METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Microbiome, Год журнала: 2022, Номер 10(1)

Опубликована: Фев. 16, 2022

Advances in microbiome science are being driven large part due to our ability study and infer microbial ecology from genomes reconstructed mixed communities using metagenomics single-cell genomics. Such omics-based techniques allow us read genomic blueprints of microorganisms, decipher their functional capacities activities, reconstruct roles biogeochemical processes. Currently available tools for analyses data can annotate depict metabolic functions some extent; however, no standardized approaches currently the comprehensive characterization predictions, metabolite exchanges, interactions, contributions cycling.

Язык: Английский

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Implications of hydrogen sulfide in colorectal cancer: Mechanistic insights and diagnostic and therapeutic strategies

Redox Biology, Год журнала: 2023, Номер 59, С. 102601 - 102601

Опубликована: Янв. 7, 2023

Hydrogen sulfide (H2S) is an important signaling molecule in colorectal cancer (CRC). It produced the colon by catalytic synthesis of colonocytes' enzymatic systems and release intestinal microbes, oxidatively metabolized mitochondria. Both endogenous H2S colonic epithelial cells exogenous lumen contribute to onset progression CRC. The up-regulation synthetases thought be cause elevated levels CRC cells. Different diagnostic probes combination therapies, as well tumor treatment approaches through modulation, have been developed recent years become active area investigation for diagnosis In this review, we focus on specific mechanisms production oxidative metabolism function occurrence, progression, diagnosis, We also discuss present challenges provide insights into future research burgeoning field.

Язык: Английский

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Another renaissance for bile acid gastrointestinal microbiology

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2024, Номер 21(5), С. 348 - 364

Опубликована: Фев. 21, 2024

Язык: Английский

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Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota

Nature Metabolism, Год журнала: 2023, Номер 5(9), С. 1526 - 1543

Опубликована: Авг. 3, 2023

Abstract Restriction of methionine (MR), a sulfur-containing essential amino acid, has been reported to repress cancer growth and improve therapeutic responses in several preclinical settings. However, how MR impacts progression the context intact immune system is unknown. Here we report that while inhibiting immunocompromised mice, reduces T cell abundance, exacerbates tumour impairs response immunotherapy immunocompetent male female mice. Mechanistically, microbial production hydrogen sulfide, which critical for survