimental models. We further discuss potential links among gut microbial dysfunction, placental oxidative stress, fetal cardiac injury, neurodevelopmental risk, offspring metabolic susceptibility, and iatrogenic prematurity. Although ursodeoxycholic acid (UDCA) improves maternal pruritus and selected biochemical indices, its effect on major perinatal outcomes remains uncertain. Ileal bile acid transporter (IBAT) inhibitors and microbiota-targeted interventions remain investigational, with insufficient pregnancy-specific evidence regarding their efficacy and maternal-fetal safety. Future studies should clarify the associated causal mechanisms and integrate metagenomic, metabolomic, and placental data to identify clinically relevant biomarkers and therapeutic targets.},
}

Humans
Female
*Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology
Pregnancy
*Pregnancy Complications/metabolism/microbiology/therapy/etiology
*Placenta/metabolism
Bile Acids and Salts/metabolism
Animals
*Liver/metabolism/pathology
*Gastrointestinal Microbiome
Dysbiosis

@article {pmid42883733,
year = {2026},
author = {Abdulkhakov, SR and Safina, DD and Markelova, MI and Ponomareva, ER and Siniagina, MN and Khusnutdinova, DR and Kupriyanova, OV and Abdulkhakov, RA and Grigoryeva, TV},
title = {Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198485},
pmid = {42883733},
issn = {1422-0067},
support = {12/2025-PD-KFU//Tatarstan Academy of Sciences/ ; },
mesh = {Humans ; *Inulin/pharmacology/therapeutic use/administration & dosage ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/metabolism ; Adult ; *Butyric Acid/pharmacology/therapeutic use/administration & dosage ; Middle Aged ; Metagenomics/methods ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Female ; Male ; Fatty Acids, Volatile/metabolism ; Metabolomics/methods ; *Metabolome ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; Metagenome ; },
abstract = {The long-term impact of eradication therapy for Helicobacter pylori on the gut microbiota is a subject of significant interest. To evaluate the influence of the bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin on functional alterations within the gut microbial community, metagenomic and metabolomic profiling were performed. Fecal samples were collected from 15 patients (aged 19-64 years) prior to the treatment, immediately after the treatment, and one month after the therapy. A significant decrease in the relative abundance of Actinobacteria, such as Bifidobacterium and Collinsella, was observed after the therapeutic intervention. In contrast, the levels of Faecalibacterium prausnitzii remained consistent, while Roseburia faecis levels exhibited a substantial decline, suggesting a disruption in key butyrate-producing bacteria. A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed. A comprehensive analysis of short-chain fatty acids (SCFAs) levels in the feces of the patients revealed a decline in the butyric acid concentration in response to the therapy, followed by a return to baseline levels. However, the level of valeric acid declined, and there was no tendency for it to increase after a month-long course of therapy. It is important to note that these shifts persisted for a period of four weeks. Consequently, the H. pylori eradication therapy intervention promotes a persistent microbial reorganization, and the observed recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation. To confirm the conclusions, a larger sample size and longer-duration studies are required.},
}

Humans
*Inulin/pharmacology/therapeutic use/administration & dosage
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/metabolism
Adult
*Butyric Acid/pharmacology/therapeutic use/administration & dosage
Middle Aged
Metagenomics/methods
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Female
Male
Fatty Acids, Volatile/metabolism
Metabolomics/methods
*Metabolome
Young Adult
Anti-Bacterial Agents/therapeutic use
Metagenome

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198493},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42883855,
year = {2026},
author = {Dessalegn, B and Debelo, M and Palmieri, N and Dublecz, K and Hess, M and Awad, WA},
title = {Early-Life Oat Supplementation Is Associated with Altered Cecal Microbiota and Microbial Metabolic Profiles and Reduced Campylobacter jejuni Colonization in Broiler Chickens.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198607},
pmid = {42883855},
issn = {1422-0067},
support = {FWF; P 36720//FWF Austrian Science Fund/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology/metabolism ; *Campylobacter jejuni ; *Avena/chemistry ; *Dietary Supplements ; *Campylobacter Infections/veterinary/microbiology ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Amino Acids/metabolism ; Fatty Acids, Volatile/metabolism ; Diet ; *Metabolome ; *Poultry Diseases/microbiology/prevention & control ; },
abstract = {Campylobacter jejuni is a leading foodborne pathogen that commonly colonizes the intestinal tract of broiler chickens and represents a significant food safety concern. Dietary intervention may provide a practical approach to modulate the gut microbiota and reduce pathogen colonization. This study investigated the effects of oat supplementation on C. jejuni colonization and dissemination, cecal microbiota and predicted functions, and cecal short-chain fatty acids (SCFAs) and ileal amino acid profiles during early-life infection in broiler chickens. One-day-old Ross 308 broiler chickens were fed a basal diet or diets containing 10% oat (MDF) or 20% oat (HDF) and orally infected with C. jejuni at 2 days of age. C. jejuni loads in the cecum, jejunum, liver, and spleen were quantified by culture. Cecal microbiota composition and predicted functional profiles were characterized by shotgun metagenomic sequencing, while cecal SCFAs and ileal amino acids were quantified at 21 and 35 dpi using gas chromatography and an automatic amino acid analyzer, respectively. Oat supplementation reduced intestinal C. jejuni loads and limited dissemination to the liver and spleen, with the MDF diet reducing cecal loads by up to 3.3 log10 CFU/g at 35 dpi (p < 0.05). Infection altered cecal microbial diversity and community structure, while oat supplementation modified these infection-associated microbial patterns, with MDF showing the most consistent effects. Differential abundance analysis identified changes in taxa, including Bacteroides, Parabacteroides, and Phocaeicola, together with changes in predicted functions related to motility and chemotaxis, iron acquisition, and dormancy/sporulation. These microbial changes coincided with alterations in cecal isobutyrate and ileal amino acids, particularly glutamate, serine, proline, and aspartate, in MDF-fed infected chickens. Overall, MDF supplementation was most consistently associated with reduced C. jejuni colonization and dissemination and concurrent changes in the developing cecal microbial and metabolic profiles.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology/metabolism
*Campylobacter jejuni
*Avena/chemistry
*Dietary Supplements
*Campylobacter Infections/veterinary/microbiology
Animal Feed
*Gastrointestinal Microbiome/drug effects
Amino Acids/metabolism
Fatty Acids, Volatile/metabolism
Diet
*Metabolome
*Poultry Diseases/microbiology/prevention & control

@article {pmid42884152,
year = {2026},
author = {Jenkins Sánchez, L and Poppe, J and Baudot, A and Vu, LD and Villella, W and Van den Abbeele, P},
title = {Impact of Triacetin- and Tributyrin-Based Formulations on IBS Microbiome Composition and SCFA Profiles: A Preclinical Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198910},
pmid = {42884152},
issn = {1422-0067},
mesh = {Humans ; *Triglycerides/pharmacology ; *Fatty Acids, Volatile/metabolism ; *Triacetin/pharmacology ; *Irritable Bowel Syndrome/microbiology/drug therapy/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Adult ; Male ; Prebiotics/administration & dosage ; Female ; Butyrates/metabolism ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent yet poorly understood functional gut disorder frequently associated with microbial dysbiosis, making microbiome-targeting interventions a promising management strategy. In this study, we evaluated the microbiome-modulating potential of three doses of triacetin (TA; ReBiome™; 100, 200 and 300 mg/day) and two finished formulations containing TA and/or tributyrin (TB): Active Biome™ (AB) and Bio Complete 3™ (BC3). Inulin served as a benchmark prebiotic. The validated ex vivo Systemic Intestinal Fermentation Research (SIFR[®]) technology pipeline was applied using fecal microbiota from eight adults with IBS. TA dose-dependently increased short-chain fatty acid (SCFA) levels from 100 mg/day, significantly increasing acetate and butyrate while maintaining low gas formation. In addition to acetate and butyrate, AB and BC3 also promoted propionate while BC3 induced a particularly pronounced butyrate increase. Overall, both formulations induced stronger SCFA but milder gas increases than inulin. TA, AB and BC3 enriched IBS-depleted, butyrate-associated OTUs related to Faecalibacterium and Anaerobutyricum species. AB and BC3 increased microbial diversity (community modulation score (CMS)) by promoting Bifidobacteriaceae, Lachnospiraceae and Bacteroidaceae. Overall, TA and TA/TB-containing formulations promoted butyrate production, potentially helping mitigate IBS symptom severity by inducing a favorable fermentation profile with limited gas formation.},
}

Humans
*Triglycerides/pharmacology
*Fatty Acids, Volatile/metabolism
*Triacetin/pharmacology
*Irritable Bowel Syndrome/microbiology/drug therapy/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Fermentation
Adult
Male
Prebiotics/administration & dosage
Female
Butyrates/metabolism

@article {pmid42884177,
year = {2026},
author = {Rodríguez-Costas, N and Rodríguez-Blanco, A and Expósito, CR and Cubiella, J and Stompel, ES and Fernández-de-Ana Portela, C and Martín, AID and Taboada-Rodríguez, P and Silva, BF and Fernández, MDR and Zarraquiños, S and Remedios, D and Gómez, CAS and Lorenzo, SA and Poceiro, RF and Parga, MLC and Ramírez, VH and Pérez-Castro, S},
title = {Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198936},
pmid = {42884177},
issn = {1422-0067},
support = {N.º Solicitud SOL-00105490, N.º Expediente EXP0010549//Centre for Industrial Technological Development/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Fungi/chemistry ; Female ; Male ; Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Aged ; },
abstract = {The gut microbiome is increasingly recognized as an important determinant of host immune regulation, intestinal homeostasis, and recovery after colorectal cancer (CRC) surgery. Although our previous randomized, double-blind, placebo-controlled clinical trial demonstrated that fungal nutraceutical supplementation with Micodigest[®] was associated with favorable taxonomic and systemic inflammatory changes in patients undergoing CRC surgery with curative intent, the functional consequences of this intervention remain poorly understood. Here, we performed a functional metagenomic analysis of fecal samples collected from patients enrolled in the original clinical trial to investigate whether Micodigest[®] supplementation was associated with changes in the functional potential of the gut microbiome. A total of 37 patients were analyzed, including 24 receiving Micodigest[®] and 13 receiving placebo, with paired samples collected before supplementation and after 4-6 weeks of intervention. Shallow shotgun metagenomic sequencing was performed, and microbial functional potential was characterized using KEGG Orthologues (KOs). Differential abundance analysis identified 14 significantly different KOs between groups at baseline and 23 after intervention, with no overlap between the two sets of orthologues. Following supplementation, Micodigest[®]-treated patients exhibited increased representation of functions related to CRISPR-associated systems, bacteriophage biology, and chitin-derived carbohydrate utilization, together with reduced representation of nutrient acquisition systems, conjugative transfer, sulfur metabolism, and components of the Wood-Ljungdahl pathway. These functional signatures suggest coordinated changes in microbial ecological adaptation, nutrient utilization, genetic exchange, and metabolic activity following fungal nutraceutical supplementation. Integration with previously reported taxonomic and inflammatory findings supports the hypothesis that Micodigest[®] may promote coordinated remodeling of the gut microbiome and host-microbiota interactions during the perioperative period. Although the present study cannot establish causality or directly infer microbial activity from metagenomic potential, these findings provide novel functional insights into the microbiome response to fungal nutraceutical supplementation in patients with CRC and highlight functional metagenomics as a valuable complement to taxonomic profiling.},
}

Humans
*Colorectal Neoplasms/microbiology
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Fungi/chemistry
Female
Male
Feces/microbiology
Metagenomics/methods
Middle Aged
Aged

@article {pmid42884562,
year = {2026},
author = {Xu, Z and Lau, RI and Qi, H and Wong, MCS and Chan, KHN and Lau, ISF and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {Synbiotic HQP08 Supplementation for Hair Loss and Depressive Symptoms: An Open-Label Pilot Study of Clinical Outcomes and Gut Microbiome Changes.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193111},
pmid = {42884562},
issn = {2072-6643},
support = {//InnoHK/ ; },
mesh = {Humans ; Pilot Projects ; *Alopecia/microbiology/therapy ; Female ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Synbiotics/administration & dosage ; Treatment Outcome ; *Depression/therapy/microbiology ; *Bifidobacterium longum ; Dietary Supplements ; Young Adult ; },
abstract = {Background: Gut microbiota dysregulation has been implicated in hair loss via the gut-skin axis, but human interventional data are limited. We previously showed that Bifidobacterium longum HK003 reverses alopecia-like phenotypes in mice. Methods: We conducted an open-label, single-arm pilot study to evaluate an HK003-containing synbiotic (HQP08) in 32 adults with self-reported hair loss over 8 weeks. The primary endpoint was the proportion of participants reporting improvement on the Patient Global Impression of Change (PGI-C) scale at week 8. Secondary outcomes included changes in hair loss severity, 60 s hair count, depressive symptoms (PHQ-9), safety, and gut microbiome composition (Chinese Clinical Trial Registry ChiCTR2500112698). Results: At week 8, 62.5% (20/32) of participants reported PGI-C improvement. Significant reductions were observed in hair loss severity (p = 0.0008), 60 s hair count (p = 0.0048), and PHQ-9 scores (p = 0.002). Younger age was associated with PGI-C response (OR per year 0.86, 95% CI: 0.73-0.98, p = 0.037). Metagenomic analysis identified engraftment of B. longum HK003-like profiles in a subset of participants at week 12. Changes in microbial pathways related to thiamine metabolism, vitamin B12 salvage, and lipopolysaccharide biosynthesis were associated with ΔPHQ-9 (FDR-adjusted p < 0.05), but not with hair-related endpoints. No serious adverse events occurred. Conclusions: This first-in-human pilot study suggests that HQP08 was well tolerated and was associated with within-participant changes in hair-loss measurements and PHQ-9 scores. Randomized controlled trials are warranted to confirm efficacy and further elucidate mechanisms within the gut-brain-skin axis.},
}

Humans
Pilot Projects
*Alopecia/microbiology/therapy
Female
Male
Adult
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Synbiotics/administration & dosage
Treatment Outcome
*Depression/therapy/microbiology
*Bifidobacterium longum
Dietary Supplements
Young Adult

@article {pmid42884650,
year = {2026},
author = {Zhao, X and Yang, C and Gao, L and Gao, Y and Qian, W and Liu, H and Sun, Z and Wang, G and Zhao, F},
title = {Heat-Inactivated Lacticaseibacillus paracasei PC-01 Alleviates DSS-Induced Colitis in Mice by Modulating Gut Microbiota and Intestinal Barrier Function.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193199},
pmid = {42884650},
issn = {2072-6643},
support = {23402050//National Natural Science Foundation of China/ ; 2024YFA1307002//National Key Research and Development Program of China/ ; 2024QN03052//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; SPKJ202206//Science and technology project of the Food Science and Engineering College, Inner Mongolia Agricultural University/ ; },
mesh = {Animals ; Mice, Inbred C57BL ; *Lacticaseibacillus paracasei/physiology ; *Gastrointestinal Microbiome ; Mice ; Intestinal Barrier Function ; Dextran Sulfate ; *Colitis/chemically induced/microbiology/therapy ; Cytokines/blood/metabolism ; Disease Models, Animal ; Male ; Hot Temperature ; *Probiotics/pharmacology ; Intestinal Mucosa/microbiology/metabolism ; },
abstract = {Background: Inflammatory bowel disease (IBD) is a chronic, progressive, immune-mediated inflammatory disorder of the gastrointestinal tract. Methods: This study used C57BL/6J mice induced by DSS to construct an intestinal inflammation model, and explored the alleviating effect and potential mechanism of heat inactivated Lactobacillus paracasei PC-01 (PC-01) on intestinal inflammation. Results: The results showed that heat-inactivated PC-01 significantly decreased the Disease Activity Index and H&E histopathological scores (p < 0.05). It also reduced the serum levels of pro-inflammatory cytokines, including IL-6, IL-1β, TNF-α, and malondialdehyde (p < 0.01), increased the levels of the anti-inflammatory factor IL-10 (p < 0.001) and antioxidant enzymes SOD and GSH-Px (p < 0.01), and restored the integrity of the intestinal epithelial barrier in DSS-induced colitis mice. Metagenomic analysis showed that PC-01 treatment restored the abundance of beneficial bacteria, including Barnesiella and Muribaculum, and reduced the enrichment of opportunistic pathogens such as Angelakisella and Lawsonibacter (p < 0.05). Further functional annotation of the microbial community indicated that PC-01 significantly enriched pathways related to the TCA cycle, riboflavin metabolism, Toll and Imd signaling, and lipopolysaccharide biosynthesis. In addition, the relative abundances of auxiliary activities, polysaccharide lyases, and S-layer homology modules were lower than those in the DSS group, whereas those of glycoside hydrolases, glycosyltransferases, and carbohydrate esterases were higher. At the transcriptional level, intervention with heat-inactivated PC-01 resulted in a downward trend in the expression of TLR4, Nfkb1, and Rela, accompanied by reduced expression of the chemokines MCP-1 and Cxcl10, and inflammasome-related genes NLRP3, Casp1, and IL-1β. Conclusions: In summary, heat-inactivated Lacticaseibacillus paracasei PC-01 effectively alleviated intestinal inflammatory injury in mice by regulating gut microbiota homeostasis and suppressing intestinal inflammatory responses.},
}

Animals
Mice, Inbred C57BL
*Lacticaseibacillus paracasei/physiology
*Gastrointestinal Microbiome
Mice
Intestinal Barrier Function
Dextran Sulfate
*Colitis/chemically induced/microbiology/therapy
Cytokines/blood/metabolism
Disease Models, Animal
Male
Hot Temperature
*Probiotics/pharmacology
Intestinal Mucosa/microbiology/metabolism

@article {pmid42885240,
year = {2026},
author = {Ghosh, SK and Wassel, MA and Wong, MK and Hyodo, S and Hamasaki, K},
title = {Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70448},
doi = {10.1111/1462-2920.70448},
pmid = {42885240},
issn = {1462-2920},
support = {//University of Tokyo/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; *Oncorhynchus keta/microbiology/metabolism/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Amino Acids/biosynthesis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; },
abstract = {The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.},
}

Animals
*Oncorhynchus keta/microbiology/metabolism/genetics
Metagenomics
*Gastrointestinal Microbiome
Amino Acids/biosynthesis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome

@article {pmid42482126,
year = {2026},
author = {Zhai, Y and Kim, Y and Ban, GH and Kim, YM and Kim, SC and Bae, D and Jeong, KC and Kim, SA},
title = {Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42482126},
issn = {2049-2618},
mesh = {Animals ; Swine ; Gene Transfer, Horizontal ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Abattoirs ; Microbiota/genetics ; Acinetobacter/genetics/drug effects/isolation & purification ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Pseudomonas/genetics/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Farms ; *Pork Meat/microbiology ; Humans ; Metagenome ; Genes, Bacterial ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health, yet the contribution of food production environments to resistance transmission remains poorly understood.

RESULTS: We conducted a longitudinal shotgun metagenomic study across the pork production continuum from farm to retail to identify environmental AMR reservoirs and transmission pathways of antimicrobial resistance genes (ARGs). Assembly-based, genome-resolved, and source-tracking analyses were integrated to characterize resistomes, microbial communities, and horizontal gene transfer dynamics. ARG abundance and diversity were highest at farms, slaughterhouses, and processing plants and declined toward retail, although clinically relevant resistance determinants persisted throughout processing. Slaughterhouse environments emerged as major contributors to ARG contamination on carcasses, highlighting the importance of environmental exposure at intermediate stages. Resistome structure was closely linked to microbial community composition, with persistent taxa such as Acinetobacter and Pseudomonas serving as key ARG carriers, including genes conferring resistance to tetracycline, aminoglycosides, macrolide-lincosamide-streptogramin, and β-lactams, multidrug efflux. Co-localization of ARGs with mobile genetic elements demonstrated ongoing potential for horizontal transfer across production stages, and genome-resolved metagenome-assembled genome analyses revealed overlapping resistance and virulence profiles between slaughterhouse- and processing plant-associated bacteria, indicating adaptive persistence within pork production environments.

CONCLUSIONS: Resistome composition across the pork production chain is largely shaped by stage-specific environmental sources, highlighting potential intervention points to mitigate AMR transmission. Video Abstract.},
}

Animals
Swine
Gene Transfer, Horizontal
Metagenomics/methods
Anti-Bacterial Agents/pharmacology
Abattoirs
Microbiota/genetics
Acinetobacter/genetics/drug effects/isolation & purification
*Bacteria/genetics/drug effects/classification/isolation & purification
Pseudomonas/genetics/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
Farms
*Pork Meat/microbiology
Humans
Metagenome
Genes, Bacterial

@article {pmid42525291,
year = {2026},
author = {Gutiérrez-Ávila, JL and Gutiérrez-Rebolledo, GA and Avila-Bonilla, RG and Pardo, MES},
title = {Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis.},
journal = {Journal of molecular evolution},
volume = {94},
number = {5},
pages = {814-834},
pmid = {42525291},
issn = {1432-1432},
mesh = {Animals ; Humans ; Female ; Male ; Sex Characteristics ; Mice ; *Gastrointestinal Microbiome/genetics/physiology ; Drosophila melanogaster/genetics ; Metagenome/genetics ; Metagenomics/methods ; Metabolic Networks and Pathways ; },
abstract = {The murine model is a standard system in translational microbiome research, yet its functional equivalence to the human microbiome remains debated. To evaluate its translational validity, we conducted a comparative whole-genome shotgun (WGS) metagenomic meta-analysis, integrating an initial retrieval of 520 datasets from 5 independent cohorts (BioProjects) across Homo sapiens (n = 202), Mus musculus (n = 75), and Drosophila melanogaster (n = 243) samples. Taxonomic and functional profiles were evaluated using strict bioinformatic quality control and batch-effect mitigation. Taxonomic profiling revealed pronounced divergence driven by host-specific ecological constraints and filtering. However, metabolic reconstruction demonstrated substantial functional equivalence, supporting the functional redundancy hypothesis for core mammalian metabolic circuits. We also noted a methodological vulnerability in our dataset: a low-depth murine sample clustered with invertebrate profiles, suggesting that technical noise or insufficient depth might artificially compress mammalian functional diversity. Comparative analysis identified sex-biased metabolic pathways conserved across mammalian hosts. Specifically, we observed a consistent enrichment of steroid metabolism in females and mineralocorticoid regulation in males. These findings indicate that functional conservation between humans and mice is modular rather than global. Consequently, the translational value of the murine model lies in domain-specific functional equivalence rather than taxonomic imitation. Moreover, the conservation of sex-specific metabolic signatures suggests that biological sex is a fundamental organising principle of microbiome function. This study highlights the necessity of mapping conserved metabolic modules and rigorously controlling inter-study variance to effectively deploy murine models in biomedical research.},
}

Animals
Humans
Female
Male
Sex Characteristics
Mice
*Gastrointestinal Microbiome/genetics/physiology
Drosophila melanogaster/genetics
Metagenome/genetics
Metagenomics/methods
Metabolic Networks and Pathways

@article {pmid42660482,
year = {2026},
author = {Li, X and Yang, H and Xu, Z and Peng, L and Jiang, Z and Zhou, X and Xiang, J and Cui, B},
title = {Artificial light pollution alters epilithic microbial communities and functional biodeterioration-related functional potentials in subterranean sandstone environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {409},
number = {},
pages = {129056},
doi = {10.1016/j.envpol.2026.129056},
pmid = {42660482},
issn = {1873-6424},
mesh = {Bacteria/classification/genetics ; *Microbiota ; *Caves/microbiology ; *Light Pollution/adverse effects ; China ; *Soil Microbiology ; RNA, Ribosomal, 16S ; Light ; Biodegradation, Environmental ; },
abstract = {Artificial light pollution represents an important anthropogenic disturbance in subterranean heritage environments, yet its associations with epilithic microbial communities and biodeterioration processes remain poorly understood. In tourist-accessible subterranean caves, artificial light creates persistent illuminated areas on stone surfaces that may alter microbial community assembly and biogeochemical functions associated with biofilm development. Here, the Longyou Grottoes, a large underground sandstone cave complex in Zhejiang, China, were investigated using 16S rRNA gene sequencing and metagenomics. Bacterial communities dominated all samples (>98% relative abundance). Cyanobacteriota were enriched under artificial light and sunlight (>40%), whereas Pseudomonadota and Actinomycetota prevailed in darkness. Dark sites exhibited higher bacterial alpha diversity and more complex co-occurrence networks. Compared with sunlight and dark environments, the artificial-light environment was associated with greater stochasticity in bacterial community assembly, broader niche breadth, and lower niche overlap. Metabolic potential analysis further revealed light-dependent metabolic shifts: artificial light enhanced assimilatory nitrogen and sulfur metabolism, sunlight promoted nitrogen fixation, and darkness favored nitrification, denitrification, and sulfur oxidation. However, bacterial community patterns were also associated with temperature, humidity, pH, and soluble salts, indicating that the observed differentiation reflected the combined influence of light and environmental heterogeneity. These findings identify artificial lighting as an important and manageable environmental factor associated with epilithic bacterial communities and provide a basis for integrating lighting management with environmental control in the preventive conservation of subterranean sandstone heritage.},
}

Bacteria/classification/genetics
*Microbiota
*Caves/microbiology
*Light Pollution/adverse effects
China
*Soil Microbiology
RNA, Ribosomal, 16S
Light
Biodegradation, Environmental

@article {pmid42665077,
year = {2026},
author = {Fan, Q and Bai, J and Wang, X and Zhao, Z and Zhao, X},
title = {Metagenomic characterization of potential exposure to genetic hazards at the interface between grazing livestock and Przewalski's gazelle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {409},
number = {},
pages = {129059},
doi = {10.1016/j.envpol.2026.129059},
pmid = {42665077},
issn = {1873-6424},
mesh = {Animals ; *Livestock/microbiology ; *Antelopes/microbiology ; Metagenomics ; Sheep ; *Metagenome ; Microbiota ; Cattle ; },
abstract = {Livestock and endangered wildlife increasingly share grazing landscapes, yet the sources, mobility-associated contexts, and bacterial hosts of livestock-associated genetic hazards in wildlife microbiomes remain poorly resolved. We analyzed metagenomes from yak, Tibetan sheep, Przewalski's gazelle, and local topsoil within an Acquired Genetic Risk (AGR) conceptual framework integrating genetic hazard burden, compositional source attribution, mobility-associated evidence, and bacterial genomic context. MRGs and Rank I and Rank III ARGs were more abundant in livestock than in Przewalski's gazelle, whereas VF abundance was highest in yak. FEAST attributed approximately 64% of the Przewalski's gazelle resistome composition to the two livestock source profiles, less than 1% to sampled topsoil, and approximately 36% remained unassigned. MGE profiles were associated with ARGs, MRGs, and VFs, while tnpA ranked highest in random forest models and was associated with total ARG abundance (R[2] = 0.618). Short-read contigs containing hazard genes and MGE markers provided localized mobility-associated sequence context. Genome-resolved analysis identified distinct bacterial contexts: TS.Bin143, an Escherichia coli MAG from Tibetan sheep, contained ARGs, MRGs, VFs, tnpA, and IS91, whereas PG.Bin275, a Hylemonella sp. MAG from Przewalski's gazelle, contained tnpA. These findings extend wildlife resistome assessment beyond abundance profiling toward source attribution, mobility-associated sequence context, and bacterial host resolution, supporting multilevel surveillance of genetic hazard exposure at livestock-wildlife interfaces.},
}

Animals
*Livestock/microbiology
*Antelopes/microbiology
Metagenomics
Sheep
*Metagenome
Microbiota
Cattle

@article {pmid42863410,
year = {2027},
author = {Villa-Rodríguez, E and Ferguson, S and Stougaard, J and Radutoiu, S},
title = {Understanding genetic determinants of bacterial adaptation to plant niches: Toward more robust bioinoculant design.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128760},
doi = {10.1016/j.micres.2026.128760},
pmid = {42863410},
issn = {1618-0623},
mesh = {*Bacteria/genetics/metabolism/growth & development ; Soil Microbiology ; *Plants/microbiology ; Plant Roots/microbiology ; *Adaptation, Physiological/genetics ; Rhizosphere ; *Bacterial Physiological Phenomena ; Microbiota/genetics ; Biofilms/growth & development ; },
abstract = {Plant-associated bacteria offer a sustainable alternative to chemical inputs in agriculture, yet the field performance of microbial inoculants remains inconsistent. A central but frequently overlooked cause is that bioprospecting pipelines still select strains on the basis of plant-growth-promoting activities, while the bacterial genetic traits that determine whether a strain can reach, colonise and persist in a given root compartment are rarely assessed. Previous reviews have largely catalogued growth-promoting functions or described root microbiome assembly from the plant's perspective, here we take the bacterium's. We trace the journey of a bacterium from bulk soil to its final niche and, at each stage, identify the genes and pathways (genetic determinants) that encode key bacterial traits involved, such as chemotaxis and motility, nutrient acquisition and metabolic independence, competitive and defensive arsenals, attachment and biofilm formation, evasion of plant immunity, and endophytic entry and persistence. Throughout, we use evidence from comparative genomics and metagenomics, (meta)transcriptomics, targeted mutagenesis and genome-wide screens such as Tn-seq, obtained in systems ranging from binary interactions to synthetic communities and natural soils. For each stage we examine the current state of knowledge, identify critical gaps, and propose avenues to deepen our mechanistic understanding of the bacterial traits involved in plant colonisation. We argue that this mechanistic understanding is the missing foundation for developing inoculants with more consistent and robust performance across diverse agroecosystems.},
}

*Bacteria/genetics/metabolism/growth & development
Soil Microbiology
*Plants/microbiology
Plant Roots/microbiology
*Adaptation, Physiological/genetics
Rhizosphere
*Bacterial Physiological Phenomena
Microbiota/genetics
Biofilms/growth & development

@article {pmid42874540,
year = {2026},
author = {Dara, M and Calabrisotto, LS and Bisanti, L and Torreagrossa, N and La Corte, C and Bertini, F and Catania, V and Quatrini, P and Parrinello, D and Piazzese, D and Cammarata, M and Banni, M and Parisi, MG},
title = {Integrated assessment of bioplastic materials effects on microbial communities and macroinvertebrate model, Mytilus galloprovincialis, in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120459},
doi = {10.1016/j.marpolbul.2026.120459},
pmid = {42874540},
issn = {1879-3363},
abstract = {The increasing use of biopolymer derivatives raises concerns about their actual environmental sustainability, which remains insufficiently understood. In this study, we adopted an integrated approach combining microbial and ecotoxicological perspectives to evaluate their impact in marine ecosystems. We investigated the plastisphere composition of conventional petroleum-based High Density Polyethylene (HDPE) and polyhydroxyalkanoates (PHA), polyhydroxybutyric acid (PHB), and polylactic acid (PLLA) scaffolds after 60 days of exposition in marine ecosystem or microcosm, by high throughput metagenomics 16S rRNA gene sequencing and culture dependent approach. A variation in terms of composition and abundance of plastisphere, between petroleum-derived and bio-based degradable scaffolds, was observed. A high abundance of Proteobacteria was detected in all polymers, with Alpha and Gamma Proteobacteria dominant. At the genera level, high abundance of sequences assigned to hydrocarbon-degrading bacteria (i.e. Oleibacter, Labrenzia, Alcanivorax) was detected in biopolymeric plastic compared to petroleum-based plastic. To link microbial colonization and material degradation with biological effects on marine fauna, the impact of biopolymer-derived micro- and nanoparticles on the mussel Mytilus galloprovincialis was assessed. Both in vitro and in vivo assays demonstrated immune system activation through phagocytosis and encapsulation, while in vivo exposures influenced several biomarkers (phagocytosis, haemocyte density, lysozyme, glutathione peroxidase, phenoloxidase, alkaline phosphatase, esterase), suggesting potential detrimental effects after 72 h. By bridging microbial ecology with immunological responses in a bioindicator species, this multidisciplinary study provides novel insights into the complex ecological footprint of biodegradable plastics in marine environments.},
}

@article {pmid42875131,
year = {2026},
author = {Kang, C and Zheng, X and Liu, Z and Wang, W and Zeng, W and He, Y and Huang, J and Nie, W and Wang, J and Wang, F},
title = {Cryptic microheterogeneity of the casing-layer microbiome and metabolome is associated with primordium fate in Phallus rubrovolvatus.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101864},
doi = {10.1016/j.funbio.2026.101864},
pmid = {42875131},
issn = {1878-6146},
mesh = {*Microbiota ; *Metabolome ; *Agaricales/growth & development/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {Commercial cultivation of Phallus rubrovolvatus relies on casing layers, yet yields remain unstable, with primordium development varying among individual microsites. This cryptic microheterogeneity is masked by conventional bulk sampling, limiting insight into casing-layer performance. Here, we combined phenotype-guided back-tracing with multi-omics to characterize microecological signatures associated with primordium fate. We identified two contrasting ecological regimes associated with reproductive outcomes. Productive microsites were characterized by a "Cooperative state" enriched in oligotrophic bacteria (e.g., Hyphomicrobium) and basidiomycetes (e.g., Clathrus columnatus). Productive microsites also showed lower available potassium (K[+]) and elevated catalase activity. Conversely, non-productive microsites were characterized by a Rhizopus-dominated "Disruptive state". This state was associated with elevated urease activity, lower catalase activity, and stress-associated metagenomic functional signatures. Overall, primordium fate was associated with distinct local microbial, functional, and metabolic configurations that were not fully explained by bulk physicochemical properties. We propose the "Cooperative vs. Disruptive" model as a conceptual framework and identify candidate microbial and metabolic features for future validation in microbiome-informed cultivation management.},
}

*Microbiota
*Metabolome
*Agaricales/growth & development/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Multiomics

@article {pmid42876779,
year = {2026},
author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Obi, AMM and Nguema, OAM},
title = {The mosquito gut microbiome and Plasmodium development: a scoping review of molecular approaches and implications for malaria vector control.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1906816},
pmid = {42876779},
issn = {2235-2988},
mesh = {Animals ; *Malaria/prevention & control/transmission/parasitology ; *Plasmodium/growth & development ; *Mosquito Vectors/microbiology/parasitology ; *Gastrointestinal Microbiome ; *Anopheles/microbiology/parasitology ; *Mosquito Control/methods ; Metagenomics ; Humans ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Malaria remains a major health burden, with an estimated 282 million cases and approximately 610,000 deaths recorded in 2024. The increasing prevalence of insecticide-resistant Anopheles vectors and drug-resistant Plasmodium strains has substantially eroded the efficacy of conventional control strategies, underscoring the critical need for innovative approaches. Accumulating evidence suggest that the mosquito midgut microbiome exerts a significant influence on Plasmodium sporogonic development; however, no scoping investigation has fully mapped the metagenomic evidence base in this field.

METHODS: Adhering to the Arksey and O'Malley framework and PRISMA-ScR guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science for publications from January 2000 to April 2026. Studies that used microbiological, molecular, or metagenomic techniques to study the gut microbiota of mosquito species related to Plasmodium were included. Descriptive mapping was used to synthesize the data in a thematic manner.

RESULTS: Thirteen primary studies met the inclusion criteria, comprising both observational field surveys and experimental infection studies. Four themes emerged: (1) gut microbiota diversity and composition are associated with Plasmodium infection status, though the direction varies by mosquito species, geography, and season; (2) several taxa, including Burkholderia, Asaia, Sphingomonas, Pseudomonas, and Serratia, are consistently associated with reduced infection or are experimentally inhibitory; (3) the Enterobacteriaceae and Serratia spp. show context-dependent, bidirectional relationships with Plasmodium that are best explained by strain-level variation; and (4) a smaller set of taxa, including Elizabethkingia, Chryseobacterium, Methylobacterium, and Pantoea, is positively associated with infection, on observational evidence only. The evidence relied predominantly on 16S rRNA amplicon sequencing, with a minority of studies adding whole-genome sequencing, transcriptomics, or metabolomics; none used shotgun metagenomics.

CONCLUSIONS: The mosquito gut microbiome exerts a net inhibitory effect on Plasmodium development, with translational potential for microbiome-based vector control, including paratransgenesis. However, the microbiota is not uniformly antagonistic to the parasite, and taxa positively associated with infection remain observational. The field is limited by a near-exclusive reliance on 16S rRNA profiling, few functional and longitudinal studies, and geographically narrow evidence. Multi-omics approaches, longitudinal designs, and broader geographic coverage will be essential to translate these associations into sustainable malaria control.},
}

Animals
*Malaria/prevention & control/transmission/parasitology
*Plasmodium/growth & development
*Mosquito Vectors/microbiology/parasitology
*Gastrointestinal Microbiome
*Anopheles/microbiology/parasitology
*Mosquito Control/methods
Metagenomics
Humans
Bacteria/classification/genetics

@article {pmid42876851,
year = {2026},
author = {Xie, W and Lu, S and Liu, Z and Zheng, J and Mo, F and Zhang, K and Huang, Z},
title = {Gut microbiome profiles of two limestone forest-dwelling langurs show stronger influence of host-associated factors than environment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953526},
pmid = {42876851},
issn = {1664-302X},
abstract = {BACKGROUND: Host-associated factor and the environment play crucial roles in shaping the composition and function of the gut microbiome. Considerable debate exists regarding the relative influence of host-associated and environmental factors on the gut microbiome. To determine the relative importance of host-associated factors and environmental factors in langurs, we employed metagenomic sequencing to examine differences in the gut microbiome of the white-headed langurs (Trachypithecus leucocephalus) and François' langurs (T. francoisi).

RESULTS: The results revealed that the alpha diversity of the gut microbiome significantly differed between white-headed langurs and François' langurs in similar habitats. However, there was no significant variation in the alpha diversity between the wild and captive François' langurs. Similarly, the proportion of Bacillota differed between the langur species, with a higher proportion in the white-headed langurs than the François' langurs. In addition, significant separation in gut microbiome functions also occurred between the two species. The functional genes related to metabolism (e.g., carbohydrate metabolism and amino acid metabolism) and Glycoside Hydrolases in wild François' langurs were more abundant than in the other langurs. The results of PCoA showed that the pathways were significantly separated between white-headed langurs and François' langurs at four levels in the KEGG database, whereas the pathways showed no significant differences between the wild and captive François' langurs except for module level. The proportion of ARGs related to multidrug resistance was higher in wild François' langurs, likely associated with the utilization of poultry manure and antibacterial biocides in the langur's habitat.

CONCLUSION: Our study demonstrates that the host-associated factors have stronger influence on shaping the gut microbiome of langurs than environmental factors. These findings provide data on the relative contributions of host-associated factors and environmental factors to the gut microbiome of langurs and identify potential driving factors for antibiotic resistance genes. In addition, these findings provide crucial insights into the influence of host-associated factors on the gut microbiome, offering a theoretical basis for future langur conservation strategies.},
}

@article {pmid42877104,
year = {2026},
author = {Tang, H and Xiong, Q and Qian, G},
title = {Exploratory microbiota-metabolite alterations associated with cognitive impairment after repeated low-dose sevoflurane exposure in mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1869293},
pmid = {42877104},
issn = {2235-2988},
mesh = {Animals ; *Sevoflurane/adverse effects/administration & dosage ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cognitive Dysfunction/chemically induced/microbiology ; Mice, Inbred C57BL ; Metabolomics ; Disease Models, Animal ; Maze Learning/drug effects ; *Microbiota/drug effects ; *Metabolome/drug effects ; },
abstract = {BACKGROUND: Repeated low-dose sevoflurane exposure may affect cognition, but the relationship between such exposure, gut microbial composition, and circulating metabolites remains unclear. This study examined an experimental proof-of-concept exposure model and treated microbiota-metabolite findings as exploratory associations.

METHODS: Mice were exposed to 100 ppm sevoflurane for 2 h/day over 7 consecutive days, followed by Morris water maze testing without a long-term recovery follow-up. Gut microbiota and serum metabolites were profiled by shotgun metagenomic sequencing and LC-MS metabolomics, respectively, and machine-learning analyses were used only for exploratory feature ranking.

RESULTS: Sevoflurane-exposed mice exhibited poorer Morris water maze performance (Day 6 escape latency: 28.6 ± 3.4 s vs. 12.5 ± 1.8 s in controls, p < 0.01), although interpretation is limited by unequal behavioral sample sizes. Serum metabolomics suggested nominal and exploratory alterations in bile acid- and sphingolipid-related pathways. Shotgun metagenomics (n = 3/group) identified preliminary relative-abundance shifts, including a lower Bacteroidota/Bacillota ratio and lower relative abundance of Akkermansia.

CONCLUSIONS: In this proof-of-concept model, repeated low-dose sevoflurane exposure was associated with impaired spatial learning and memory and with exploratory serum metabolic and gut microbial alterations. The findings do not establish persistent long-term deficits, routine occupational risk, or causal microbiota-metabolite mediation. Larger cage-aware studies, an ambient-air comparison group, targeted validation, and interventional experiments are required.},
}

Animals
*Sevoflurane/adverse effects/administration & dosage
Mice
Male
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Cognitive Dysfunction/chemically induced/microbiology
Mice, Inbred C57BL
Metabolomics
Disease Models, Animal
Maze Learning/drug effects
*Microbiota/drug effects
*Metabolome/drug effects

@article {pmid42877526,
year = {2026},
author = {Fang, YH and Liu, HN and Chen, YJ and Hsu, TW and Chiu, CA and Chiang, PN and Huang, CL},
title = {Metagenomic profiling reveals that divergent fire-adaptive strategies drive distinct fungal succession in pine litter decomposition.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201414},
pmid = {42877526},
issn = {2210-6340},
abstract = {Decomposing litter is a critical driver of fuel bed formation and forest fire regimes, yet how divergent plant fire-adaptive strategies influence litter chemistry and subsequent fungal decomposition dynamics remains poorly understood. Here, we conducted a 6-month reciprocal litterbag experiment by incubating litter from two contrasting pine species-the fire-tolerant Pinus taiwanensis and the fire-avoiding P. morrisonicola-in both their own native habitat and that of the other species, coupled with genome-resolved metagenomics to track fungal succession and lignocellulolytic functional profiles. We found that the fire-avoiding P. morrisonicola exhibited significantly accelerated decomposition, driven by inherently lower initial C:N ratio and less recalcitrant litter, whereas the fire-tolerant P. taiwanensis exhibited slower decomposition rates. Metagenomic profiling revealed a distinct functional succession underlying this process. Early decomposition was dominated by Ascomycota (e.g., Leotiomycetes), which rapidly colonized the litter to initiate biopolymer breakdown. As easily decomposable substrates depleted, a functional shift occurred. Specifically, the highly recalcitrant P. taiwanensis litter selectively recruited Basidiomycota (e.g., Agaricales and Trechisporales) equipped with diverse lignin-modifying enzymes, reflected by a late-stage temporal surge in ligninolytic gene abundances. Ultimately, these findings demonstrate that plant fire-adaptive strategies act as a strong filter, shaping litter chemistry to drive specific taxonomic and functional fungal succession. This study provides a mechanistic understanding of the eco-evolutionary linkage between plant traits, microbiome assembly, and ecosystem-level fire dynamics.},
}

@article {pmid42878177,
year = {2026},
author = {Vliex, LMM and Godinho Mimoso, IF and Le, GN and Blaak, EE and Penders, J},
title = {Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746814},
doi = {10.1080/19490976.2026.2746814},
pmid = {42878177},
issn = {1949-0984},
mesh = {Humans ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Vancomycin/administration & dosage/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Obesity/microbiology/drug therapy ; *Trisaccharides/administration & dosage ; Double-Blind Method ; *Overweight/microbiology/drug therapy ; Female ; Adult ; Male ; Middle Aged ; Prebiotics/administration & dosage ; Feces/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotics are widely used to treat bacterial infections, yet overuse and misuse causes disruption of the gut microbiome and spread of antibiotic-resistant bacteria. Presence of antibiotic resistance genes (ARGs) could be a determinant of the response to antibiotics. Supplementation with prebiotics may limit the detrimental antibiotic-induced effects on the microbiome, but whether this results in changes in the gut resistome is unclear. This study investigated the impact of eight-week 2'-fucosyllactose (2'-FL) supplementation after seven-day vancomycin use in 18 adults with overweight/obesity, a subset from a double-blind placebo-controlled randomized intervention. Whole-metagenome shotgun sequencing was used to characterize the gut microbiome and resistome at baseline, after vancomycin use and after supplementation. Seven-day vancomycin use disrupted microbial richness and diversity (p < 0.001) and changed microbial composition. No improvements in microbial recovery were detected after eight week 2'-FL supplementation compared to placebo. Resistome richness and diversity were not affected by vancomycin use, although the presence of specific ARGs changed. No differential impact of 2'-FL supplementation on resistome richness, diversity and composition was detected. While vancomycin use disrupted the gut microbiome and affected the resistome, the detectable effects of 2'-FL supplementation were limited. Future research should investigate antibiotic- and prebiotic-induced changes in the gut resistome in more detail.},
}

Humans
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Vancomycin/administration & dosage/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Obesity/microbiology/drug therapy
*Trisaccharides/administration & dosage
Double-Blind Method
*Overweight/microbiology/drug therapy
Female
Adult
Male
Middle Aged
Prebiotics/administration & dosage
Feces/microbiology
Drug Resistance, Bacterial

@article {pmid42878179,
year = {2026},
author = {Shin, MG and Park, SJ and Kang, W and Bae, Y and Kim, S and Yoo, D and Yoon, S and Park, SM and Kwon, ES and Chang, J and Yoon, JH and Park, DG and Lee, EJ},
title = {Escherichia coli hns and methylglyoxal link gut microbial metabolism to host neuronal gene regulation in Parkinson's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2739674},
doi = {10.1080/19490976.2026.2739674},
pmid = {42878179},
issn = {1949-0984},
mesh = {Animals ; *Parkinson Disease/metabolism/microbiology/genetics ; Humans ; *Escherichia coli/metabolism/genetics ; Caenorhabditis elegans/genetics/microbiology ; *Gastrointestinal Microbiome ; *Pyruvaldehyde/metabolism/blood ; Dopaminergic Neurons/metabolism ; *Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation ; Male ; Disease Models, Animal ; Female ; Neurons/metabolism ; Feces/microbiology ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra (SN). Although the gut microbiota has been implicated in PD pathogenesis, how defined bacterial genes and their metabolites influence host neuronal gene regulation remains unclear. Here, we identify a gut microbial hns-methylglyoxal (MG) pathway linking Escherichia coli (E. coli) metabolism to host neuronal gene regulation. In the stool metagenomic cohort, hns, a bacterial gene encoding the histone-like nucleoid structuring protein and primarily derived from E. coli, was enriched particularly in body-first PD, a subtype associated with gut-originating pathology. In a separate plasma MG cohort, plasma levels of MG, a reactive metabolite whose bacterial production was hns-dependent in our model system, were higher in body-first than in brain-first PD and were nominally inversely associated with cardiac meta-iodobenzylguanidine (MIBG) uptake within the body-first group. Using Caenorhabditis elegans (C. elegans) PD models, we found that feeding with Δhns E. coli protected dopaminergic neurons, whereas exogenous MG abolished this neuroprotection. Transcriptomic and neuronal RNAi analyses identified rig-5 as a host mediator of hns deletion-induced neuroprotection. Cross-species analyses identified LSAMP as a candidate mammalian ortholog of rig-5. MG suppressed LSAMP expression in human neuronal cells, and LSAMP expression was reduced in the post-mortem SN of patients with PD. Conversely, Lsamp expression was increased in the SN of mice colonized with Δhns E. coli. Together, these findings delineate a microbial gene-metabolite-host gene pathway through which E. coli hns and MG modulate rig-5-dependent dopaminergic vulnerability in C. elegans, with corresponding changes of LSAMP expression in mammalian systems.},
}

Animals
*Parkinson Disease/metabolism/microbiology/genetics
Humans
*Escherichia coli/metabolism/genetics
Caenorhabditis elegans/genetics/microbiology
*Gastrointestinal Microbiome
*Pyruvaldehyde/metabolism/blood
Dopaminergic Neurons/metabolism
*Escherichia coli Proteins/metabolism/genetics
Gene Expression Regulation
Male
Disease Models, Animal
Female
Neurons/metabolism
Feces/microbiology

@article {pmid42477662,
year = {2026},
author = {Chao-Chao, Q and Zhi-Ruo, L and Xiao-Qing, L and Yan-Hong, M and Yue-Ying, Z and Ning, P and Ji-Chan, S and Xian-Gao, J},
title = {Exploring differences in alveolar microbiome between pulmonary tuberculosis patients with different treatment outcomes: a metagenomic study from China.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42477662},
issn = {1471-2466},
mesh = {Humans ; *Tuberculosis, Pulmonary/drug therapy/microbiology ; *Microbiota/genetics ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; China ; Male ; *Antitubercular Agents/therapeutic use ; Metagenomics ; Adult ; Treatment Outcome ; Middle Aged ; *Pulmonary Alveoli/microbiology ; },
abstract = {This study aimed to investigate differences in the composition and functional characteristics of alveolar microbiota in patients with pulmonary tuberculosis (PTB) exhibiting differential therapeutic responses. Thirty-two patients with drug-sensitive PTB who had completed standard anti-tuberculosis therapy were enrolled and classified into good-response (n = 16) and poor-response (n = 16) groups. Bronchoalveolar lavage fluid (BALF) samples were collected and analysed using metagenomic sequencing to characterize microbial community and functional pathways. No significant differences were observed in α-diversity between the two groups; however, β-diversity analysis demonstrated moderate but significant in microbial community structure (ANOSIM, R = 0.381, P < 0.001). The good efficacy group was characterized by enrichment of Prevotella, Staphylococcus, and oral commensal bacteria including Fusobacterium and Rothia, together with significantly increased pathways related to peptidoglycan biosynthesis, glutathione metabolism, energy production, and DNA repair. In contrast, the poor efficacy group was characterised by enrichment of Microbacterium and activation of functional pathways associated with biofilm formation. These findings suggest that both the taxonomic composition and functional activity of the pulmonary microbiome are closely associated with anti-tuberculosis treatment outcomes.},
}

Humans
*Tuberculosis, Pulmonary/drug therapy/microbiology
*Microbiota/genetics
Female
Bronchoalveolar Lavage Fluid/microbiology
China
Male
*Antitubercular Agents/therapeutic use
Metagenomics
Adult
Treatment Outcome
Middle Aged
*Pulmonary Alveoli/microbiology

@article {pmid42671175,
year = {2026},
author = {Schärer, MR and Yu, Y and Grawe, A and Christenson, JK and Robinson, SL and Bokulich, NA},
title = {Laccase-mediated biotransformation potential for fluorinated compounds by geographically diverse human gut microbiota.},
journal = {mBio},
volume = {17},
number = {10},
pages = {e0102626},
doi = {10.1128/mbio.01026-26},
pmid = {42671175},
issn = {2150-7511},
support = {23-2 ETH-047//ETH Research Grants/ ; //Uniscientia Foundation/ ; PZPGP2_209124/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; *Laccase/metabolism/genetics ; Biotransformation ; *Gastrointestinal Microbiome ; Phylogeny ; *Bacteria/classification/genetics/enzymology/metabolism ; Metagenome ; *Hydrocarbons, Fluorinated/metabolism ; },
abstract = {The growing prevalence of synthetic organofluorine substances in agrochemicals, food packaging, and consumer products has led to increasing gastrointestinal exposure, with potential consequences for human health. Despite the extreme stability of fluorinated compounds, several microbial pathways for their transformation are known, including those involving laccases, a type of multicopper oxidase. However, the functionality of laccases in the gut microbiome, a natural contact point between food-associated chemicals and microbial biotransformation pathways, is poorly defined. Through a multi-study analysis of 1,578 human gut metagenomes spanning a global gradient from hunter-gatherer societies to industrialized urban populations, we found that laccase-coding gene homologs are widely distributed in the human gut microbiome. We identified a significant association between both the abundance and phylogenetic diversity of laccase homologs and the degree of urbanization. As human gut microbial laccase activity has not been experimentally demonstrated, eight gut metagenome-derived laccases were heterologously expressed and screened for activity with a redox mediator system. Six of the eight laccases demonstrated activity. One of these gut microbial laccases, derived from Veillonella, and three previously characterized laccases were then tested for their capacity to deplete 11 different food-associated chemicals. The Veillonella laccase depleted the agrochemicals cyflumetofen and fluazinam, as well as the industrial chemical bisphenol AF, to a lesser extent. By linking global gut metagenomes with activity assays, this work demonstrates the untapped potential of mining human gut metagenomes for laccases and other microbial enzymes that can actively modify various agricultural and industrial chemicals.IMPORTANCEAs adverse effects of fluorinated compounds on human health are emerging, the responsible enzymes from the human gut microbiome of geographically diverse human cohorts mediating interactions with fluorinated compounds in the gastrointestinal tract remain poorly characterized. In a multi-study analysis of publicly available microbiome sequencing data, we linked the abundance, diversity, and phylogeny of laccases within the gut microbiome to the degree of urbanization of human cohorts and experimentally demonstrated the ability of these laccases to deplete a range of food-associated fluorochemicals. Another significant contribution of our study is in the integration of rural catchment areas as a quantitative metric of urbanization in gut microbiome metagenomics and enzyme activity surveys.},
}

Humans
*Laccase/metabolism/genetics
Biotransformation
*Gastrointestinal Microbiome
Phylogeny
*Bacteria/classification/genetics/enzymology/metabolism
Metagenome
*Hydrocarbons, Fluorinated/metabolism

@article {pmid42700718,
year = {2026},
author = {Maglione, A and Rosso, R and Tortarolo, D and Pantini, F and Pernice, S and Contaldo, SG and Lanzillo, R and Spiezia, AL and Cordioli, C and Virgilio, E and Masuzzo, F and Matta, M and Malucchi, S and Cavalla, P and Cocolin, L and Sirovich, R and Beccuti, M and Ferrocino, I and Cordero, F and Clerico, M and Rolla, S},
title = {Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106470},
doi = {10.1016/j.ebiom.2026.106470},
pmid = {42700718},
issn = {2352-3964},
mesh = {Humans ; *Multiple Sclerosis/diagnosis/microbiology/etiology ; Prognosis ; Female ; Disease Progression ; *Gastrointestinal Microbiome ; Adult ; Male ; Biomarkers ; Metagenomics/methods ; Middle Aged ; Magnetic Resonance Imaging ; Metagenome ; Cohort Studies ; },
abstract = {BACKGROUND: Alterations in gut microbiome composition have been associated with multiple sclerosis (MS), but their impact on disease severity and early progression remains poorly understood. In this study we investigated whether gut microbiome profiling at diagnosis could identify microbial signatures associated with clinical and radiological features of early MS and provide prognostic information.

METHODS: We analysed the gut microbiome of 53 treatment-naïve patients with MS (pwMS) and 55 healthy donors (HD) using shotgun metagenomic sequencing, combined with clinical features collected over 1 year from diagnosis. To clarify whether gut microbiome composition at MS onset could have prognostic relevance, pwMS were stratified according to lesion burden, lesion localisation, and magnetic resonance imaging (MRI) activity.

FINDINGS: Overall beta diversity in Bacteria, Archaea, and Eukarya differed significantly between pwMS and HD (p-value <0.001, <0.02, <0.03, respectively). Within the MS group, glucocorticoid treatment at disease onset was the clinical factor most strongly associated with gut microbiota diversity. Stratification according to lesion burden, lesion localisation, and MRI activity identified two clinically distinct MS subgroups with different baseline clinical characteristics at onset (p-value <0.03) and different risk of early disease progression. The cluster associated with an unfavourable prognosis showed greater progression within 12 months and was enriched for motor symptoms and spinal cord lesions at diagnosis.

INTERPRETATION: Our findings suggest that gut microbiome alterations are detectable at the earliest stages of MS and are associated with clinical and radiological features linked to short-term disease evolution. Gut microbial profiling may therefore represent a promising early prognostic biomarker and may help to identify candidate targets for early intervention and therapeutic development in MS, although further validation in larger longitudinal cohorts is needed.

FUNDING: This study was supported by grants from the Italian Multiple Sclerosis Foundation, the Cassa di Risparmio di Torino Foundation, and the Italian Ministry of University and Research.},
}

Humans
*Multiple Sclerosis/diagnosis/microbiology/etiology
Prognosis
Female
Disease Progression
*Gastrointestinal Microbiome
Adult
Male
Biomarkers
Metagenomics/methods
Middle Aged
Magnetic Resonance Imaging
Metagenome
Cohort Studies

@article {pmid42716835,
year = {2026},
author = {Zhao, K and Vignolle, GA and Labus, JS and Mayer, EA and Vaughan, A and Dy, M and Vora, P and Hung, MW and Vossel, K and Gill, C and Del Rio, D and Stanton, C and Ross, RP and Cryan, JF and Kaddurah-Daouk, R and Zhang, Y and Church, A},
title = {Brain-gut crosstalk associated with brain ageing in young and mid-life adults: a multicohort cross-sectional study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106468},
pmid = {42716835},
issn = {2352-3964},
support = {R01 AG046171/AG/NIA NIH HHS/United States ; U01 AG088562/AG/NIA NIH HHS/United States ; R01 MH108348/MH/NIMH NIH HHS/United States ; R21 AG080425/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; K23 DK106528/DK/NIDDK NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG057452/AG/NIA NIH HHS/United States ; R01 AG081322/AG/NIA NIH HHS/United States ; R01 AG081768/AG/NIA NIH HHS/United States ; R03 DK121025/DK/NIDDK NIH HHS/United States ; R01 MD015904/MD/NIMHD NIH HHS/United States ; U19 AG074879/AG/NIA NIH HHS/United States ; UH2 AG083254/AG/NIA NIH HHS/United States ; U24 AG056270/AG/NIA NIH HHS/United States ; R01 AG085518/AG/NIA NIH HHS/United States ; RF1 NS033310/NS/NINDS NIH HHS/United States ; UH3 AG083254/AG/NIA NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Brain/physiology/diagnostic imaging/metabolism ; *Aging/physiology ; Female ; Magnetic Resonance Imaging ; Cross-Sectional Studies ; Male ; Adult ; Middle Aged ; Young Adult ; Cognition ; Gastrointestinal Microbiome ; Metabolomics/methods ; },
abstract = {BACKGROUND: Brain age deviation is a promising neuroimaging biomarker of brain health, but its relevance in young and mid-life adults and its biological underpinnings remain insufficiently characterised. We aimed to test whether a functional-connectivity-derived brain ageing index (BAI) captures reproducible variability in early brain ageing and whether it is associated with cognitive-affective function and gut-derived biological signatures.

METHODS: We analysed resting-state fMRI from a discovery cohort (n = 674) with validation in a replication cohort (n = 444) and an independent cohort (n = 344). Whole-brain functional connectivity was computed using a 100-region Schaefer parcellation, and Bayesian ridge regression was used to predict chronological age; BAI was defined as the age-bias-corrected residual (predicted brain age minus chronological age). We tested associations between BAI and cognitive and affective measures across cohorts. In the independent cohort, we applied multi-view sparse partial least squares to integrate stool metagenomic and metabolomic profiles with BAI, and performed KEGG pathway enrichment analyses on features with non-zero weights.

FINDINGS: Predicted brain age correlated with chronological age across cohorts (r = 0.50-0.59). Higher BAI was consistently associated with connectivity patterns involving posterior cingulate/praecuneus and medial frontal regions, poorer cognitive performance, particularly working memory and executive function, and greater depressive symptoms. Multi-omics integration identified microbial taxa and stool metabolites, including ceramides, 24-hydroxycholesterol, dicarboxylic acids, and inverse associations with estetrol, linked to BAI. Enrichment analyses suggested involvement of neuroimmune, vascular, synaptic, and mitochondrial pathways.

INTERPRETATION: A connectivity-derived BAI captures reproducible variability in early brain ageing and links large-scale brain network organisation to gut-derived biological signatures. These findings suggest that BAI captures individual variability associated with brain health-related phenotypes and support the potential association of peripheral brain-gut biological pathways in early brain ageing.

FUNDING: National Institutes of Health, National Institute on Ageing.},
}

Humans
*Brain/physiology/diagnostic imaging/metabolism
*Aging/physiology
Female
Magnetic Resonance Imaging
Cross-Sectional Studies
Male
Adult
Middle Aged
Young Adult
Cognition
Gastrointestinal Microbiome
Metabolomics/methods

@article {pmid42742206,
year = {2026},
author = {Boldogkői, Z and Tombácz, D},
title = {The canine gut microbiome as a translational model for human health and aging.},
journal = {mBio},
volume = {17},
number = {10},
pages = {e0195126},
doi = {10.1128/mbio.01951-26},
pmid = {42742206},
issn = {2150-7511},
support = {K 142674//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; ADV 152705//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; LP2020-8/2020//Magyar Tudományos Akadémia/ ; FK 142676//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; },
mesh = {Animals ; Dogs/microbiology ; *Aging ; Humans ; *Gastrointestinal Microbiome ; Translational Research, Biomedical ; Disease Models, Animal ; Models, Animal ; One Health ; },
abstract = {The domestic dog is increasingly recognized as a complementary translational model for microbiome research relevant to human health while also offering direct benefits for veterinary medicine. Dogs share environments and dietary exposures with humans and show substantial taxonomic and gene-content similarity to the human gut microbiome, although the apparent degree of similarity depends strongly on whether read recruitment, gene-catalog overlap, or functional overlap is assessed. Dogs also develop spontaneous chronic enteropathies, obesity-associated metabolic dysfunction, cancers, cognitive dysfunction, and behavioral disorders in which gut microbial changes can be examined under clinically realistic conditions. Their shorter, breed- and body-size-dependent lifespan permits repeated sampling across development, aging, disease progression, and treatment within practical timeframes. Breed structure, full-sibling cohorts, controlled dietary interventions, and access to clinically indicated samples from multiple anatomical compartments can strengthen selected study designs, although they do not provide the tighter genetic, environmental, and microbial control achievable in rodents. Here, we evaluate the research questions for which canine cohorts are especially informative, synthesize evidence linking canine and human disease-associated microbiomes, and critically assess aging, causal inference, and One Health applications. Major limitations include the need for breed and body-size stratification, heterogeneous diet and husbandry, incomplete treatment histories, the lack of routinely available gnotobiotic canine systems, and gaps in canine-specific reference resources. The canine system is therefore most informative when study designs exploit its clinical realism while acknowledging the tighter experimental control offered by reductionist models, positioning the dog as a complementary rather than a universally superior model.},
}

Animals
Dogs/microbiology
*Aging
Humans
*Gastrointestinal Microbiome
Translational Research, Biomedical
Disease Models, Animal
Models, Animal
One Health

@article {pmid42767310,
year = {2026},
author = {Guo, Y and Song, Z and Xie, H and Kong, Q and Bai, L and Zhang, J},
title = {Coupled salinity-redox gradients shape dissolved organic matter characteristics and its linkages with microbial functional potential in intertidal sediments.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125713},
doi = {10.1016/j.envres.2026.125713},
pmid = {42767310},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology/chemistry ; Seashore ; *Salinity ; Oxidation-Reduction ; *Dissolved Organic Matter/analysis/chemistry ; Estuaries ; *Microbiota ; },
abstract = {Estuarine intertidal sediments occur in freshwater-seawater mixing zones where hydrological processes simultaneously alter salinity and redox conditions, potentially regulating dissolved organic matter (DOM) transformation and microbial processes. However, how DOM and its interactions with microbial communities respond to salinity and redox gradients in natural intertidal environments remains poorly understood. Here, surface sediments and porewater from the Yellow River Estuary were analyzed by integrating constructed composite salinity and redox indicators, spectroscopy-based two-dimensional correlation analysis, metagenomics, and multivariate statistics. Results showed that overall DOM variation was significantly associated with both gradients, with redox showing stronger links to chromophoric and protein-like components, molecular-weight properties, and redox-sensitive aromatic, phenolic, oxygen-containing structures. In contrast, neither gradient was significantly associated with whole-community taxonomic composition or functional potential, whereas carbon- and nitrogen-related taxa and functions showed environmental associations. Multiple analyses consistently indicated that DOM covaried with selected functional modules, with more reducing conditions linked to DOM accumulation and fermentation-related functions, and higher salinity linked to microbially derived DOM and substrate-utilization functions. Variation partitioning attributed 20.7% of DOM variation and 39.6% of the main joint DOM-microbe pattern to the shared salinity-redox fraction, while redox retained a significant unique association with DOM (20.3%). Exploratory path models further suggested that DOM characteristics may link salinity-redox gradients to selective rather than community-wide microbial functional variation. Together, these findings support considering salinity and redox as a coupled environmental background and highlight DOM chemistry as a potential interface between their variation and selective microbial functional responses in intertidal sediments.},
}

*Geologic Sediments/microbiology/chemistry
Seashore
*Salinity
Oxidation-Reduction
*Dissolved Organic Matter/analysis/chemistry
Estuaries
*Microbiota

@article {pmid42785295,
year = {2026},
author = {Ziemski, M and Gehret, L and Simard, A and Castro Dau, S and Risch, V and Grabocka, D and Matzoros, C and Wood, C and Cabrera, PM and Hernández-Velázquez, R and Schärer, MR and Sandberg, F and Herman, C and Evans, K and Robeson, MS and Bolyen, E and Caporaso, JG and Bokulich, NA},
title = {MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework.},
journal = {Cell genomics},
volume = {6},
number = {10},
pages = {101366},
doi = {10.1016/j.xgen.2026.101366},
pmid = {42785295},
issn = {2666-979X},
mesh = {*Metagenome/genetics ; *Software ; *Metagenomics/methods ; Microbiota/genetics ; Reproducibility of Results ; *Data Science ; Computational Biology/methods ; Humans ; },
abstract = {Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems but is fraught with technical hurdles. We introduce MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking; https://moshpit.qiime2.org)-software built on the QIIME 2/rachis framework (Q2F) that integrates best-in-class CAMI II- and LEMMI-validated metagenome tools with robust provenance tracking and multiple user interfaces-enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.},
}

*Metagenome/genetics
*Software
*Metagenomics/methods
Microbiota/genetics
Reproducibility of Results
*Data Science
Computational Biology/methods
Humans

@article {pmid42785505,
year = {2026},
author = {Jiang, Y and Liu, B and Ding, Y and Li, L and Li, Z and Ren, Y and Zhong, C and Chen, J and Cui, X and Lu, A and Liu, J},
title = {Mineral-supported microbial functional differentiation across a vertical gradient in a vanadium-titanium magnetite mine.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125725},
doi = {10.1016/j.envres.2026.125725},
pmid = {42785505},
issn = {1096-0953},
mesh = {*Mining ; *Vanadium ; *Ferrosoferric Oxide ; *Titanium ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification ; *Microbiota ; China ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Vanadium-titanium magnetite (VTM) mines are often associated with metal contamination, organic carbon depletion, and ecological degradation, yet how indigenous microbiomes respond to vertical geochemical heterogeneity remains poorly understood. Here, we investigated a ∼260 m vertical gradient in the Zhulan Iron Mine, China, by integrating elemental and mineralogical analyses with 16S rRNA gene amplicon and metagenomic profiling. Pronounced vertical stratification was observed. The lower-elevation section was enriched in vanadium (V) and Fe(II)-bearing minerals and harbored microbial communities with lower diversity but a more highly connected co-occurrence network. Representative lower-section taxa, including Thiobacillus, Sulfuricaulis, and Chloroflexota members, were linked to functional potentials for V-associated redox transformation, Fe/S metabolism, extracellular electron transfer, and autotrophic carbon fixation. These patterns suggest that Fe(II)-bearing minerals, particularly magnetite, may serve as potential inorganic electron sources supporting mineral-based lithotrophy and carbon fixation under metal-rich and organic-carbon-limited conditions. In contrast, the upper-elevation section exhibited lower V stress, higher microbial diversity, sparse vegetation, and enrichment of heterotrophic and plant-associated taxa, such as Sphingomonas, Flavisolibacter, and Actinomycetota, indicating a shift toward plant-supported microbial functions during early ecological recovery. Overall, this study links vertical geochemical stratification to microbial functional differentiation and highlights indigenous mineral-microbe interactions as a potential basis for targeted, low-input restoration strategies in metal-contaminated mining ecosystems.},
}

*Mining
*Vanadium
*Ferrosoferric Oxide
*Titanium
*Soil Microbiology
*Bacteria/genetics/metabolism/classification
*Microbiota
China
RNA, Ribosomal, 16S/genetics

@article {pmid42822627,
year = {2026},
author = {Zhou, L and Sha, H and Han, H and Wang, S and Li, S and Peng, X},
title = {Oxygen-associated differentiation of TBBPA-transforming activated sludge consortia and characterization of a cultivable Klebsiella degrader.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125834},
doi = {10.1016/j.envres.2026.125834},
pmid = {42822627},
issn = {1096-0953},
mesh = {*Sewage/microbiology ; *Polybrominated Biphenyls/metabolism ; *Klebsiella/metabolism/genetics ; *Oxygen/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Anaerobiosis ; *Flame Retardants/metabolism ; *Microbial Consortia ; },
abstract = {Tetrabromobisphenol A (TBBPA), a widely used brominated flame retardant, poses increasing environmental and health concerns, yet how oxygen availability is associated with the assembly and degradation potential of TBBPA-transforming microbiomes remains poorly resolved. Here, ten enrichment consortia (six aerobic and four anaerobic) were established from activated sludge collected at six municipal wastewater treatment plants, achieving up to 63.46% TBBPA removal at an initial concentration of 5 mg/L. Metagenomic analysis revealed marked community divergence between the aerobic and anaerobic enrichment conditions, with Burkholderia predominating in the aerobic consortia and Klebsiella predominating in the anaerobic consortia. Read-mapping-based abundance profiling detected the HY4.102-affiliated Klebsiellapneumoniae population under both oxygen conditions, with higher relative abundance in the anaerobic consortia. Strain NCHT, isolated from the aerobic consortium NC_H, shared >99% ANI and AAI with HY4.102 and transformed TBBPA under both aerobic and anaerobic batch conditions. During aerobic incubation, strain NCHT transformed 51.0-68.4% of TBBPA across the tested concentrations, and UHPLC-MS/MS analysis yielded 17 putatively identified transformation intermediates consistent with an interconnected network involving debromination, hydroxylation, O-methylation, and β-scission. Molecular docking further prioritized DhmA, GSTs, CbdA/B, and PobB as candidate enzymes for debromination and downstream aromatic transformation, broadly consistent with the dehalogenation-related genes annotated in MAG HY4.102. Together, these findings provide an integrated community-to-strain framework for investigating TBBPA transformation.},
}

*Sewage/microbiology
*Polybrominated Biphenyls/metabolism
*Klebsiella/metabolism/genetics
*Oxygen/metabolism
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
Anaerobiosis
*Flame Retardants/metabolism
*Microbial Consortia

@article {pmid42862088,
year = {2026},
author = {Hoque, MN and Rahman, MS and Hossain, MG and Rahman, MT and Islam, T and Hossain, MA},
title = {Subclinical Mastitis and Antibiotic Exposure Reshape the Milk Bacteriome, Resistome, and Metabolic Functional Profiles in Dairy Cows.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70440},
pmid = {42862088},
issn = {2045-8827},
support = {LS20221764//Bangladesh Bureau of Educational Information & Statistics (BANBEIS), Ministry of Education/ ; },
mesh = {Animals ; *Milk/microbiology ; Female ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Cattle ; *Bacteria/drug effects/classification/genetics/isolation & purification ; *Mastitis, Bovine/microbiology/drug therapy ; Metagenomics ; *Microbiota/drug effects ; Drug Resistance, Bacterial ; },
abstract = {Subclinical mastitis (SCM) reduces milk yield and promotes antibiotic use, contributing to antimicrobial resistance. However, information on milk microbiome dysbiosis and resistome alterations in dairy cows remains limited. We performed shotgun metagenomic sequencing of 30 milk samples from 20 cows classified as SCM (n = 10), antibiotic-treated (ANT; n = 10), and healthy milk (HM; n = 10). Bacteriome, resistome, and metabolic functions were analyzed using bioinformatic tools. Microbial alpha diversity was significantly higher in HM than SCM and ANT samples (p < 0.05), with the greatest richness observed in Local Zebu and Middle-aged (5-8 years) cows. However, beta diversity did not differ significantly among groups (PERMANOVA, p > 0.05). A total of 665 bacterial species belonging to 15 phyla were identified, with Pseudomonadota, Actinomycetota, and Bacillota comprising 90%-99% of total abundance. SCM milk was dominated by Actinoalloteichus sp. (40.55%) and Vibrio furnissii (37.01%), while Staphylococcus aureus was enriched (1.74%) compared with HM and ANT (< 0.01%). ANT milk showed increased abundance of Acinetobacter johnsonii (10.52%), whereas HM samples contained beneficial commensals, including Pseudomonas lundensis, Bacteroides thetaiotaomicron, and Lactococcus lactis. Similar taxonomic shifts were observed across breeds and age groups. In total, 194 antimicrobial resistance genes (ARGs) were detected, with SCM harboring the largest repertoire (n = 161). Nevertheless, macrolide-, aminoglycoside-, and β-lactam-resistance genes were significantly enriched in ANT samples (p < 0.01). Correlation analyses linked Escherichia coli and A. johnsonii with multiple ARGs, while Acinetobacter and Pseudomonas were associated with lipid metabolism, membrane transport, and xenobiotic biodegradation pathways. These findings reveal bacteriome disruption, ARG enrichment, and functional alterations in SCM and antibiotic-exposed milk.},
}

Animals
*Milk/microbiology
Female
*Anti-Bacterial Agents/pharmacology/therapeutic use
Cattle
*Bacteria/drug effects/classification/genetics/isolation & purification
*Mastitis, Bovine/microbiology/drug therapy
Metagenomics
*Microbiota/drug effects
Drug Resistance, Bacterial

@article {pmid42865259,
year = {2026},
author = {Doane, MP and Martin, B and Kerr, E and Dinsdale, EA and Rangers, MM and Guida, L and Kyne, PM},
title = {Patterns of Functional Redundancy and Anaerobic Metabolic Potential Characterise the Skin Microbiome of a Critically Endangered Sawfish.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70442},
pmid = {42865259},
issn = {1462-2920},
support = {//Charles Darwin University 2021 Institute of Advanced Studies (IAS) Rainmaker Start Up/ ; //Australian Marine Conservation Society (AMCS)/ ; //Flinders Accelerator for Microbiome Exploration/ ; },
mesh = {Animals ; *Skin Microbiome ; Anaerobiosis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Endangered Species ; *Microbiota ; Metagenomics ; *Skin/microbiology ; Phylogeny ; },
abstract = {Using shotgun metagenomics of largetooth sawfish (Pristis pristis) skin and paired pool water samples, we provide the first taxonomic and functional characterisation of a sawfish skin microbiome and assess its ecological distinctiveness, assembly, and resilience relative to the surrounding water column. The skin microbiome was strongly host-associated and compositionally distinct, with lower taxonomic richness than the water column but dominated by Bacillota, particularly spore-forming Bacilli. Functional profiling revealed genes associated with sporulation, dormancy, anaerobic metabolism, and peptide transport, consistent with low-oxygen, low-flow conditions. In contrast, water-column microbiomes were more taxonomically diverse and enriched in phototrophic and polysaccharide-utilisation pathways. Sawfish skin communities exhibited patterns consistent with greater functional redundancy, with gene functions accumulating more rapidly per taxon. Together with greater among-individual taxonomic dispersion, this pattern is consistent with a host-filtered, lottery-like assembly process in which taxonomically variable communities maintain similar functional potential. The enrichment of dormancy and anaerobic pathways suggests the skin microbiome persists through periods of host quiescence and environmental stress while maintaining metabolic potential. Together, these results demonstrate that the sawfish skin supports a resilient, functionally robust microbiome distinct from ambient aquatic communities, highlighting the potential for integrating microbial functional data into conservation strategies for Critically Endangered vertebrates.},
}

Animals
*Skin Microbiome
Anaerobiosis
*Bacteria/classification/genetics/isolation & purification/metabolism
Endangered Species
*Microbiota
Metagenomics
*Skin/microbiology
Phylogeny

@article {pmid42869831,
year = {2026},
author = {Li, T and Song, ZX and Yang, DM and Ren, GX and Yin, Y and Yan, YG and Gao, J and Jiang, D and Liu, CS},
title = {[Diversity of endophytes in licorice from different habitats based on metagenomics and analysis of their correlation with accumulation of active ingredients].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {18},
pages = {5253-5261},
doi = {10.19540/j.cnki.cjcmm.20260415.406},
pmid = {42869831},
issn = {1001-5302},
mesh = {*Endophytes/genetics/classification/metabolism/isolation & purification ; *Glycyrrhiza/microbiology/chemistry/metabolism ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; Glycyrrhizic Acid/metabolism/analysis ; Biodiversity ; },
abstract = {Licorice is an important TCM. Its medicinal quality mainly depends on the accumulation of active ingredients such as flavonoids(such as liquiritin and isoliquiritin) and triterpenoids(such as glycyrrhizic acid), and the endogenous microbial community is considered an important environmental factor influencing the synthesis of these components. To analyze the regulatory effect of endophytes on secondary metabolites of licorice, metagenomic sequencing and ultra-high performance liquid chromatography were used to compare and analyze the composition and function of endophytes in wild and cultivated licorice roots as well as their relationship with the main active ingredients. The results showed that the content of liquiritin, isoliquiritin, and glycyrrhizic acid in wild licorice was significantly higher than that in cultivated licorice. The metagenomic analysis annotated that the endophytes in wild licorice belonged to 31 phyla and 315 genera, while those in cultivated licorice belonged to 24 phyla and 125 genera. Among them, Rathayibacter, Plantibacter, and other genera were significantly enriched in wild licorice, while only Lysobacter was significantly enriched in cultivated licorice. Functional annotations indicated that the endophytes in wild licorice were enriched in pathways such as two-component systems, nitrogen metabolism, and aminoacyl tRNA synthesis, while those in cultivated licorice were enriched in pathways such as photosynthesis and carbon fixation. Further correlation analysis revealed that some endophyte genera(such as Phenylobacterium and Microbacterium) and functional pathways(such as signal transduction and terpenoid metabolism) were significantly positively correlated with the content of glycyrrhizic acid and liquiritin. In addition, the abundance of glycosyltransferases and cytochrome P450 in endophytes in wild licorice was significantly higher than that in cultivated licorice. This indicated that they had an enzymatic basis for participating in the synthesis of host glycosides. This research systematically reveals the differences in endophytic community structure, function, and accumulation of active ingredients between wild and cultivated licorice, providing a theoretical basis for understanding the microbial mechanism of endophytes regulating the quality of licorice, and also offering references for developing microbial fertilizers to improve the quality of licorice.},
}

*Endophytes/genetics/classification/metabolism/isolation & purification
*Glycyrrhiza/microbiology/chemistry/metabolism
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
Glycyrrhizic Acid/metabolism/analysis
Biodiversity

@article {pmid42870454,
year = {2026},
author = {Khafagy, ES and El-Kimary, GI and Al Saqr, A and Hegazy, WAH},
title = {The Oral Virome in Dental Caries: From Ecological Disruptors to Therapeutic Opportunities.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604028},
doi = {10.4014/jmb.2604.04028},
pmid = {42870454},
issn = {1738-8872},
mesh = {*Dental Caries/therapy/virology/microbiology ; Humans ; Biofilms/growth & development ; *Virome ; *Mouth/virology/microbiology ; Bacteriophages/physiology/genetics ; Animals ; Dysbiosis ; Streptococcus mutans/virology ; Microbiota ; },
abstract = {Dental caries results from ecological dysbiosis of oral biofilms driven by frequent sugar exposure, yet the role of viruses, particularly bacteriophages, in this process remains underexplored. This review synthesizes current evidence on how the oral virome contributes to caries pathogenesis and examines emerging phage-based therapeutic strategies. The oral cavity harbors diverse viral communities, including eukaryotic viruses (herpesviruses, papillomaviruses) and prokaryotic viruses (bacteriophages). While herpesviruses like EBV, CMV, and HSV-1 do not directly demineralize teeth, they may act as ecological stressors by modulating host immunity, altering gingival crevicular fluid composition, and promoting inflammation that favors cariogenic bacterial activity. Bacteriophages function as key ecological regulators through "kill-the-winner" dynamics, maintaining microbial diversity by preying on dominant species. However, temperate phages can horizontally transfer genes encoding acidogenicity, biofilm formation, or antibiotic resistance, potentially accelerating dysbiosis. Metagenomic studies reveal distinct salivary phage signatures associated with caries, suggesting diagnostic potential. Preclinical evidence demonstrates that lytic phages targeting Streptococcus mutans (e.g., SMHBZ8, ΦAPCM01) disrupt biofilms in vitro and prevent caries in ex vivo and murine models. Phage-derived enzymes (endolysins, depolymerases) and peptides offer additional precision antimicrobials with minimal commensal disruption. Despite promising advances, significant translational gaps remain, including limited well-characterized phages, insufficient polymicrobial model testing, and absence of human clinical trials. Integrating virome ecology into caries management represents a paradigm shift from pathogencentric approaches toward ecosystem-based therapeutics, with phages offering targeted, self-replicating, and evolutionarily dynamic tools for restoring oral health.},
}

*Dental Caries/therapy/virology/microbiology
Humans
Biofilms/growth & development
*Virome
*Mouth/virology/microbiology
Bacteriophages/physiology/genetics
Animals
Dysbiosis
Streptococcus mutans/virology
Microbiota

@article {pmid42870579,
year = {2026},
author = {Zhu, YH and Li, X and Liu, Z and Liu, J and Ye, R and Xue, W and Jiang, G},
title = {DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag571},
pmid = {42870579},
issn = {1477-4054},
support = {2025AIYJSZX-YB006//Fundamental Research Funds for the Central Universities/ ; BK20230102//Natural Science Foundation of Jiangsu Province/ ; 62402227//National Natural Science Foundation of China/ ; 42677660//National Natural Science Foundation of China/ ; 42477122//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Bayes Theorem ; Clustering Algorithms ; *Metagenome ; Microbiota ; Cluster Analysis ; Algorithms ; Autoencoder ; },
abstract = {Accurate metagenomic binning is essential for reconstructing microbial genomes, thereby facilitating the discovery of novel taxa, the identification of pathogens, and the characterization of antimicrobial resistance genes. Most existing methods are designed for assembled contigs and cannot be directly applied to raw long reads. Although a few dedicated long-read binning methods have emerged, challenges remain in bin-number estimation and representation learning. Here, we propose Deep Embedded Clustering for Long-read Binning (DecBin), an adaptive method for directly binning raw long reads through integrating a variational autoencoder (VAE), Bayesian optimization, and deep embedded clustering within a unified framework. Computational experiments on large-scale simulated and mock-community datasets demonstrate that DecBin outperforms state-of-the-art methods in both long-read binning and metagenome-assembled genome recovery, while also achieving strain-level resolution in a low-complexity natural microbiome. Further analysis shows that the advantage of DecBin is partly attributable to its Davies-Bouldin index-guided Bayesian optimization, which explicitly evaluates candidate cluster numbers using a global cluster-validity criterion, thereby improving bin-number estimation across communities of varying complexity. Meanwhile, joint fine-tuning of the VAE encoder and clustering layer enables clustering feedback to refine the latent space, yielding representations better aligned with genome partitions. These findings highlight the potential of adaptive deep clustering for metagenomic binning directly from raw long reads without prior assembly. The source code of DecBin is freely available at https://github.com/LorMeBioAI/DecBin.},
}

*Metagenomics/methods
Bayes Theorem
Clustering Algorithms
*Metagenome
Microbiota
Cluster Analysis
Algorithms
Autoencoder

@article {pmid42871043,
year = {2026},
author = {Zou, Y and Zhang, W and Gao, A and Fu, J and Sui, Y},
title = {Beyond community state types: vaginal microbial diversity and CST-IV signatures are associated with pregnancy in euploid embryo transfer cycles.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1881146},
pmid = {42871043},
issn = {1664-2392},
mesh = {Female ; Humans ; *Embryo Transfer/methods ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; Pregnancy Outcome ; Adult ; Fertilization in Vitro ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Pregnancy Rate ; },
abstract = {BACKGROUND: Despite significant progress in assisted reproductive technology, in vitro fertilization (IVF) pregnancy rates remain suboptimal. Although the vaginal microbiome has been implicated in IVF outcomes, prior studies often overlooked embryonic aneuploidy, a major confounder. This study aimed to investigate the association between the vaginal microbiome and pregnancy outcomes in euploid embryo transfer cycles.

METHODS: This prospective study included 109 single euploid blastocyst transfer cycles. Upper vaginal swabs were collected on the transfer day and subjected to 16S rRNA gene sequencing. Microbial α- and β-diversity, community state types (CSTs), and differentially abundant taxa were compared between the clinical pregnancy (CP, n = 55) and non-clinical pregnancy (NCP, n = 54) groups.

RESULTS: The NCP group exhibited significantly higher vaginal microbial richness (Chao1, p = 0.029; ACE, p = 0.029) and distinct β-diversity compared with the CP group (R² = 0.049, p = 0.002), whereas CST distribution did not differ between groups. Within the non-Lactobacillus-dominant CST-IV subgroup, the CP group was relatively enriched in Bifidobacteriaceae (LDA = 5.0) with predicted fermentative pathways, whereas the NCP group showed higher relative abundances of Prevotella (LDA = -4.1), Dialister (LDA = -3.6), and Peptoniphilus (LDA = -2.3), accompanied by predicted tryptophan degradation and oxidative stress pathways.

DISCUSSION: These findings, derived mainly from computational prediction, suggest that fine-scale taxonomic and functional composition, rather than broad CST classification, may influence pregnancy outcomes following euploid embryo transfer, offering preliminary insights for microbiome-informed strategies to optimize reproductive outcomes. Future longitudinal studies incorporating shotgun metagenomics and metabolomics in independent cohorts are warranted to validate these preliminary observations and to clarify the dynamic association between vaginal microbiota and IVF pregnancy outcomes.},
}

Female
Humans
*Embryo Transfer/methods
*Vagina/microbiology
Pregnancy
*Microbiota
Pregnancy Outcome
Adult
Fertilization in Vitro
Prospective Studies
RNA, Ribosomal, 16S/genetics
Pregnancy Rate

@article {pmid42873652,
year = {2026},
author = {Pulvino, AT and Sardaro, MLS and Quinn, WG and Christopher, ER and Koenig, S and Lucore, JM and Vidal-Cruchez, O and Mallott, EK and Kuthyar, S and Lee, W and Chitta, S and Gray, S and Williams, LE and Curley, JP and Liechty, ER and Ben-Sahra, I and Amato, KR},
title = {Bile, sulphur and carbohydrate metabolic variation co-occur with host adiposity in mice colonized with primate microbiota.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001848},
pmid = {42873652},
issn = {2057-5858},
mesh = {Animals ; Mice ; Humans ; *Adiposity ; *Bile/metabolism ; Macaca mulatta ; *Sulfur/metabolism ; *Carbohydrate Metabolism ; Multiomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Cecum/microbiology ; Liver/metabolism ; Metagenomics ; Primates/microbiology ; Microbiota ; },
abstract = {Although mechanistic links between the microbiome and chronic disease are increasingly well defined, how microbiomes facilitate normal variation in host metabolism remains less clear. Building on our recent demonstration that pooled faecal inocula from different primate species can cause relative differences in mouse host adiposity, we define potential mechanisms by which this could occur. Using existing samples from germ-free mice inoculated with faecal samples from humans (Homo sapiens), rhesus macaques (Macaca mulatta) and squirrel monkeys (Saimiri boliviensis), we integrate shotgun metagenomics of caecal contents, liquid chromatography-MS-MS metabolomics of serum and caecal contents and hepatic RNA-sequencing. Our multi-omic analysis reveals that the relative increase in adiposity previously observed in macaque-donor mice is associated with differences in hepatic cysteine catabolism and bile metabolism pathway features. These data suggest that bile and sulphur co-metabolic variation may mediate increased bile pool hydrophobicity. We also observed variation in caecal microbiome composition as well as host hepatic retinol signalling and lipid metabolism between treatments. When considered together with the observation that macaque-donor mice consumed less food than the other treatment groups, our results support the hypothesis that increased bile pool hydrophobicity results in increased dietary energy extraction. Our findings provide a foundation for future mechanistic testing of new hypotheses for understanding how the intestinal microbiomes of different primate species regulate lipid homeostasis in a mouse host.},
}

Animals
Mice
Humans
*Adiposity
*Bile/metabolism
Macaca mulatta
*Sulfur/metabolism
*Carbohydrate Metabolism
Multiomics
Feces/microbiology
*Gastrointestinal Microbiome
Cecum/microbiology
Liver/metabolism
Metagenomics
Primates/microbiology
Microbiota

@article {pmid42152807,
year = {2026},
author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A},
title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {133},
number = {12},
pages = {2092-2102},
doi = {10.1111/1471-0528.70266},
pmid = {42152807},
issn = {1471-0528},
support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
mesh = {Female ; Humans ; *Polycystic Ovary Syndrome/microbiology/physiopathology/complications/metabolism ; Animals ; Pregnancy ; Adult ; *Gastrointestinal Microbiome/physiology ; Rats ; *Endometrium/physiopathology/metabolism ; Prospective Studies ; *Abortion, Spontaneous/microbiology/etiology ; *Dysbiosis/microbiology/complications ; Disease Models, Animal ; Case-Control Studies ; Pregnancy Outcome ; Isoleucine/blood ; Cellular Senescence ; Rats, Sprague-Dawley ; Stromal Cells ; Amino Acids, Branched-Chain/blood ; },
abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.

DESIGN: Prospective cohort study integrated with mechanistic experiments.

SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).

POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.

METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.

MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.

RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.

CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.},
}

Female
Humans
*Polycystic Ovary Syndrome/microbiology/physiopathology/complications/metabolism
Animals
Pregnancy
Adult
*Gastrointestinal Microbiome/physiology
Rats
*Endometrium/physiopathology/metabolism
Prospective Studies
*Abortion, Spontaneous/microbiology/etiology
*Dysbiosis/microbiology/complications
Disease Models, Animal
Case-Control Studies
Pregnancy Outcome
Isoleucine/blood
Cellular Senescence
Rats, Sprague-Dawley
Stromal Cells
Amino Acids, Branched-Chain/blood

@article {pmid42861600,
year = {2026},
author = {Liu, Y and Ning, X and Liu, Y and Yu, Z and Liu, J and Xu, X and Zhao, J and Sun, S},
title = {Potential Roles of Escherichia coli in IgA Nephropathy: Evidence, Mechanistic Hypotheses and Microbiota-Targeted Strategies.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70455},
pmid = {42861600},
issn = {1751-7915},
support = {82470735//National Natural Science Foundation of China/ ; 2023TD-02//Shaanxi Provincial Health Commission/ ; 2023-ZDLSF-15//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLSF03-12//Key Research and Development Projects of Shaanxi Province/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/therapy/pathology ; *Escherichia coli/pathogenicity ; Animals ; *Gastrointestinal Microbiome ; Immunoglobulin A/metabolism ; },
abstract = {IgA nephropathy (IgAN), the most common primary glomerular disease, involves mucosa-kidney axis dysregulation, with gut dysbiosis increasingly implicated in its pathogenesis. Certain Escherichia coli (E. coli) strains harbour virulence-associated features that promote intestinal colonization, barrier disruption and immune activation. Recent microbiome and metagenomic studies have reported an enrichment of E. coli in patients with IgAN, suggesting a potential link to the mucosa-kidney axis. Nevertheless, E. coli may contribute to IgAN through two major pathways. First, sustained LPS exposure may induce aberrant production of galactose-deficient IgA1 (Gd-IgA1) by stimulating B cells and activate the NLR family pyrin domain containing 3 (NLRP3) inflammasome in macrophages, thereby amplifying systemic and renal inflammation. Second, metabolic reprogramming is associated with increased circulating sphingosine-1-phosphate (S1P) and altered production of indole and trimethylamine (TMA); S1P may promote mesangial proliferation and fibrosis, whereas indole- and TMA-related pathways may contribute to tubulointerstitial injury and chronic kidney disease (CKD) progression. Beyond conventional gut microbiota-targeted interventions, emerging precision therapeutic strategies offer promising new directions for the etiological treatment of IgAN. This review summarizes E. coli virulence factors, pathogenesis, and host, environmental, and ecological factors driving its gut expansion in IgAN patients and outlines corresponding therapeutic strategies.},
}

Humans
*Glomerulonephritis, IGA/microbiology/therapy/pathology
*Escherichia coli/pathogenicity
Animals
*Gastrointestinal Microbiome
Immunoglobulin A/metabolism

@article {pmid42336879,
year = {2026},
author = {Feng, C and Lu, H and Bian, J and Wang, H and Jia, H and Li, X and Yang, M and Song, H and Tan, W and Wang, L},
title = {Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42336879},
issn = {2055-5008},
support = {2025ZD01900200//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; },
mesh = {Animals ; *Bacteriophages/genetics/physiology ; Mice ; *Virulence Factors/genetics ; Humans ; Metagenomics/methods ; Virulence/genetics ; *Bacteria/genetics/pathogenicity/classification/virology ; Microbiota ; Ecosystem ; Animals, Wild/microbiology ; },
abstract = {Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.},
}

Animals
*Bacteriophages/genetics/physiology
Mice
*Virulence Factors/genetics
Humans
Metagenomics/methods
Virulence/genetics
*Bacteria/genetics/pathogenicity/classification/virology
Microbiota
Ecosystem
Animals, Wild/microbiology

@article {pmid42458473,
year = {2026},
author = {Gupta, E and Sharma, S and Tikar, SN and Dash, PK},
title = {Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42458473},
issn = {1743-422X},
mesh = {Animals ; *Aedes/virology ; *Metagenomics/methods ; India ; Computational Biology/methods ; Genome, Viral ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation & purification ; *Genetic Variation ; Larva/virology ; Shotgun Sequencing ; },
abstract = {Metagenomics or metaviromics is emerging as a powerful technology for pathogen surveillance and pandemic preparedness. Mosquitoes are important vectors for transmission of many emerging viruses responsible for numerous outbreaks. Monitoring mosquitoes becomes essential to investigate its virome which leads to understanding of disease dynamics and allow preventive actions. In this study, shotgun metagenomic methodology using Ion GeneStudio S5 System was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season of 2024. Aedes larvae reared to adulthood and processed for sequencing using Ion Torrent S5 platform. Computational analyses were performed using three bioinformatic pipelines: Chan Zuckerberg ID (CZ ID), Genome Detective Platform and the Galaxy Platform. A mock database of 11 known viruses was created as well as publicly available NCBI Sequence Read Archive (SRA) datasets were used to validate all three pipelines. In terms of detection accuracy, Genome Detective and CZ ID performed exceptionally well and therefore may be suitable for future mosquito virome surveillance studies. We found presence of viruses viz. Alphamesonivirus cavallynense and Phasivirus phasiense dominating in all samples. Dengue virus was detected in one sample by CZ ID, whereas Wenzhou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus found most commonly among samples. Other viruses found like Aedes anphevirus (AeAV; genus Glybovirus), Aedes totivirus, Verdadero virus and Chaq-like virus. Variation in the result among different pipelines are likely attributable to incorporation of different viral reference databases, classification algorithms, metrics and analysis parameters. To the best of our knowledge, this study represents the first metagenomic study of mosquitoes using Ion GeneStudio S5 platform in India. The findings provide a comparative evaluation of the metagenomic pipelines and elucidates detailed information of each pipeline and its working for future studies.},
}

Animals
*Aedes/virology
*Metagenomics/methods
India
Computational Biology/methods
Genome, Viral
*Virome
*Mosquito Vectors/virology
*Viruses/classification/genetics/isolation & purification
*Genetic Variation
Larva/virology
Shotgun Sequencing

@article {pmid42464266,
year = {2026},
author = {He, C and Du, Y and Lloyd, KG and Vishnivetskaya, TA and Rivkina, EM and Jiang, H and Liang, R},
title = {Diversity and potential ecological roles of viruses in Pleistocene permafrost.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
pmid = {42464266},
issn = {1741-7007},
mesh = {*Permafrost/virology ; Siberia ; *Viruses/classification/genetics/isolation & purification ; Arctic Regions ; *Biodiversity ; Metagenomics ; },
abstract = {BACKGROUND: Ancient permafrost, formed during past glacial periods, is widespread in Siberia and other Arctic regions. Even though these soils have remained below 0 °C over geological time periods, the widespread presence of bacteria and archaea in permafrost is well documented. However, the diversity of viruses in ancient permafrost of different geological ages and their potential ecological roles are still poorly understood.

RESULTS: We applied metagenomics to characterize viruses from Middle to Late Pleistocene permafrost sediments from Siberia. A total of 2697 viral operational taxonomic units (vOTUs) were recovered through metagenomic assembly and virus identification. Viral diversity in the Middle Pleistocene permafrost was much higher than that in the Late Pleistocene. The virus communities at different depths of the Middle Pleistocene permafrost showed great similarity to each other but were significantly different from those of the Late Pleistocene, with Azeredovirinae, Peduoviridae, and Fiersviridae being the predominant viruses in Pleistocene permafrost. The viruses were predicted to carry auxiliary metabolic genes potentially involved in cold adaptation and elemental (C and N) biogeochemical cycling in ancient permafrost. The virus-host prediction revealed that microorganisms such as bacteria and archaea are the main hosts and only a few eukaryotic hosts were identified.

CONCLUSIONS: Our results show that permafrost viral communities in Siberia exhibit remarkable diversity and may have played a significant ecological role in ancient permafrost over geological time. While the release of viruses from thawing deep permafrost could pose a relatively small risk to human health and environment, it could have significant impacts on the carbon cycle, potentially influencing climate change feedback in permafrost regions.},
}

*Permafrost/virology
Siberia
*Viruses/classification/genetics/isolation & purification
Arctic Regions
*Biodiversity
Metagenomics

@article {pmid42571869,
year = {2026},
author = {Manzoor, M and Leskelä, J and Könönen, E and Lahti, L and Putaala, J and Pussinen, PJ and Paju, S},
title = {Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression.},
journal = {Journal of clinical periodontology},
volume = {53},
number = {11},
pages = {1650-1662},
doi = {10.1111/jcpe.70184},
pmid = {42571869},
issn = {1600-051X},
support = {296541//Research Council of Finland/ ; 316777//Research Council of Finland/ ; 355532//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 369310//Research Council of Finland/ ; 286246//Research Council of Finland/ ; 318075//Research Council of Finland/ ; 322656//Research Council of Finland/ ; //Finnish Dental Society Apollonia/ ; //Sigrid Juselius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
mesh = {Humans ; *Saliva/microbiology ; Disease Progression ; *Metagenomics/methods ; Cross-Sectional Studies ; *Microbiota/genetics ; Female ; Adult ; Male ; *Periodontal Diseases/microbiology ; Gingivitis/microbiology ; Periodontitis/microbiology ; },
abstract = {AIM: To characterise multi-kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage-specific taxonomic and functional alterations using shotgun metagenomic sequencing.

MATERIALS AND METHODS: In this cross-sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I-II) and severe periodontitis (Stages III-IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways.

RESULTS: Beta diversity differed between periodontal health and the different disease states (Bray-Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease-associated species Porphyromonas gingivalis , Tannerella forsythia , Treponema denticola , Porphyromonas endodontalis , Fusobacterium nucleatum and Parvimonas micra . Among non-bacterial taxa, Candida, Moineauvirus, Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770-1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762-0.968).

CONCLUSION: Salivary multi-kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at-risk individuals.},
}

Humans
*Saliva/microbiology
Disease Progression
*Metagenomics/methods
Cross-Sectional Studies
*Microbiota/genetics
Female
Adult
Male
*Periodontal Diseases/microbiology
Gingivitis/microbiology
Periodontitis/microbiology

@article {pmid42859015,
year = {2026},
author = {Yu, Z and Wang, W and Chen, F and Li, L and Luo, L and Zhong, X and Liu, D and Tang, W and Liu, X and Huang, M},
title = {Temporal dynamics and metabolic potential of microbial dark matter during dry storage of high-temperature Daqu revealed by metagenome-assembled genomes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120539},
doi = {10.1016/j.foodres.2026.120539},
pmid = {42859015},
issn = {1873-7145},
mesh = {*Metagenome ; *Alcoholic Beverages/microbiology/analysis ; *Hot Temperature ; Fermentation ; *Food Microbiology ; Metagenomics ; *Food Storage/methods ; Bacillota/genetics/metabolism ; Archaea/genetics/metabolism ; *Microbiota/genetics ; },
abstract = {High-temperature Daqu is the core starter culture for Jiang-flavor Baijiu production, whose microbial community directly shapes the enzymatic properties and flavor precursor profiles of fermentation systems. Dry storage drives microbial succession and functional maturation of Daqu, yet existing studies have predominantly focused on cultivable and well-characterized taxa, leaving the temporal dynamics and metabolic contributions of microbial dark matter (MDM) largely unexplored at the genome-resolved level. Using genome-resolved metagenomics, we reconstructed 52 medium- to high-quality metagenome-assembled genomes (MAGs) from high-temperature Daqu samples across a six-month dry storage period and identified five novel unclassified MDM lineages comprising four Bacillota-affiliated bacterial lineages and one archaeal lineage. Comparative genomic analysis revealed distinct functional differentiation between MDM lineages and dominant culturable taxa, as MDM lineages were enriched in genes associated with carbohydrate uptake and fermentative acid production and harbored a streamlined biosynthetic gene cluster (BGC) profile with uniformly high sequence novelty. Temporal dynamic analysis showed that MDM lineages from different storage microhabitats exhibited divergent succession patterns, and conventional physicochemical parameters showed limited explanatory power for MDM community variation, with only glucoamylase activity displaying a marginal association trend. This study provides genome-resolved insights into uncultured MDM lineages during high-temperature Daqu dry storage, expands the genomic repertoire of uncultured microbiota in traditional fermentation ecosystems, and offers novel perspectives for deciphering Daqu maturation mechanisms and quality regulation.},
}

*Metagenome
*Alcoholic Beverages/microbiology/analysis
*Hot Temperature
Fermentation
*Food Microbiology
Metagenomics
*Food Storage/methods
Bacillota/genetics/metabolism
Archaea/genetics/metabolism
*Microbiota/genetics

@article {pmid42859016,
year = {2026},
author = {Ji, Q and Qu, H and Chen, D and Li, Q and Zong, L and Liu, Y and Huang, Y and Gu, R},
title = {Matrix-associated spatial structure contributes to compositional stability of a complex multispecies starter culture under microbial perturbation: Insights from kefir grains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120540},
doi = {10.1016/j.foodres.2026.120540},
pmid = {42859016},
issn = {1873-7145},
mesh = {*Kefir/microbiology ; Fermentation ; *Food Microbiology/methods ; *Microbiota ; Cultured Milk Products/microbiology ; },
abstract = {Complex multispecies starter cultures can enrich the metabolic and sensory diversity of fermented foods, but industrial use is limited by compositional drift, overgrowth of dominant taxa, and vulnerability to exogenous microbial contamination. Kefir grains (KG), a matrix-encapsulated complex starter culture with stable serial propagation, provide a model for how spatial structure contributes to starter stability. We compared matrix-associated KG with free kefir-fermented milk (FKFM), representing a grain-free liquid-phase kefir microbial community, under a large-scale microbial challenge. During the acute 24 h challenge, target-taxon drift estimated from PMA-qPCR data was lower in KG than in the liquid compartments. Ten-generation serial transfer caused stronger community restructuring and Shannon diversity loss in FKFM, whereas KG showed constrained compositional adjustment and remained relatively clustered in Bray-Curtis ordination space. Species-level metagenomic tracking showed broader expansion, retention, and cumulative drift of species-level signals corresponding to exogenous challenge strains in FKFM, while more of these signals in KG followed restricted/stable trajectories. Kefir cell-free supernatant inhibited multiple challenge strains beyond the effect of low pH, indicating a contribution of diffusible inhibitory factors. SEM and live/dead staining revealed rough matrix-associated surfaces and heterogeneous cell states in KG. Together, the results support a model in which spatial structure, prior niche occupancy, and diffusible inhibition jointly contribute to the compositional stability and anti-perturbation capacity of this complex starter culture, informing the design of spatially structured synthetic starter consortia for industrial fermentation.},
}

*Kefir/microbiology
Fermentation
*Food Microbiology/methods
*Microbiota
Cultured Milk Products/microbiology

@article {pmid42860401,
year = {2026},
author = {Xu, Z and Jiang, H and Huang, W and Chan, A and Lin, Y and Chan, T and Lui, RN and Wong, MTL and Mak, JWY and Chan, FKL and Chevarin, C and Colombel, JF and Buisson, A and Ng, SC},
title = {Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42860401},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/therapy/microbiology ; Pilot Projects ; *Fecal Microbiota Transplantation/methods/adverse effects ; Female ; *Escherichia coli/genetics/physiology ; Male ; Feces/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli Infections/therapy/microbiology ; Young Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {Adherent-invasive Escherichia coli (AIEC) is implicated in Crohn's disease (CD) pathogenesis, but whether fecal microbiota transplantation (FMT) clears mucosal AIEC and alters fecal and mucosal microbiomes has not been studied. In this open-label pilot study, thirty adults with CD and seropositivity for serum anti-E.coli antibody (AEcAb) received a single colonoscopic FMT from one of two donors (ClinicalTrials.gov identifier NCT05611866). The primary outcome was adverse events (AEs) within 12 weeks after FMT; secondary outcomes included changes in mucosal AIEC, clinical measures, and fecal and mucosal microbiome profiles. Shotgun metagenomic sequencing for fecal samples and 16S rRNA sequencing for ileal mucosal samples were performed at baseline and after FMT. Baseline AEcAb levels were higher in patients with mucosal AIEC colonization (p = 0.019) and remained elevated after FMT. No FMT-related serious adverse events were reported. FMT was associated with mucosal AIEC decolonization in all 8 evaluable baseline-positive patients. Mucosal alpha diversity increased after FMT (p = 0.023), which correlated with reduced fecal calprotectin (p = 0.034). Microbial pathway profiles in CD patients resembled those of their respective donors with reduced donor-recipient dissimilarity post-FMT (p = 0.030), particularly among recipients with mucosal AIEC decolonization (p = 0.039). In conclusion, this open-label pilot study demonstrates the feasibility of FMT for modulating mucosal AIEC colonization in CD and highlights the importance of capturing microbial changes at the disease site that may be undetectable in fecal samples.},
}

Humans
*Crohn Disease/therapy/microbiology
Pilot Projects
*Fecal Microbiota Transplantation/methods/adverse effects
Female
*Escherichia coli/genetics/physiology
Male
Feces/microbiology
Adult
*Intestinal Mucosa/microbiology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Escherichia coli Infections/therapy/microbiology
Young Adult
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid42215825,
year = {2026},
author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L},
title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {7},
pages = {1209-1227},
pmid = {42215825},
issn = {1618-1905},
support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Hypertriglyceridemia/microbiology ; China ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Machine Learning ; Adult ; Triglycerides/blood ; Feces/microbiology ; East Asian People ; },
abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.},
}

Humans
*Hypertriglyceridemia/microbiology
China
Metagenomics
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
Male
Female
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Middle Aged
Machine Learning
Adult
Triglycerides/blood
Feces/microbiology
East Asian People

@article {pmid42800338,
year = {2026},
author = {Gui, Y and Yu, W and Shi, Y and Li, Y and Yang, X and Zhang, H and Yan, W and Liu, Q and Jiang, G},
title = {Microbial filtering and functional reprogramming in soil exposed to spent NCM battery black powder.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120847},
doi = {10.1016/j.ecoenv.2026.120847},
pmid = {42800338},
issn = {1090-2414},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics/classification ; Manganese/toxicity ; *Electric Power Supplies ; Cobalt/toxicity ; Nickel/toxicity ; Powders ; Soil/chemistry ; },
abstract = {Spent lithium-ion battery black powder is an emerging complex contaminant, which contains transition metals, residual electrolyte salts, and compounds derived from organic electrolytes or binders. Its ecological effects on soil microbiomes remain poorly understood. Here, we designed a soil microcosm experiment with using red soil exposed to a concentration gradient of black powder derived from nickel-cobalt-manganese (NCM) lithium-ion batteries. Samples were collected at two incubation time points and analyzed by shotgun metagenomic sequencing. Black powder exposure produced a nonlinear taxonomic response, with species-level alpha diversity increasing under intermediate exposure, while rare-taxon abundance distributions shifted markedly under medium and high exposure. The LEfSe and PLS-DA analyses identified concentration- and time-dependent indicator taxa, including enrichment of Actinomycetota-related taxa and depletion of Nitrospira and Candidatus Methylomirabilis under high exposure. Community structure diverged significantly along the concentration gradient, and PERMANOVA attributed 23.2% of taxonomic variation to treatment. Structural equation modeling showed no significant direct path from black powder concentration to functional potential; instead, the model was consistent with a possible indirect association through community restructuring. Functional alpha diversity generally declined with increasing black powder concentration. High concentration exposure was associated with reduced relative abundance of KEGG Orthology entries (KOs) related to nitrogen cycling and increased stress-response and organic-matter-decomposition signatures. Overall, these results suggest that NCM-derived black powder can alter soil microbial functional profiles by reshaping community composition.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
*Microbiota/drug effects
*Bacteria/drug effects/genetics/classification
Manganese/toxicity
*Electric Power Supplies
Cobalt/toxicity
Nickel/toxicity
Powders
Soil/chemistry

@article {pmid42852388,
year = {2026},
author = {Laue, HE and Fleisch, AF and Calafat, AM and Lanphear, BP and Cecil, KM and Yolton, K and Buckley, JP and Karagas, MR and Madan, JC and Willis, AD and Braun, JM},
title = {Associations of Urinary Triclosan Concentrations Across Gestation and Childhood with the Adolescent Gut Microbiome.},
journal = {Environmental health perspectives},
volume = {134},
number = {6},
pages = {672-687},
pmid = {42852388},
issn = {1552-9924},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; K99 ES034086/ES/NIEHS NIH HHS/United States ; P01 ES011261/ES/NIEHS NIH HHS/United States ; R01 ES014575/ES/NIEHS NIH HHS/United States ; R00 ES034086/ES/NIEHS NIH HHS/United States ; UL1 TR001425/TR/NCATS NIH HHS/United States ; R01 ES024381/ES/NIEHS NIH HHS/United States ; R01 ES025214/ES/NIEHS NIH HHS/United States ; R01 ES020349/ES/NIEHS NIH HHS/United States ; },
mesh = {*Triclosan/urine ; Humans ; Female ; Pregnancy ; Adolescent ; Child ; *Gastrointestinal Microbiome/drug effects ; Child, Preschool ; Male ; Infant ; *Anti-Infective Agents, Local/urine ; Ohio ; Prospective Studies ; Feces/microbiology ; },
abstract = {Research on the influence of repeated exposure to antimicrobial chemicals, such as triclosan, on the microbiome is lacking. The goal of this study was to elucidate the associations of time-varying urinary triclosan concentrations with the adolescent gut microbiome. We used data from a prospective cohort based in Cincinnati, OH (enrolled 2003-2006, n = 146), to assess the time-varying associations of urinary triclosan concentrations with adolescent (age ∼ 12 years) gut microbiome diversity and composition. Individuals ≥ 18-years-old were recruited during the second trimester of pregnancy, and urinary triclosan concentrations were measured in pregnant women up to 2 times in pregnancy and up to 7 times in the child from ages 1 through 12 years. At age ∼ 12 years, fecal microbiome diversity and composition was characterized with metagenomic sequencing. We estimated differences in the relative abundance of prevalent (≥50%) bacterial species and gene pathways using linear regression and generalized estimating equations to assess windows of heightened susceptibility adjusted for sociodemographic characteristics. Additionally, we examined sex-specific associations by including an interaction term. The adolescent median Shannon diversity was 3.5 (IQR: 3.3, 3.5). Higher gestational triclosan concentrations with lower gut microbiome diversity [β = -0.13 per 10-fold increase (95%CI: -0.24, -0.02)]. Triclosan concentrations were also positively associated with higher abundance of antibiotic resistance genes and differential abundance of some bacterial species, with the strongest associations observed in early life and at age 12 years. We also found differences depending on sex, with more significant associations observed among males. Our findings provide insight into windows of triclosan exposure that are relevant to gut microbiome composition and the impacts of antimicrobial agents.},
}

*Triclosan/urine
Humans
Female
Pregnancy
Adolescent
Child
*Gastrointestinal Microbiome/drug effects
Child, Preschool
Male
Infant
*Anti-Infective Agents, Local/urine
Ohio
Prospective Studies
Feces/microbiology

@article {pmid42853629,
year = {2026},
author = {Jin, JX and Ye, ZC and Zhang, GF and Wang, Y and Jiang, ZC and Lan, FL and He, YF},
title = {Geographic differentiation of the gut microbiota in Lissorhoptrus oryzophilus (Coleoptera: Curculionidae): associations with environmental gradients and predicted functional potential.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {5},
pages = {},
pmid = {42853629},
issn = {1536-2442},
support = {568//Guizhou Provincial Science and Technology Program Project/ ; 011//Innovative capabilities Buildup of Green Prevention and Control for Invasive Species in Agriculture/ ; 2017YFC1200600//National Key R&D Program of China/ ; 024//Guizhou Key Laboratory of Agricultural Biosecurity/ ; },
mesh = {Animals ; *Weevils/microbiology ; China ; *Gastrointestinal Microbiome ; Altitude ; Bacteria/classification/genetics ; Metagenomics ; },
abstract = {The rice water weevil, Lissorhoptrus oryzophilus (Kuschel), is a major invasive pest native to rice that has expanded far beyond its native North American range to establish widespread populations across Asia and Europe. However, how altitudinal gradients shape this microbial ecosystem remains unclear. We performed shotgun metagenomics to profile the gut microbiota of 3 geographically distinct populations-Pingba District (PB), Yibin City (SC), and Mudanjiang (MDJ) City-of L. oryzophilus across elevational gradients in China. Though low-abundance archaeal, fungal, and viral sequences were detected, bacterial taxa (>89% of annotated genes) dominated functional profiles. All populations were Proteobacteria-dominated, but PB was enriched in Erwiniaceae (Pantoea deleyi), while SC/MDJ were dominated by Rickettsiaceae (Rickettsia/Wolbachia). Population-specific taxa were most abundant in MDJ (19 species), followed by PB (15), with SC harboring only 1 unique species. Predicted functional profiles aligned with taxonomy: PB showed elevated amino acid/carbohydrate metabolism, carbohydrate-active enzyme, and efflux pump gene abundances. SC and MDJ shared similar functional profiles. Principal coordinates analysis revealed distinct clustering of PB across taxonomic and functional dimensions, while SC/MDJ partially overlapped. These correlative findings suggest microbial metabolic plasticity may support the weevil's persistence across heterogeneous environments, though causal links require experimental validation.},
}

Animals
*Weevils/microbiology
China
*Gastrointestinal Microbiome
Altitude
Bacteria/classification/genetics
Metagenomics

@article {pmid42858079,
year = {2026},
author = {Yang, X and Ye, T and He, Y and Zhao, J and Wang, J and Cheng, X},
title = {Qi-Fu-Yin Attenuates Frailty by Regulating Gut Microbiota and Neuroendocrine Hormones in 5xFamilial Alzheimer's Disease Transgenic Mice.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/73003},
pmid = {42858079},
issn = {1940-087X},
mesh = {Animals ; *Alzheimer Disease/drug therapy/microbiology/blood/metabolism ; Mice, Transgenic ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; *Frailty/drug therapy/microbiology ; Female ; Male ; Disease Models, Animal ; },
abstract = {Frailty is a common and debilitating feature of Alzheimer's disease (AD), yet effective therapeutic strategies targeting both cognitive decline and physical frailty remain limited. Qi-Fu-Yin (QFY), a traditional Chinese herbal formulation, has been used to treat aging-related disorders, but its effects on frailty in AD and the underlying mechanisms are unclear. This study aimed to evaluate whether QFY alleviates frailty in 5xFamilial Alzheimer's Disease (FAD) transgenic mice and to explore the potential involvement of gut microbiota and neuroendocrine hormones. Mice were treated with QFY at low (2.8 g/kg), medium (5.6 g/kg), or high (11.2 g/kg) doses, or with donepezil as a positive control, for 194 days. Frailty-related behaviors were assessed using CatWalk gait analysis, grip strength, rotarod, nest-building, and aging scoring. Plasma hormone levels were measured, and fecal gut microbiota composition and function were analyzed by 16S rRNA sequencing and metagenomic analysis. QFY treatment significantly improved gait parameters, grip strength, motor coordination, nesting ability, and reduced aging scores in 5xFAD mice, with effects comparable to or superior to those of donepezil. QFY also restored aberrant levels of estradiol, testosterone, and corticosterone, and reshaped gut microbiota composition, particularly by increasing the abundance of Adlercreutzia, which negatively correlated with senescence and testosterone levels. Functional metagenomics revealed that QFY partially restored disease-associated microbial pathways, including those involved in carbohydrate metabolism and virulence. These findings suggest that QFY alleviates frailty in 5xFAD mice, with effects associated with concurrent modulation of gut microbiota and neuroendocrine function, though causal relationships require further validation. These findings support further investigation of QFY as a potential intervention for AD-associated frailty.},
}

Animals
*Alzheimer Disease/drug therapy/microbiology/blood/metabolism
Mice, Transgenic
Mice
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/administration & dosage
*Frailty/drug therapy/microbiology
Female
Male
Disease Models, Animal

@article {pmid42858083,
year = {2026},
author = {Zheng, Y and Yang, Y and Mei, X and Guo, T and Gu, L and Liu, X and Yu, J and Yang, X and Yang, M and Li, Y and Zhang, X and Zhou, Y and Zheng, J and Hu, X},
title = {Paired Exploratory Metagenomic Analysis of Gut Microbiota Before and After Ceftizoxime Treatment in College Students with Acute Enteritis.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {236},
pages = {},
doi = {10.3791/71529},
pmid = {42858083},
issn = {1940-087X},
mesh = {Humans ; *Ceftizoxime/therapeutic use/pharmacology/administration & dosage ; Female ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Metagenomics/methods ; Young Adult ; Adolescent ; *Enteritis/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/microbiology ; Students ; Acute Disease ; Metagenome/drug effects ; },
abstract = {This study explored the short-term changes in gut microbiota concurrent with ceftizoxime sodium therapy and clinical recovery in college students with acute enteritis. A retrospective, self-controlled before-and-after design was adopted, enrolling 10 college students (5 males, 5 females; aged 18-24 years) with acute enteritis admitted to Southwest University Hospital. Fecal samples were collected before intravenous antibiotic treatment and at the time of clinical recovery (5-7 days later). All patients received intravenous ceftizoxime sodium (1.0 g every 12 h). Metagenomic sequencing was performed to analyze microbiota composition and diversity. We hypothesized that short-term ceftizoxime therapy would induce detectable species-level restructuring without substantially altering higher-level diversity. Phylum-level analyses showed no statistically significant differences between the two groups. Also, α-diversity analysis at the genus level revealed that the Shannon, Simpson, and Chao1 showed no differences between the two groups (q = 0.054, 0.054 and 0.084, respectively). PERMANOVA based on Bray-Curtis distances at the genus level demonstrated a statistically significant difference in overall microbial community structure between the two groups before and after treatment (F = 1.81, P = 0.043), but no significant difference after adjustment (P = 0.054). ANOSIM performed on the raw full-species abundance table at the species level further detected significant separation between the two groups (R = 0.114, P = 0.016). No species remained statistically significant after false-discovery-rate correction. These exploratory, descriptive findings indicate that species-level temporal changes in the gut microbiota occurred concurrently with ceftizoxime exposure and clinical recovery, but cannot be attributed specifically to the antibiotic. The study provides hypothesis-generating data for future controlled investigations of antibiotic-microbiota interactions in young adults.},
}

Humans
*Ceftizoxime/therapeutic use/pharmacology/administration & dosage
Female
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Metagenomics/methods
Young Adult
Adolescent
*Enteritis/drug therapy/microbiology
Male
*Gastrointestinal Microbiome/drug effects/genetics
Feces/microbiology
Students
Acute Disease
Metagenome/drug effects

@article {pmid42858216,
year = {2026},
author = {Khan, A and Ullah, Z and Siraj, M and Younas, S and Wahab, S and Waris, A and Hong, ST},
title = {The Gut Microbiota-Epilepsy Axis: Bibliometric Trends, Mechanistic Insights, and Microbiota-Targeted Next-Generation Therapeutic Opportunities.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42858216},
issn = {1559-1182},
mesh = {Humans ; *Epilepsy/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Brain ; },
abstract = {Epilepsy is a complex neurological disorder with diverse underlying causes. Growing evidence suggests that gut dysbiosis may promote epileptogenesis by disrupting short-chain fatty acids, tryptophan-kynurenine metabolism, immune signaling, and neuronal excitability. In this review, we combine findings from human and animal studies to explain how gut dysbiosis may influence seizures through the gut-brain axis. We highlight emerging and less-discussed mechanisms, including vagus nerve signaling, microbial amyloids, bacterial extracellular vesicles (BEVs), the queuosine salvage pathway, and multi-kingdom microbiota interactions. We also summarize microbiota profiling studies and describe dysbiosis patterns linked to seizure. To support translation, we propose a peri-ictal multi-omics strategy for biomarker discovery. This includes standardized sampling and integration of metagenomics, metabolomics, and host transcriptomics. In addition, our bibliometric analysis further shows rapidly growing global interest in this topic. Recent studies increasingly focus on the gut-brain axis, ketogenic diet, and inflammation-driven mechanisms. Finally, we outline both established approaches and emerging next-generation microbiome-based therapeutic strategies, including SCFA-restoring synbiotics, engineered psychobiotics, bacteriophage therapy, and AI-guided personalization. These advances highlight the microbiota as modifiable target for adjunctive epilepsy management and provide a translational roadmap for future mechanistically informed research and clinical interventions.},
}

Humans
*Epilepsy/therapy/microbiology
Animals
*Gastrointestinal Microbiome/physiology
Dysbiosis
Brain

@article {pmid42858532,
year = {2026},
author = {Paladsing, Y and Linsuwanon, P and Jittmittraphap, A and Leaungwutiwong, P and Morand, S and Chaisiri, K},
title = {Rodent-associated viruses in Asia: ecological drivers, host-virus associations and insights from a systematic review.},
journal = {Research in veterinary science},
volume = {213},
number = {},
pages = {106394},
doi = {10.1016/j.rvsc.2026.106394},
pmid = {42858532},
issn = {1532-2661},
abstract = {Rodent-associated viruses are important zoonotic agents of increasing relevance to public and veterinary health. Muroid rodents occupy diverse natural and human-modified environments, facilitating interactions with humans, livestock and wildlife. However, knowledge of rodent-associated viral diversity and the ecological processes influencing viral maintenance and transmission remains fragmented. This review synthesizes published literature on viral diversity, host-virus associations, research trends, and ecological drivers of viral occurrence in Asian muroid rodents. PubMed and Scopus were systematically searched using terms related to rodents, viruses, and Asian regions. Extracted data included publication characteristics, diagnostic methods, host and virus taxonomy, geography, and ecological metadata. Descriptive analyses, geospatial mapping, and network approaches were applied to identify patterns and knowledge gaps. Of 1,049 records retrieved, 165 studies published between 1968-2025 from 30 Asian countries met the inclusion criteria. These studies documented 106 viral taxa representing 74 genera and 35 families. Research activity increased markedly after 2000 alongside advances in molecular diagnostics and metagenomic sequencing. Studies were concentrated in East and mainland Southeast Asia. Orthohantavirus spp. were the most studied viral group, whereas many other viruses remained poorly characterized. Network analyses identified core murine genera, particularly Rattus, Apodemus, Niviventer, Bandicota and Mus, sharing extensive viral associations. Host age, sex, population density, habitat disturbance, climate, and biodiversity were commonly linked with viral prevalence and dynamics. Despite substantial progress, gaps remain in ecological integration, longitudinal surveillance, and comparative study design. Future research should prioritize standardized, ecologically informed surveillance within an integrated One Health framework to improve zoonotic risk assessment and prevention.},
}

@article {pmid42859003,
year = {2026},
author = {Dong, L and Luo, S and Misbahullah, SM and Xu, J and Wan, S and Gao, H and Qin, Z},
title = {Polymerization-dependent gut microbiome responses to curdlan β-1,3-glucan and its oligosaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120524},
doi = {10.1016/j.foodres.2026.120524},
pmid = {42859003},
issn = {1873-7145},
mesh = {*beta-Glucans/metabolism/chemistry ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Feces/microbiology ; *Oligosaccharides/metabolism/chemistry ; Polymerization ; Fermentation ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {β-1,3-Glucan is a dietary fiber with microbiome-modulating potential, yet the role of polymerization degree on microbial composition and metabolism remains unclear. Curdlan is an insoluble linear β-1,3-glucan widely used as a food hydrocolloid that provides a model to examine structure-dependent microbiome responses. We compared glucose, curdlan (CBG), and curdlan-derived β-1,3-glucan oligosaccharides (OBG) using anaerobic in vitro fermentation of pooled human feces. A multi-omics approach integrating 16S rRNA sequencing, shotgun metagenomics, short-chain fatty acid (SCFA) quantification, and untargeted metabolomics was applied to resolve taxonomic, functional, and metabolic shifts. Both CBG and OBG enriched Bacteroidota and enhanced carbohydrate metabolism relative to glucose, but through distinct pathways. CBG promoted polymer-associated carbohydrate processing, with enrichment of β-1,3-glucan-degrading enzymes such as GH16, Sus-like transport systems, and polysaccharide-specialized taxa (e.g., Prevotella and Bifidobacterium), and butyrate production. In contrast, OBG favored transporter-mediated substrate uptake, broader microbial participation (e.g. Parabacteroides and Enterobacteriaceae), and a metabolite profile enriched in amino acid-derived compounds and branched-chain SCFAs. These findings demonstrate that β-1,3-glucan polymerization degree governs microbiome functional routing and highlight polymerization degree as a tunable parameter for designing microbiome-directed carbohydrate ingredients with predictable metabolic outcomes.},
}

*beta-Glucans/metabolism/chemistry
Humans
*Gastrointestinal Microbiome/drug effects/physiology
Feces/microbiology
*Oligosaccharides/metabolism/chemistry
Polymerization
Fermentation
Dietary Fiber/metabolism
Fatty Acids, Volatile/metabolism
Glucose/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42680679,
year = {2026},
author = {Yang, X and Peng, AD and Cheng, JH and Huang, YH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG and Wen, G},
title = {A legacy pollutant deciphered by multiomics toxicology and targeted remediation by a synthetic microbial consortium: a case study of 2-chloroacetophenone from abandoned chemical weapons.},
journal = {Water research},
volume = {306},
number = {},
pages = {126776},
doi = {10.1016/j.watres.2026.126776},
pmid = {42680679},
issn = {1879-2448},
mesh = {Biodegradation, Environmental ; Multiomics ; *Water Pollutants, Chemical ; *Microbial Consortia ; *Acetophenones ; },
abstract = {2-Chloroacetophenone (2-CA) is a typical organic poison found in abandoned Japanese chemical weapons, yet systematic research on its ecological risks and bioremediation strategies in aquatic environments remains scarce. Through a 120-day exposure experiment across three concentration gradients (10, 50, and 100 mg·L[-1]) coupled with multiomics analysis (physicochemical profiling, ionomics, 16S rRNA sequencing, metagenomics, and metabolomics), we systematically characterized the toxic effects of 2-CA on aquatic microbial communities and their molecular response mechanisms. The glutathione (GSH) metabolic pathway was identified as the core defense hub against 2-CA-induced oxidative stress, with multiomics data revealing its transition from compensatory activation to irreversible collapse. Guided by these mechanistic insights, we directionally isolated three cascade-degrading bacteria (Pseudomonas abietaniphila, Bacillus sp., and Arthrobacter agilis) harboring the key genes hapA, yjfP, and catA, which encode the three consecutive steps of Baeyer-Villiger oxidation, ester bond hydrolysis, and aromatic ring cleavage. The synthetic microbiome assembled from these three wild-type strains achieved 100% removal of 100 mg·L[-1] 2-CA within 24 h in vitro and within 10 days in simulated contaminated water, with the sequential detection of predicted intermediates (phenyl 2-chloroacetate, phenol, and pyruvic acid) confirming the operation of the cascade pathway. This study establishes a "toxicology diagnosis-functional deconstruction-synthetic reconstruction" paradigm, providing mechanistic understanding and a potential bioremediation strategy for organic toxicants at sites contaminated by relic Japanese chemical weapons, although direct ecotoxicological validation of detoxification remains to be confirmed.},
}

Biodegradation, Environmental
Multiomics
*Water Pollutants, Chemical
*Microbial Consortia
*Acetophenones

@article {pmid41672081,
year = {2026},
author = {Miller, KJ and Wolff, IM and Montes de Oca Valeriano, LA and Soto-Giron, MJ and Jangi, S and Schott, EM and Charbonneau, MR and Ballok, AE and Toledo, GV},
title = {Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial.},
journal = {Beneficial microbes},
volume = {17},
number = {5},
pages = {477-489},
doi = {10.1163/18762891-bja00109},
pmid = {41672081},
issn = {1876-2891},
mesh = {Humans ; *Synbiotics/administration & dosage/analysis ; Feces/microbiology ; Female ; Middle Aged ; Adult ; Young Adult ; Adolescent ; *Gastrointestinal Microbiome ; Metagenomics ; *Bacteria/isolation & purification/genetics/classification ; Microbial Viability ; },
abstract = {The viability and persistence of orally administered microbes in the human gut are essential to their biological function. We previously described the development of two synbiotic medical foods, SBD111 and SBD121, each comprising four food-derived microbial strains and prebiotic fibres for the dietary management of postmenopausal bone loss and rheumatoid arthritis, respectively. Here, we report a randomised, open-label clinical study examining gut persistence of SBD111 and SBD121 microbes by testing faecal samples from healthy adults following administration for seven days. Thirty-eight participants, aged 18-64 years with a body mass index (BMI) of 18.5-35 kg/m2, were randomised to receive one of the two synbiotic medical foods daily for one week, followed by a four-week monitoring period. Employing quantitative PCR (qPCR), shotgun metagenomics, and culture-based assays, we evaluated the presence and viability of the microbial strains comprising each synbiotic medical food during and after administration. SBD111 and SBD121 were well-tolerated with minimal adverse events reported. Strains were detected in over 80% of participants during the administration period, with strain abundance peaking in the first week. Persistence in the follow-up period varied by strain and detection method. The microbial strains were detected by qPCR and metagenomic sequencing for a median of seven days and three days during the follow-up period, respectively. However, Bacillus amyloliquefaciens was consistently detected for seven days by both methods. Culture-based assays confirmed the presence of viable strains from both synbiotic medical foods in stool samples up to one-week post-consumption. Faecal metagenome diversity and metabolic functional potential remained stable throughout the administration and follow-up periods. Collectively, these results establish that SBD111 and SBD121 deliver viable microbes that transiently persist in the gut, reinforcing their promise for safe and targeted dietary interventions and highlighting the value of multi-platform detection strategies for comprehensive microbial persistence assessment. This trial, funded by Sōlarea biō, is registered at ClinicalTrials.gov (NCT06614166).},
}

Humans
*Synbiotics/administration & dosage/analysis
Feces/microbiology
Female
Middle Aged
Adult
Young Adult
Adolescent
*Gastrointestinal Microbiome
Metagenomics
*Bacteria/isolation & purification/genetics/classification
Microbial Viability

@article {pmid42189388,
year = {2026},
author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G},
title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.},
journal = {Science China. Life sciences},
volume = {69},
number = {9},
pages = {3112-3126},
pmid = {42189388},
issn = {1869-1889},
mesh = {Male ; Animals ; *Testis/drug effects/metabolism ; *Carbon Quantum Dots/toxicity ; Mice ; *Fertility/drug effects ; *Gastrointestinal Microbiome/drug effects ; Blood-Testis Barrier/drug effects ; Testosterone ; *Infertility, Male/chemically induced ; Intestinal Barrier Function ; },
abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.},
}

Male
Animals
*Testis/drug effects/metabolism
*Carbon Quantum Dots/toxicity
Mice
*Fertility/drug effects
*Gastrointestinal Microbiome/drug effects
Blood-Testis Barrier/drug effects
Testosterone
*Infertility, Male/chemically induced
Intestinal Barrier Function

@article {pmid42437920,
year = {2026},
author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A},
title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.},
journal = {Cardiovascular diabetology},
volume = {25},
number = {1},
pages = {},
pmid = {42437920},
issn = {1475-2840},
mesh = {Humans ; Male ; Middle Aged ; *Prediabetic State/blood/physiopathology/diagnosis/therapy/microbiology ; Adult ; *Cardiorespiratory Fitness ; Multiomics ; *Proteomics/methods ; *High-Intensity Interval Training ; *Metabolomics/methods ; Obesity/blood/physiopathology ; Adaptation, Physiological ; Biomarkers/blood ; Oxygen Consumption ; Young Adult ; Time Factors ; Gastrointestinal Microbiome ; Treatment Outcome ; Feces/microbiology ; China ; Metagenomics/methods ; },
abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.},
}

Humans
Male
Middle Aged
*Prediabetic State/blood/physiopathology/diagnosis/therapy/microbiology
Adult
*Cardiorespiratory Fitness
Multiomics
*Proteomics/methods
*High-Intensity Interval Training
*Metabolomics/methods
Obesity/blood/physiopathology
Adaptation, Physiological
Biomarkers/blood
Oxygen Consumption
Young Adult
Time Factors
Gastrointestinal Microbiome
Treatment Outcome
Feces/microbiology
China
Metagenomics/methods

@article {pmid42505077,
year = {2026},
author = {Zhang, Q and Li, D and Liu, B and Zhang, Y and Li, M and Guo, R and Ni, Y and Chen, S and Ni, B and Qiu, L and Xing, G and Dong, H and Yan, Q and Li, S and Zou, X and Cao, B},
title = {A Comprehensive Microbial Gene Catalog of the Human Airway Microbiome Across Anatomical Sites and Geographic Regions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {56},
pages = {e76589},
pmid = {42505077},
issn = {2198-3844},
support = {BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; 82341113//National Natural Science Foundation of China/ ; 025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Respiratory System/microbiology ; Virulence Factors/genetics ; Antimicrobial Peptides/genetics ; Metagenomics/methods ; *Bacteria/genetics ; },
abstract = {The respiratory microbiota is a critical determinant of airway health, yet functional characterization remains challenging due to the lack of a high-resolution reference catalog. To address this gap and enable systematic investigation at both species and gene levels, we constructed the integrated Human Airway Microbiome Gene Catalog (iHAMGC) through high-throughput metagenomic analysis of 12,273 airway samples. This catalog comprises 24,185,985 non-redundant microbial genes and provides extensive taxonomic and functional annotations, with a particular focus on clinically relevant elements, including antibiotic resistance genes, virulence factors, and antimicrobial peptides. We further resolved the bacterial hosts of resistance genes and virulence factor genes, as well as taxa contributing to antimicrobial peptide activity. The iHAMGC captures site-specific microbial and functional variations across distinct airway niches and reveals regional differences in functional potential. By offering a comprehensive, publicly accessible reference for airway microbial genes, the iHAMGC serves as a foundational resource for advancing our understanding of the airway microbiota in respiratory health and disease.},
}

Humans
*Microbiota/genetics
*Respiratory System/microbiology
Virulence Factors/genetics
Antimicrobial Peptides/genetics
Metagenomics/methods
*Bacteria/genetics

@article {pmid42685687,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Chang, K and Li, S and Zhang, Y and Yu, H and Wang, C and Yao, X and Chen, S and Nie, X and Zhao, J and Lu, B and Li, Y and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {The human oral and airway viral genome catalog from metagenomes enables virome characterization informing respiratory health.},
journal = {Med (New York, N.Y.)},
volume = {7},
number = {10},
pages = {101269},
doi = {10.1016/j.medj.2026.101269},
pmid = {42685687},
issn = {2666-6340},
mesh = {Humans ; *Virome/genetics ; *Metagenome/genetics ; *Genome, Viral/genetics ; *Mouth/virology ; *Respiratory Tract Infections/virology ; Female ; *Respiratory System/virology ; Prospective Studies ; Male ; Aged ; Metagenomics ; },
abstract = {BACKGROUND: Viral communities of the upper aerodigestive tract represent an important component of the human microbial ecosystem but remain poorly characterized due to the limited availability of habitat-specific reference resources.

METHODS: We integrated 19,997 public and 2,673 newly sequenced oral and airway metagenomes to establish the Oral and Airway Viral Genome Catalogue (OAVGC). Viral genomes were reconstructed and characterized through taxonomic assignment, prokaryotic host prediction, functional annotation, and assessment of putative antibacterial activity. Our prospective longitudinal aging cohort, alongside 5 in-house datasets and publicly cohorts, were analyzed to investigate associations between airway virome profiles and respiratory health.

FINDINGS: The OAVGC comprised 141,459 high-quality viral genomes (completeness ≥90%) clustered into 68,708 viral operational taxonomic units (vOTUs). Approximately half of these viruses and families are previously undescribed, with independent cross-cohort detection and PCR assays providing additional support for their occurrence. Across multiple respiratory infection cohorts, the virome exhibited convergent diversity reductions and compositional signatures. In the prospective cohort, the baseline airway virome was correlated with host lung function and geriatric health scores. Virome-based machine learning classifiers demonstrated potential for predicting the future occurrence of upper respiratory tract infections up to 12 months in advance, outperforming bacteriome-based models in our prediction analyses.

CONCLUSIONS: The OAVGC provides an unprecedented genomic and functional resource for investigating the ecological and clinical associations of the oral-airway virome, revealing its potential impact on respiratory health and capacity to predict future infections.

FUNDING: National Natural Science Foundation of China (82341113) and National Key R&D Program of China (2022YFA1304303).},
}

Humans
*Virome/genetics
*Metagenome/genetics
*Genome, Viral/genetics
*Mouth/virology
*Respiratory Tract Infections/virology
Female
*Respiratory System/virology
Prospective Studies
Male
Aged
Metagenomics

@article {pmid42848247,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Tumor microenvironment and gut microbiome in immunotherapy resistance in gastric cancer: clinical questions, biological mechanisms, and evidence-based therapeutic perspectives.},
journal = {Medical oncology (Northwood, London, England)},
volume = {43},
number = {11},
pages = {},
pmid = {42848247},
issn = {1559-131X},
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology ; *Tumor Microenvironment/immunology ; *Drug Resistance, Neoplasm/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Immunotherapy/methods ; },
abstract = {Immune checkpoint inhibitors (ICIs) have improved systemic therapy for advanced gastric and gastroesophageal junction cancer, yet primary and acquired resistance remain common and are incompletely explained by established tumor biomarkers. This narrative review evaluates the connected roles of the tumor microenvironment (TME), host immunity, and the gut microbiome in shaping ICI resistance in gastric cancer. We performed a structured PubMed search through 28 August 2026 and prioritized gastric cancer-specific clinical and translational evidence, supplemented by systematic reviews, meta-analyses, and mechanistically relevant studies from other tumor types when necessary. Within the gastric cancer TME, cancer-associated fibroblasts, myeloid cells, regulatory T cells, extracellular matrix remodeling, hypoxia, angiogenesis, and T-cell exhaustion can promote immune exclusion or dysfunction. Microbial diversity, microbial metabolites, antibiotics, proton pump inhibitors, defined live biotherapeutics, fecal microbiota transplantation, and diet may influence systemic antitumor immunity, but most human evidence is retrospective, cross-sectional, or derived from non-gastric cancers. Clinically, antibiotic stewardship, reassessment of unnecessary acid suppression, and nutritional optimization are reasonable supportive measures, whereas routine probiotic supplementation, Clostridium butyricum MIYAIRI 588 for ICI sensitization, and fecal microbiota transplantation remain investigational in gastric cancer. Future studies should integrate longitudinal exposures, serial TME profiling, stool metagenomics, medication use, nutritional status, and clinical outcomes. The TME-gut microbiome axis is therefore a biologically plausible framework for biomarker-guided research, but current evidence does not justify empiric microbiome-directed anticancer therapy in gastric cancer.},
}

Humans
*Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology
*Tumor Microenvironment/immunology
*Drug Resistance, Neoplasm/immunology
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Immunotherapy/methods

@article {pmid42849679,
year = {2026},
author = {De Lise, F and Sacco, O and Shaikh-Ibrahim, A and Di Fenza, M and Strazzulli, A and Moracci, M and Terrapon, N and Curci, N and Cobucci-Ponzano, B},
title = {Seeding subfamilies in glycoside hydrolase family 116: New insights into the function and inhibitor sensitivity of subfamily 2.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {154792},
doi = {10.1016/j.ijbiomac.2026.154792},
pmid = {42849679},
issn = {1879-0003},
abstract = {Among glycoside hydrolase (GH) families and characterized enzymes reported in CAZy, GHs from Archaea remain largely underrepresented. Recent 'omics' studies have uncovered numerous uncharacterized GH sequences from extremophilic Archaea, providing unprecedented opportunities to study their diversity, structure, function, and properties. The GH family 116 (GH116) was originally built around a characterized archaeal member, revealing homologous sequences in Eukaryota and Bacteria. Although previous studies proposed or attempted GH116 subdivision into distinct subfamilies associated with different substrate specificity and inhibitor sensitivity, such a classification has never been formally established, mainly because few GH116 enzymes have been biochemically characterized. As a result, its functional landscape remains poorly understood. Here, we formally establish GH116 subfamilies, starting from the discovery of nine novel archaeal GH116 sequences identified from metagenomics samples collected from two mud/water pools in the extreme environment of Pisciarelli solfatara. These sequences were assigned to subfamilies 2 and 3, mainly hyperthermophilic archaeal enzymes. By combining phylogenetic analyses, structural modeling, and biochemical studies, we identified subfamily-specific structural domains that may serve as structural markers and suggest that these subfamilies represent functionally specialized groups. Focusing on subfamily 2, previously with only one characterized member, we biochemically characterized two novel enzymes. Our results expand GH116 functional diversity, reporting for the first time β-galactosidase activity within this family and showing β-xylosidase activity in subfamily 2, previously observed only in subfamily 3. We also examined active-site inhibition profiles and, through active-site mapping and mutational analysis, elucidated the molecular basis of inhibitor sensitivity in one enzyme of this subgroup.},
}

@article {pmid42850249,
year = {2026},
author = {Chen, S and Bahadur, A and Zhu, J and Liu, E and Gu, Y and Liang, H and Zhang, W and Li, S and Li, A and Wei, P and Liu, Q and Wu, T and Yang, P and Zou, Y and Han, M and Malard, LA},
title = {Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to alpine permafrost degradation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42850249},
issn = {2041-1723},
support = {U23A2062//National Natural Science Foundation of China (National Science Foundation of China)/ ; U24A20586//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Permafrost/microbiology ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification ; Soil Microbiology ; Tibet ; Metagenome ; Nitrogen/metabolism ; },
abstract = {Deciphering microbiomes across vertical profiles is critical for understanding biogeochemical cycling and potential biosafety hazards associated with permafrost degradation under climate warming. However, knowledge about microbiome patterns over key profile layers in response to degradation remains limited in the Qinghai-Tibet Plateau. Using metagenomic data obtained from 150 samples of six 15 m-depth alpine permafrost cores along a degradation gradient, we analyzed microbial community structure and functional potential across different main-layers, including the active, frozen fringe, and frozen layers. We found the recovered microbial and functional diversity decreased with profile depth, and declined only in the active layer as permafrost degraded. Interestingly, Pithoviridae, Caulimoviridae, and virulence factors related to adhesion, biofilm formation, and immune regulation were enriched in the frozen fringe layer, along with increasing relative abundance of Lavidaviridae under the degradation. Along the degradation gradient, carbohydrate-active enzymes diversity decreased in the active layer, while the ratio of nitrite reductase genes to nitrous oxide reductase genes increased in the active and the frozen fringe layers. Hydrothermal regimes emerged as the primary controls shaping microbiome distributions across the vertical profile and along the degradation gradient. Notably, hydrothermal and microbiome attributes jointly regulated carbon/nitrogen loss during the degradation. Taken together, these findings offer crucial insights into microbiome patterns, carbon/nitrogen loss and biosecurity concerning permafrost degradation under global warming.},
}

*Permafrost/microbiology
*Microbiota/genetics/physiology
Bacteria/genetics/classification
Soil Microbiology
Tibet
Metagenome
Nitrogen/metabolism

@article {pmid42402715,
year = {2026},
author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD},
title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.},
journal = {Plant, cell & environment},
volume = {49},
number = {11},
pages = {7997-8013},
pmid = {42402715},
issn = {1365-3040},
support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; },
mesh = {*Hemiterpenes/metabolism ; *Plant Roots/microbiology/growth & development ; *Butadienes/metabolism ; *Nicotiana/microbiology/growth & development/genetics/metabolism ; Plants, Genetically Modified ; *Microbiota ; *Pentanes/metabolism ; Rhizosphere ; Soil Microbiology ; Biomass ; Bacteria ; },
abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.},
}

*Hemiterpenes/metabolism
*Plant Roots/microbiology/growth & development
*Butadienes/metabolism
*Nicotiana/microbiology/growth & development/genetics/metabolism
Plants, Genetically Modified
*Microbiota
*Pentanes/metabolism
Rhizosphere
Soil Microbiology
Biomass
Bacteria

@article {pmid42444523,
year = {2026},
author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M},
title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {83},
number = {4},
pages = {728-736},
pmid = {42444523},
issn = {1536-4801},
support = {K01 DK135647/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; K23 AT009458/AT/NCCIH NIH HHS/United States ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; R03 DK147916/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; K23 DK135797/DK/NIDDK NIH HHS/United States ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; P30 DK078392/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Crohn Disease/microbiology ; *Irritable Bowel Syndrome/microbiology ; Child ; Female ; *Pancreatitis/microbiology ; Adolescent ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; *Dysbiosis/microbiology ; Case-Control Studies ; Acute Disease ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.

METHODS: Stool was collected from 120 subjects (AP [n = 30], CD [n = 29], IBS Rome IV [n = 27], and healthy controls [HC, n = 34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.

RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p < 0.0001) and similar to CD (p = 0.97). CD differed from IBS (p = 0.001) and HC (p < 0.0001) while IBS and HC were similar (p = 0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2] = 0.12, p < 0.001), and differences between all conditions in pairwise comparisons (p < 0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC = 0.97), followed by AP (AUC = 0.92), HC (AUC = 0.88), and IBS (AUC = 0.83).

CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.},
}

Humans
*Crohn Disease/microbiology
*Irritable Bowel Syndrome/microbiology
Child
Female
*Pancreatitis/microbiology
Adolescent
Feces/microbiology
*Gastrointestinal Microbiome
Male
*Dysbiosis/microbiology
Case-Control Studies
Acute Disease

@article {pmid42478878,
year = {2026},
author = {Davis, EC and Jackson, CM and Diaz, NS and Susana, J and Nelson, A and Insel, R and Seppo, AE and Järvinen, KM},
title = {Maternal Perinatal Gut Microbiome Is Shaped by Traditional Farming Lifestyle and Associated With Early Childhood Atopic Disease.},
journal = {Allergy},
volume = {81},
number = {10},
pages = {3707-3724},
pmid = {42478878},
issn = {1398-9995},
support = {U01 AI131344/AI/NIAID NIH HHS/United States ; //University of Rochester University Research Award/ ; NIFA 67012-35010//U.S. Department of Agriculture/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; T32 HL066988/HL/NHLBI NIH HHS/United States ; U01 AI131344//National Institute of Allergy and Infectious Diseases/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247//University of Rochester Environmental Health Sciences Center/ ; T32 HL066988/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; Pregnancy ; *Life Style ; *Gastrointestinal Microbiome ; *Hypersensitivity, Immediate/etiology/epidemiology ; *Maternal Exposure/adverse effects ; *Agriculture ; Infant ; Adult ; *Prenatal Exposure Delayed Effects ; Developmental Origins of Health and Disease ; },
abstract = {Maternal exposure to a traditional farming lifestyle during pregnancy is associated with protection against allergic disease in childhood; however, the mechanism remains unclear. Pre-clinical work has demonstrated a role for the maternal gut microbiome in fetal immune programming. Given the diverse microbial exposure on farms, we sought to assess whether the maternal gut microbiome may mediate the relationship between maternal farm exposure and protection against offspring allergic disease. Deep shotgun metagenomic analysis of the perinatal fecal microbiome showed that women from an Old Order Mennonite traditional farming community (OOM, n = 68) harbored a more diverse gut microbiome relative to women from urban/suburban Rochester, NY (ROC, n = 55). We identified several bacterial species differentially abundant between lifestyle groups, including those from Dorea, Anaerobutyricum, Bifidobacterium, and Bacteroides genera, which translated to marked differences in microbiome functional capacity. These differences in the gut microbiome composition were accompanied by targeted metabolite findings indicating higher serum acetate and isobutyrate levels in OOM women that were positively correlated with cord plasma levels and infant systemic IgA concentrations. Among urban women, maternal microbiome composition was associated with early childhood atopic disease outcomes. Specifically, Dorea longicatena and Segatella copri were least abundant in urban mothers whose infants developed atopic disease (atopic dermatitis) or IgE-mediated food allergy alone, respectively, and were most abundant in the OOM mothers. Together, these findings highlight the maternal gut microbiome and metabolites as potential contributors to prenatal farming lifestyle protection against early childhood allergic disease.},
}

Humans
Female
Pregnancy
*Life Style
*Gastrointestinal Microbiome
*Hypersensitivity, Immediate/etiology/epidemiology
*Maternal Exposure/adverse effects
*Agriculture
Infant
Adult
*Prenatal Exposure Delayed Effects
Developmental Origins of Health and Disease

@article {pmid42517538,
year = {2026},
author = {Fehr, D and Flack, N and Masenga, G and Mosha, N and Li, N and White, A and Semango, G and Distler, M and Lang, C and Grimm, F and Scharl, M and Mavura, D and Masenga, JE and Schmid-Grendelmeier, P and Brüggen, MC},
title = {Dietary Habits and Atopic Dermatitis Significantly Influence the Fecal Microbiome.},
journal = {Allergy},
volume = {81},
number = {10},
pages = {3584-3598},
pmid = {42517538},
issn = {1398-9995},
support = {LF-OC-20-000418//LEO Fondet/ ; 0456/2024//Vontobel-Stiftung/ ; //Bruno Bloch Stiftung/ ; },
mesh = {Humans ; *Dermatitis, Atopic/etiology/microbiology/epidemiology ; *Feces/microbiology ; Female ; Male ; *Feeding Behavior ; Case-Control Studies ; Metagenomics/methods ; *Microbiota ; Child, Preschool ; *Gastrointestinal Microbiome ; Child ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) has been associated with microbial gut dysbiosis in children. Data in adults is scarce.

OBJECTIVE: We sought to explore the fecal microbiome composition in AD patients versus healthy controls (HC) and investigate the impact of environmental aspects such as the geographical location and dietary habits.

METHODS: In this case control study, a total of 140 fecal samples from 69 AD patients and 71 HC from Tanzania (TZ) and Switzerland (CH) were analyzed. Illumina shotgun metagenomics sequencing was performed followed by taxonomic profiling, calculation of alpha/beta diversity, and permutational multivariate analysis of variance. Differentially abundant species and genera between AD and HC were evaluated.

RESULTS: Alpha diversity (Shannon Index) did not significantly differ between AD and HC. The presence of AD was identified as a significant source of fecal microbiome variation (Bray-Curtis beta diversity). On the species level, Faecalibacterium taiwanense was more abundant in AD, and Vescimonas sp000435555 in HC. On the genus level, CAG-302 (NCBI: Clostridium) was more abundant in HC. Geographical location was associated with distinct dietary habits. Prevotella was significantly more abundant in TZ, whereas Alistipes and Bacteroides were significantly more abundant in CH.

CONCLUSIONS: The presence of AD significantly impacted the fecal microbiome variation and was associated with a particular microbial composition. The impact of geographical location on the fecal microbiome may be related to nutritional differences. Our data support the rationale of a gut-skin axis and pave the way towards therapeutic approaches modulating the microbiome.},
}

Humans
*Dermatitis, Atopic/etiology/microbiology/epidemiology
*Feces/microbiology
Female
Male
*Feeding Behavior
Case-Control Studies
Metagenomics/methods
*Microbiota
Child, Preschool
*Gastrointestinal Microbiome
Child

@article {pmid42571819,
year = {2026},
author = {Li, S and Cai, M and Chen, L and Liang, J and Luo, X and Meng, J and Cao, Y and Liu, G and Hu, Y and Cai, S and Zou, M},
title = {Serine synergizes with lipopolysaccharide to induce macrophage pyroptosis through extracellular Hsp90α and early skin immune microenvironment disruption in diabetic foot.},
journal = {Metabolism: clinical and experimental},
volume = {184},
number = {},
pages = {156732},
doi = {10.1016/j.metabol.2026.156732},
pmid = {42571819},
issn = {1532-8600},
mesh = {*HSP90 Heat-Shock Proteins/metabolism ; *Macrophages/drug effects/metabolism ; Humans ; *Serine/pharmacology/metabolism ; *Lipopolysaccharides/pharmacology ; *Skin/immunology/metabolism/drug effects ; *Diabetic Foot/metabolism/immunology/pathology/microbiology ; Animals ; Skin Microbiome ; Cellular Microenvironment/drug effects ; Keratinocytes/metabolism/drug effects ; Female ; Male ; Dysbiosis/metabolism ; },
abstract = {BACKGROUND: The pathogenesis of early-stage skin lesions in diabetic foot (DF) remains poorly understood, and cannot be fully explained by conventional theories. Skin microbiota dysbiosis has recently emerged as a critical factor, but the underlying mechanisms remain unclear.

METHODS: In this study, we integrated metabolomics and metagenomics analyses of skin samples to investigate metabolic dysregulation driven by microbial dysbiosis.

RESULTS: We identified elevated serine as a key metabolic alteration strongly correlated with a dysbiotic microbiota structure. Functionally, we demonstrate that abnormal serine accumulation contributes to the dysregulation of the early skin immune microenvironment in the diabetic foot. Mechanistically, our results reveal that excess serine synergizes with lipopolysaccharide (LPS) to stimulate the release of eHsp90α from keratinocytes, which was strictly dependent on the Akt/mTOR/HIF-1α pathway. This released eHsp90α then acts as a damage-associated molecular pattern, promoting both the migration and subsequent pyroptotic cell death of macrophages.

CONCLUSIONS: Collectively, our findings suggest a novel pathogenic axis where a microbiota-host derived metabolite collaborates with a bacterial endotoxin to promote inflammatory cell death, which is closely associated with early skin lesions in DF. This work not only elucidates a new mechanism for DF pathogenesis but also suggests that the serine-eHsp90α-pyroptosis axis may serve as a potential candidate for future therapeutic exploration.},
}

*HSP90 Heat-Shock Proteins/metabolism
*Macrophages/drug effects/metabolism
Humans
*Serine/pharmacology/metabolism
*Lipopolysaccharides/pharmacology
*Skin/immunology/metabolism/drug effects
*Diabetic Foot/metabolism/immunology/pathology/microbiology
Animals
Skin Microbiome
Cellular Microenvironment/drug effects
Keratinocytes/metabolism/drug effects
Female
Male
Dysbiosis/metabolism

@article {pmid42714846,
year = {2026},
author = {Cui, Y and Zhang, B and Jiang, X and Rehemujiang, H and Xu, G and Li, Y and Wang, B},
title = {Perilla seed oil reshapes the rumen microbiome and increases fermentation end-products in vitro.},
journal = {Journal of applied microbiology},
volume = {137},
number = {10},
pages = {},
doi = {10.1093/jambio/lxag233},
pmid = {42714846},
issn = {1365-2672},
support = {2025ZY0108//Central Government-Guided Local Science and Technology Development Fund Project/ ; 326YXQN0947//Natural Science Foundation of China/ ; 324QN289//Natural Science Foundation of China/ ; CARS-37//China Agriculture Research System/ ; },
mesh = {Animals ; *Rumen/microbiology ; Fermentation/drug effects ; *alpha-Linolenic Acid/pharmacology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; *Plant Oils/pharmacology ; RNA, Ribosomal, 16S/genetics ; Animal Feed/analysis ; },
abstract = {AIMS: The effect of Perilla frutescens seed oil (PSO) on an in vitro rumen microbial ecosystem was evaluated by integrating fermentation measurements, microbiome profiling, metagenomics, and untargeted metabolomics.

METHODS AND RESULTS: Rumen inoculum was incubated for 24 h with a control TMR substrate (CK), TMR supplemented with 23.7 mg of Perilla seeds per bottle (PS), or TMR supplemented with 8.5 μL of Perilla seed oil per bottle (PSO), with the PS and PSO treatments providing equivalent amounts of seed oil. Fermentation kinetics and volatile fatty acids were measured, and microbial and metabolic responses were characterized using 16S rRNA gene sequencing, metagenomics, KEGG and CAZy annotation, untargeted metabolomics, and MetOrigin2 source tracing. PSO increased maximum gas production and total volatile fatty acid concentrations while maintaining pH within the physiological range. Community diversity was unchanged, but PSO altered microbial composition, including increases in Firmicutes, Verrucomicrobia, Vagococcus, Clostridium, and Lactobacillus and decreases in Shigella sonnei and Methanosarcina sp. Ant1. PSO also altered microbial functional profiles and increased several lipid- and vitamin-associated metabolites, including linoleic acid, 13-HODE, 9-oxoODE, pantothenic acid, and thiamine, while reducing lactate.

CONCLUSIONS: PSO changed rumen microbial community structure and functional potential in parallel with increased fermentation end-products and extensive metabolic shifts. These in vitro findings identify microbial and metabolic responses that warrant validation in vivo.},
}

Animals
*Rumen/microbiology
Fermentation/drug effects
*alpha-Linolenic Acid/pharmacology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
*Microbiota/drug effects
Fatty Acids, Volatile/metabolism
*Plant Oils/pharmacology
RNA, Ribosomal, 16S/genetics
Animal Feed/analysis

@article {pmid42732816,
year = {2026},
author = {Hao, F and Zhu, W and Tang, A and Chen, Q and Guo, M and Xin, Y and Zhu, X and Zhao, Y and Hu, X and Luo, M and Zhou, N and Qin, K and Zhu, H and Li, W},
title = {Akkermansia muciniphila alleviates osteoporosis by suppressing bone marrow adiposity through the gut microbiota-UDCA-TGR5 axis.},
journal = {Life sciences},
volume = {405},
number = {},
pages = {124676},
doi = {10.1016/j.lfs.2026.124676},
pmid = {42732816},
issn = {1879-0631},
mesh = {Animals ; *Osteoporosis/metabolism/microbiology ; Female ; Rats ; *Gastrointestinal Microbiome/physiology ; *Adiposity ; *Bone Marrow/metabolism ; *Ursodeoxycholic Acid/metabolism ; Rats, Sprague-Dawley ; Ovariectomy ; *Receptors, G-Protein-Coupled/metabolism ; Akkermansia ; Mesenchymal Stem Cells/metabolism ; Signal Transduction ; },
abstract = {Osteoporosis (OP) is characterized not only by progressive bone loss but also frequently by pathological bone marrow adiposity (BMA) expansion. Akkermansia muciniphila (AKK), implicated in lipid metabolic homeostasis, was previously found to be markedly depleted during estrogen deficiency-associated bone loss. However, whether AKK suppresses pathological BMA expansion and the corresponding receptor-mediated mechanisms remain poorly understood. Here, we demonstrated that AKK significantly attenuated bone loss and potently suppressed pathological BMA expansion in ovariectomized rats. Integrated untargeted metabolomics and targeted bile acid profiling revealed that AKK supplementation notably restored ursodeoxycholic acid (UDCA) levels in both serum and feces. Metagenomic analyses showed that AKK reshaped bile salt hydrolase (BSH)-related microbial functions, thereby promoting the intestinal deconjugation of tauroursodeoxycholic acid to generate UDCA. The enhanced UDCA-producing capacity of gut microbiota from the AKK-treated group was abolished by inhibition of microbial BSHs. Consistently, oral UDCA supplementation replenished circulating UDCA levels and reproduced the bone- and marrow-protective effects of AKK. In the host, elevated circulating UDCA activated TGR5-dependent TGF-β/SMAD2 signaling in bone marrow mesenchymal stem cells (BMSCs), thereby suppressing adipogenic differentiation and promoting osteogenesis. These effects were reversed by a TGR5 inhibitor and Tgfbr1 knockdown. Collectively, our study reveals a novel mechanism underlying the anti-osteoporotic effects of AKK, whereby AKK suppresses pathological BMA expansion through the gut microbiota-UDCA-TGR5 signaling axis. These findings provide a potential therapeutic strategy for osteoporosis and bone marrow lipid metabolic dysfunction.},
}

Animals
*Osteoporosis/metabolism/microbiology
Female
Rats
*Gastrointestinal Microbiome/physiology
*Adiposity
*Bone Marrow/metabolism
*Ursodeoxycholic Acid/metabolism
Rats, Sprague-Dawley
Ovariectomy
*Receptors, G-Protein-Coupled/metabolism
Akkermansia
Mesenchymal Stem Cells/metabolism
Signal Transduction

@article {pmid42767176,
year = {2026},
author = {Delican, D and Kılıçkaya, O and Ozden, O and Ensari, Y},
title = {Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity.},
journal = {Bioorganic chemistry},
volume = {182},
number = {},
pages = {110550},
doi = {10.1016/j.bioorg.2026.110550},
pmid = {42767176},
issn = {1090-2120},
mesh = {Humans ; *Asparaginase/pharmacology/metabolism/chemistry/genetics ; *Antineoplastic Agents/pharmacology/chemistry/metabolism ; *Gastrointestinal Microbiome ; Drug Screening Assays, Antitumor ; Structure-Activity Relationship ; Cell Proliferation/drug effects ; Dose-Response Relationship, Drug ; Molecular Structure ; },
abstract = {L-asparaginase is essential for acute lymphoblastic leukemia treatment; however, current Escherichia coli and Erwinia chrysanthemi formulations face significant limitations, including immunogenicity, glutaminase-associated toxicity, and short plasma half-life. The human gut microbiome represents an unexplored reservoir of therapeutic enzymes that may offer superior biocompatibility due to host-commensal co-evolution. We employed a systematic genome-mining approach to screen human gut metagenomic data for novel L-asparaginase candidates. Five candidate enzymes from the genera Bacteroides, Ruminococcus, Clostridium, and Prevotella were identified using virtual screening. These enzymes were subsequently codon-optimized and heterologously expressed in E. coli, thereby validating our computational selection strategy. Biochemical characterization revealed optimal activity at alkaline pH (8.0-9.0), robust performance at physiological temperature (37 °C), and excellent storage stability. Ruminococcus_seq7 exhibited exceptional kinetic properties (Km = 0.53 ± 0.19 mM; Vmax = 78.6 ± 5.59 U/mg), whereas Bacteroides_seq104 showed intermediate kinetics (Km = 2.04 ± 0.57 mM; Vmax = 75.4 ± 5.75 U/mg). These lead candidates demonstrated complementary anti-leukemic profiles: Ruminococcus_seq7 showed broad-spectrum activity against T-cell leukemias (IC50: 5.1-8.6 U/mL for Jurkat, MOLT-4, and THP-1), while Bacteroides_seq104 exhibited remarkable potency against THP-1 cells (IC50 = 0.9 U/mL) and successfully overcame resistance in REH cells (IC50 = 36.9 U/mL). Both enzymes maintained >95% viability in healthy HUVEC cells. This study provides proof-of-concept for the discovery of therapeutic enzyme from the human gut microbiome. The identified L-asparaginases exhibited favorable biochemical properties, potent and selective anti-leukemic activity, and enhanced safety profiles. The absence of glutaminase activity and high biocompatibility position these gut microbiome-derived enzymes as promising biotherapeutic scaffolds for next-generation leukemia treatment, pending further optimization of substrate affinity to meet clinical standards.},
}

Humans
*Asparaginase/pharmacology/metabolism/chemistry/genetics
*Antineoplastic Agents/pharmacology/chemistry/metabolism
*Gastrointestinal Microbiome
Drug Screening Assays, Antitumor
Structure-Activity Relationship
Cell Proliferation/drug effects
Dose-Response Relationship, Drug
Molecular Structure

@article {pmid42841652,
year = {2026},
author = {Voulgari-Kokota, A and Janson, E and Heikamp de Jong, I and Knol, J and van Elburg, R and van der Aa, NE and Hortensius, LM and Dudink, J and de Theije, CGM and Schipper, L and Kozior, M and van de Lagemaat, M and Groenendaal, F and van Bel, F and Wildt-Grootendorst, A and Drost-Verhoef, S and Hennink, A and Obihara, CC and van Hillegersberg-Schilder, JLAM and Dassel, CM and Oudshoorn, JH and Meijssen, CB and de Boer, IP and Illy, KE and Claessens, N and Viergever, MA and Isgum, I and Shetty, S and Wopereis, H and Benders, M and Belzer, C},
title = {Synbiotic supplementation leads to gut microbiome communities with functional capacity linked to better brain white matter development in preterm infants.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743949},
doi = {10.1080/19490976.2026.2743949},
pmid = {42841652},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; *Infant, Premature/growth & development ; *White Matter/growth & development ; *Brain/growth & development ; *Gastrointestinal Microbiome ; *Synbiotics/administration & dosage ; Dietary Supplements ; Male ; Bifidobacterium breve ; Glutamine/administration & dosage ; Female ; Oligosaccharides/administration & dosage ; Neurodevelopment ; Magnetic Resonance Imaging ; Infant ; },
abstract = {Preterm birth, a major cause of brain injury, is often linked to dysregulated gut microbiome development. This association underscores microbial metabolic function as a modifiable target to support neurodevelopment. In this secondary analysis of data derived from a randomized controlled trial (Trial Registration: ISRCTN96620855), we tested whether daily nutritional supplementation with Bifidobacterium breve M-16V, short- and long-chain oligosaccharides, and L-glutamine could steer the gut microbiome of very and extremely preterm infants toward communities that support brain maturation. The gut microbiome was profiled with longitudinal shotgun metagenomics at nine time points during the intervention, which started at 48-72 h after birth and continued until 36 weeks postmenstrual age. Additionally, MRI scans were conducted when infants reached term-equivalent age to evaluate brain maturation. Supplementation promoted the early establishment of Bifidobacterium-rich communities in the test group, with enhanced capacity for amino acid biosynthesis and pyruvate fermentation towards acetate and lactate production. Integration of microbiome data with brain developmental markers post hoc showed that the same functions were markedly reduced in infants with delayed white-matter myelination. By integrating microbiome functional capacity profiling and evaluation of brain maturation via MRI, this study demonstrated that early microbial modulation could influence brain development, positioning the preterm gut microbiome as a clinically actionable target.},
}

Humans
Infant, Newborn
*Infant, Premature/growth & development
*White Matter/growth & development
*Brain/growth & development
*Gastrointestinal Microbiome
*Synbiotics/administration & dosage
Dietary Supplements
Male
Bifidobacterium breve
Glutamine/administration & dosage
Female
Oligosaccharides/administration & dosage
Neurodevelopment
Magnetic Resonance Imaging
Infant

@article {pmid42842295,
year = {2026},
author = {Lin, WY and Chang, YJ and Gill, T and Ching, J and Anderson, D and Creek, DJ and Ayub, Q and Rahman, S and Chong, CW},
title = {Association of microbial pathways predicted/inferred using 16S and shotgun metagenome with faecal metabolite abundances.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001855},
pmid = {42842295},
issn = {2057-5858},
mesh = {*Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Metagenomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; *Bacteria/genetics/classification/metabolism ; Metabolome ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {The gut microbiome is an essential metabolic organ influencing host health through metabolite production. While metabolite production levels can be directly measured by gas or liquid chromatography, they are commonly inferred from the abundance of metagenomic functional pathways. To evaluate the accuracy of these inferences, we established a single, manually curated metabolite-pathway/enzyme mapping list as a standardized biological reference. We then compared liquid chromatography-mass spectrometry (LC-MS)-based faecal metabolites with functional pathways/enzymes inferred from four approaches: 16S rRNA gene amplicons, reference-based shotgun, de novo assembly-based contigs and de novo assembly-based metagenome-assembled genomes (MAGs). Our results demonstrate that predictive accuracy is strongly metabolite-specific and method-dependent rather than a uniform characteristic of metagenomic data. While 16S (9.9%), ref-shotgun (14.2%) and de novo-contigs (5.5%) yielded only a small fraction of well-predicted metabolites, the de novo-MAGs approach significantly outperformed other approaches, achieving a 36.9% well-predicted rate for mapped metabolites. Notably, this approach provided the most robust functional-metabolite associations for indicators of gut health. In conclusion, while microbial functional potential does not always mirror metabolic reality, high-quality genomic binning via MAGs offers a significantly more robust framework for selective metabolite prediction.},
}

*Feces/microbiology/chemistry
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Metagenomics/methods
Humans
Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
*Bacteria/genetics/classification/metabolism
Metabolome
Liquid Chromatography-Mass Spectrometry

@article {pmid42844285,
year = {2026},
author = {Pearman, JK and Sissons, J and Kanyi Kihika, J and Waters, S and Rees, ABH and Howarth, JD and Vandergoes, MJ and Wood, SA},
title = {Divergent microbial functional pathways and declining redundancy in lake sediments across eutrophication gradients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844285},
issn = {2041-1723},
support = {CAWX2305//Ministry of Business, Innovation and Employment (MBIE)/ ; C05X1707//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; *Geologic Sediments/microbiology/chemistry ; New Zealand ; Phosphorus/metabolism ; Ecosystem ; *Microbiota/genetics ; *Bacteria/metabolism/genetics/classification ; Nitrification ; Denitrification ; Metagenomics ; Nitrogen/metabolism ; },
abstract = {Microbial communities underpin nutrient cycling across aquatic ecosystems and are strongly influenced by human disturbance, yet the implication for functional redundancy remains poorly understood. Lake eutrophication is a global threat to freshwater systems, primarily driven by human activities within lakes and surrounding catchments. We hypothesize that eutrophication alters functional redundancy of key metabolic pathways in lake sediments. To test this, we conducted a national scale metagenomic study of surface sediments from 144 New Zealand lakes spanning a broad nutrient gradient. Increasing eutrophication is associated with reduced taxon-based functional redundancy, the potential of multiple species to perform the same function, indicating a narrower taxa pool supporting core functions. In contrast, abundance-based functional redundancy, characterized by the abundance of organisms that can perform the function, showed pathway-specific responses across trophic gradients. For example, nitrification and denitrification have greater abundance-based functional redundancy under higher nutrient conditions, whereas phosphorus transport shows reduced redundancy. By eroding microbial functional redundancy, eutrophication may increase susceptibility of microbial communities to environmental perturbations, potentially compromising their ability to sustain key metabolic processes. As lakes play key roles in biogeochemical cycles, the lower stability of vital biogeochemical pathways in lake sediments is likely to have an impact across ecosystems globally.},
}

*Lakes/microbiology/chemistry
*Eutrophication
*Geologic Sediments/microbiology/chemistry
New Zealand
Phosphorus/metabolism
Ecosystem
*Microbiota/genetics
*Bacteria/metabolism/genetics/classification
Nitrification
Denitrification
Metagenomics
Nitrogen/metabolism

@article {pmid42844483,
year = {2026},
author = {Carter, MM and Liu, Z and Olm, MR and Martin, M and Sprockett, DD and Ghadermazi, P and Trumble, BC and Kaplan, H and Stieglitz, J and Rodriguez, DE and Relman, DA and Sonnenburg, ED and Gurven, M and Good, BH and Sonnenburg, JL},
title = {Prehistoric global migration of vanishing gut microbes with humans.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42844483},
issn = {1476-4687},
abstract = {The gut microbiome is crucial for health and is affected strongly by lifestyle[1]. Many microorganisms commonly found in non-industrialized populations are disappearing or have become extinct in industrialized populations[2-6]. Studying which microorganisms have been long-term residents of the human gut and may have co-evolved with humans[2,7,8] could provide insights into how microbial biodiversity loss affects human health. However, the genetic complexities of microbial evolution and the plasticity of gut microbiome composition have made it challenging to resolve the evolutionary history of these long-term associations. Here we performed deep metagenomic sequencing of the Tsimane horticulturalists of Bolivia and compared their gut microbiomes with those of the Hadza hunter-gatherers of Tanzania[3]. These two populations, whose ancestors have been separated for tens of thousands of years, share 1,231 microbial species, most of which are rare in or absent from industrialized populations. Population genetic analyses of 636 of the shared species revealed patterns of microbial divergence and gene flow consistent with prehistoric human co-migration, with estimated split times that approximately align with human migration out of Africa and into the Americas. Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia. However, many of these species are now vanishing from industrialized populations and the consequences for human health remain uncertain.},
}

@article {pmid42844624,
year = {2026},
author = {Yoon, J and Lee, B and Yoo, KC and Kwak, MJ and Song, HJ and Hwang, CY and Chung, Y and Kim, K and Kwon, SK and Song, JY and Yoon, HS and Kim, JF},
title = {Novel Antarctic chemolithotroph drives iron biomineralization.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42844624},
issn = {2049-2618},
mesh = {*Iron/metabolism ; *Geologic Sediments/microbiology/chemistry ; Antarctic Regions ; *Biomineralization ; Oxidation-Reduction ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; *Chemoautotrophic Growth ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Iron, the most abundant redox-active metal in the Earth's crust, is coupled to numerous biogeochemical cycles. However, the mechanisms of iron oxidation and the organisms involved remain incompletely understood. Banded iron formations (BIFs) are a major reservoir of iron ore in the Precambrian sedimentary record, yet the biological contribution to their genesis remains a subject of unresolved debate. While large-scale BIF deposition largely ceased after the Proterozoic, microbial activity in modern Holocene sediments under fluctuating redox conditions provides a unique opportunity to examine mechanisms reminiscent of ancient iron cycling. Here, we report the stratigraphic sequence of microbiome profiles recorded in laminated facies with iron-containing crystalline illite in the embayment sediments beneath the Larsen C Ice Shelf (LCIS) in Antarctica during the Holocene.

RESULTS: LCIS sediments record microbial community shifts tightly coupled to environmental changes throughout the Holocene. Metagenomic analyses revealed three dominant microbial phases corresponding to geological facies boundaries. The open marine setting (phase A) showed higher taxonomic richness, whereas the sub-ice shelf sediments (phases B and C) were largely anoxic and characterized by diverse chemolithoautotrophic metabolisms. Keystone taxa including uncultured members of Thermodesulfovibrionia, as well as unique microbial communities and metabolisms, were evident in the aphotic, anoxic seawater; metagenomic analyses further revealed chemolithotrophy. The Thermodesulfovibrionia bacterium, visualized using fluorescence in situ hybridization and designated as "Candidatus Mariimomonas ferrooxydans", formed a novel clade in the phylum Nitrospirota. Metagenome-assembled genome analysis identified a putative outer-membrane Fe(II) oxidase, Cyc2, whose Fe(II)-oxidation activity was experimentally confirmed.

CONCLUSION: Our findings document the interaction between microbiome and environment, illustrating how LCIS sediments preserve a dynamic record of microbial community responses to environmental transitions. These results provide critical insights into microbial iron mineralization, echoing the biogeochemistry of the geologic past, particularly synglacial iron formation during the Neoproterozoic Snowball Earth. Video Abstract.},
}

*Iron/metabolism
*Geologic Sediments/microbiology/chemistry
Antarctic Regions
*Biomineralization
Oxidation-Reduction
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
*Chemoautotrophic Growth
RNA, Ribosomal, 16S/genetics
Phylogeny
Metagenomics/methods
Seawater/microbiology

@article {pmid42845172,
year = {2026},
author = {Xu, Q and Song, Y and Yu, H and Wang, Y and Gu, HF},
title = {Gut Microbiota Modulation by Abelmoschus manihot (L.) Improves Circulating Metabolites and Alleviates Diabetic Nephropathy in db/db Mice.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e5630909},
pmid = {42845172},
issn = {2314-6141},
support = {CPU20200228//Suzhong Pharmaceutical Group Co. Ltd/ ; },
mesh = {Animals ; *Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Abelmoschus/chemistry ; Male ; Metabolomics ; Metabolome/drug effects ; Diabetes Mellitus, Experimental/drug therapy ; *Plant Extracts/pharmacology ; Diabetes Mellitus, Type 2/drug therapy ; Disease Models, Animal ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; },
abstract = {BACKGROUND: Huangkui capsule (HKC), derived from the ethanol extract of Abelmoschus manihot (L.) flowers, is widely used in China for treating kidney diseases, including diabetic nephropathy (DN). Our previous study demonstrated that HKC modulates the intestinal microbiota and circulating metabolites in non-obese diabetic mice, a type 1 diabetes model. To further explore its efficacy, we evaluated HKC in db/db mice, a well-established type 2 diabetes and DN model.

METHODS: An HKC cohort studied in 2022 was compared with historical Ctrl and DN cohorts studied in 2021. Shotgun metagenomic sequencing was performed to characterize intestinal microbiota changes, while liquid chromatography-mass spectrometry (LC-MS)-based plasma metabolomics was used to identify alterations in circulating metabolites. The biological functions of the altered microbiota and plasma metabolites were analyzed, and the potential association between the intestinal microbiome and plasma metabolome was evaluated.

RESULTS: Compared with the historical DN cohort, the HKC cohort had higher abundances of Streptococcaceae, Streptococcus, and Massilimaliae and lower abundances of Alloprevotella and Prevotellamassilia in exploratory comparisons. In the HKC-versus-DN comparison, the archived gene set enrichment analysis reported 15 pathways with nominal positive enrichment. Additionally, 12 plasma metabolites were upregulated and 14 downregulated, including branched-chain amino acids (DL-leucine, DL-valine, D-isoleucine), organic acids (N-methyl-α-aminoisobutyric acid, guanidineacetic acid), and choline.

CONCLUSION: In db/db mice, the cohort receiving A. manihot (L.)-derived HKC had lower urinary albumin-to-creatinine ratio (UACR) and different intestinal microbiota and plasma metabolite profiles than the historical DN cohort, highlighting its therapeutic potential for DN.},
}

Animals
*Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Abelmoschus/chemistry
Male
Metabolomics
Metabolome/drug effects
Diabetes Mellitus, Experimental/drug therapy
*Plant Extracts/pharmacology
Diabetes Mellitus, Type 2/drug therapy
Disease Models, Animal
Mice, Inbred C57BL
*Drugs, Chinese Herbal/pharmacology

@article {pmid42845237,
year = {2026},
author = {Shannon, E and Devotta, H and Ndwandwe, C and Kim, S and Yao, L and Kareem, L and Walters, A and Korpela, K and Hurley, S and Lunjani, N and Koc, F and Mathur, H and Ambikan, A and Neogi, U and Friess, L and van Sinderen, D and Stanton, C and Venter, C and Walter, J and Hourihane, J and O'Mahony, L},
title = {Gut microbial metabolism of peanuts generates immunoregulatory metabolites.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743944},
doi = {10.1080/19490976.2026.2743944},
pmid = {42845237},
issn = {1949-0984},
mesh = {Humans ; *Arachis/metabolism/immunology/microbiology/chemistry ; Bifidobacterium/metabolism/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Leukocytes, Mononuclear/immunology ; Fermentation ; Infant ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fatty Acids, Volatile/metabolism ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Interleukin-10/immunology ; Cytokines ; },
abstract = {Early life introduction of potentially allergenic foods such as peanuts is important for the prevention of food allergy. We hypothesized that peanut consumption may indirectly influence the immune system via effects on gut microbiota composition and metabolism. In vitro human fecal fermentations with peanuts were performed. Changes in taxa and metabolism were measured using 16S rRNA gene sequencing and untargeted metabolomics respectively. Ten Bifidobacterium strains were cultured in vitro in the presence of peanuts and human peripheral blood mononuclear cells (PBMCs) were used to assess culture supernatant immunomodulatory effects. Fecal samples were sequenced from children at 12 months (n = 343) using whole genome metagenomic sequencing. An online questionnaire was used to collect dietary data. Human fecal bioreactor fermentation of peanut flour, previously subjected to in vitro simulated gastrointestinal digestion, resulted in significant production of short-chain fatty acids (SCFA), associated with increased relative abundance of Megasphaera and bifidobacteria. 188 metabolites were significantly altered following peanut fermentation. Bifidobacterium longum subspecies longum strain 160 efficiently metabolized peanut associated with secretion of indole-3-lactic acid (ILA). Following growth on peanuts, bifidobacterial supernatants enhanced IL-10 secretion, but reduced TNF-alpha and IL-5 secretion from stimulated PBMCs. Peanut consumption by 12-month-old children was associated with significant changes in gut microbiota composition including increased levels of Prevotella buccae, Megasphaera micronuciformis and Blautia wexlerae. Peanuts are metabolized by microbes generating immunoregulatory metabolites such as SCFAs and ILA. These metabolites may represent one potential mechanism underlying the allergy-protective effects of early peanut consumption, which requires further validation in high-risk allergy cohorts.},
}

Humans
*Arachis/metabolism/immunology/microbiology/chemistry
Bifidobacterium/metabolism/genetics
Feces/microbiology
*Gastrointestinal Microbiome
Leukocytes, Mononuclear/immunology
Fermentation
Infant
*Bacteria/classification/genetics/metabolism/isolation & purification
Fatty Acids, Volatile/metabolism
RNA, Ribosomal, 16S/genetics
Female
Male
Interleukin-10/immunology
Cytokines

@article {pmid41791848,
year = {2026},
author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ},
title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.},
journal = {Gut},
volume = {75},
number = {11},
pages = {2118-2129},
doi = {10.1136/gutjnl-2025-337478},
pmid = {41791848},
issn = {1468-3288},
mesh = {Humans ; Cross-Sectional Studies ; *Colorectal Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Aged ; Colonoscopy ; Feces/microbiology ; Metagenome ; Neoplasm Staging ; },
abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.},
}

Humans
Cross-Sectional Studies
*Colorectal Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
Aged
Colonoscopy
Feces/microbiology
Metagenome
Neoplasm Staging

@article {pmid41806991,
year = {2026},
author = {Martinez-Tellez, B and Schönke, M and Kovynev, A and Garcia-Dominguez, E and Ortiz-Alvarez, L and Verhoeven, A and Gacesa, R and Vich Vila, A and Ducarmon, QR and Jimenez-Pavon, D and Gomez-Cabrera, MDC and Weersma, RK and Smits, WK and Giera, M and Ruiz, JR and Rensen, PC},
title = {Roseburia inulinivorans increases muscle strength.},
journal = {Gut},
volume = {75},
number = {11},
pages = {2130-2142},
doi = {10.1136/gutjnl-2025-336980},
pmid = {41806991},
issn = {1468-3288},
mesh = {Animals ; Humans ; *Muscle Strength/physiology ; Mice ; Female ; Male ; *Eubacteriales/physiology ; *Gastrointestinal Microbiome/physiology ; Muscle, Skeletal/physiology ; Adult ; Aged ; Young Adult ; Hand Strength/physiology ; Mice, Inbred C57BL ; *Probiotics/administration & dosage ; Middle Aged ; },
abstract = {BACKGROUND: Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored.

OBJECTIVE: We aimed to investigate whether specific gut microbial species are associated with muscle strength and to explore underlying mechanisms linking the gut microbiota to muscle health.

DESIGN: We conducted metagenomic analyses in cohorts of younger and older adults extensively phenotyped for muscle strength. Associations were tested between bacterial taxa and performance measures. Causality was assessed by oral supplementation of candidate species in antibiotic-treated mice. Metabolomic profiling and muscle phenotyping were performed to elucidate mechanisms.

RESULTS: The relative abundance of Roseburia inulinivorans, but not other Roseburia species, was positively associated with multiple strength measures including handgrip, leg press and bench press in humans. Supplementation of R. inulinivorans in mice significantly enhanced forelimb grip strength, whereas other Roseburia species had no effect. Metabolomic analyses revealed that R. inulinivorans reduced amino acid concentrations in the caecum and plasma, while activating the purine and pentose phosphate pathway in muscle. These changes coincided with increased muscle fibre size and a shift from type I to type II fibres. Accordingly, we observed that the relative abundance of R. inulinivorans is lower in older adults compared with young adults.

CONCLUSION: R. inulinivorans emerges as a species-specific modulator of muscle strength, linking gut microbiota to muscle metabolism and function. These findings support its potential as a probiotic candidate for nutraceutical interventions targeting age-related muscle-wasting diseases.

TRIAL REGISTRATION NUMBER: NCT02365129.},
}

Animals
Humans
*Muscle Strength/physiology
Mice
Female
Male
*Eubacteriales/physiology
*Gastrointestinal Microbiome/physiology
Muscle, Skeletal/physiology
Adult
Aged
Young Adult
Hand Strength/physiology
Mice, Inbred C57BL
*Probiotics/administration & dosage
Middle Aged

@article {pmid42319773,
year = {2026},
author = {Ali, H and Rieuwpassa, IE and Hamrun, N and Marlina, E and Yulianty, R and Akbar, FH and Siti Hartina Dewang, DA},
title = {Longitudinal effects of antiretroviral therapy on the oral microbiota in people living with HIV: A systematic review.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {73},
number = {3},
pages = {279-287},
doi = {10.1556/030.2026.02910},
pmid = {42319773},
issn = {1588-2640},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; *Microbiota/drug effects ; *Mouth/microbiology ; Longitudinal Studies ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {People living with HIV frequently experience oral microbial dysbiosis, contributing to oral disease burden and reduced quality of life. Although antiretroviral therapy (ART) effectively suppresses viral replication and promotes immune recovery, its longitudinal effects on the oral microbiota remain incompletely understood. This systematic review aimed to evaluate longitudinal changes in oral microbiota composition and diversity in people living with HIV before and after ART initiation. A systematic review was conducted in accordance with PRISMA guidelines and registered in PROSPERO (CRD420251164326). Electronic searches were performed in PubMed, ScienceDirect, Wiley Online Library, DOAJ, and Google Scholar for studies published between 2015 and 2024. Eligible studies included longitudinal human studies reporting pre- and post-ART oral microbiota data using 16S rRNA gene sequencing or metagenomic approaches. Methodological quality was assessed using Joanna Briggs Institute critical appraisal tools. Due to substantial heterogeneity, findings were synthesized narratively. Six longitudinal studies met the inclusion criteria. ART was associated with partial and non-uniform modulation of the oral microbiota. Changes in beta diversity and selective taxonomic shifts were commonly reported, whereas changes in alpha diversity were inconsistent. Taxonomic alterations were more evident at the genus level, while several dominant oral genera remained stable before and after ART. Evidence linking oral microbiota changes with immune recovery was limited. Longitudinal evidence indicates that ART induces selective and heterogeneous changes in the oral microbiota without consistent normalization toward a non-HIV microbial profile, underscoring the importance of integrating oral health into long-term HIV care.},
}

Humans
*HIV Infections/drug therapy/microbiology
*Microbiota/drug effects
*Mouth/microbiology
Longitudinal Studies
*Anti-HIV Agents/therapeutic use
Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid42321256,
year = {2026},
author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L},
title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42321256},
issn = {2055-5008},
support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; },
mesh = {Animals ; *Methane/metabolism ; Cattle ; *Polyphenols/metabolism/pharmacology ; *Hydrogen/metabolism ; Archaea/metabolism/genetics/classification ; Rumen/microbiology ; Female ; *Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Multiomics ; Animal Feed/analysis ; Microbiota ; },
abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.},
}

Animals
*Methane/metabolism
Cattle
*Polyphenols/metabolism/pharmacology
*Hydrogen/metabolism
Archaea/metabolism/genetics/classification
Rumen/microbiology
Female
*Bacteria/metabolism/genetics/classification
Metagenomics/methods
Multiomics
Animal Feed/analysis
Microbiota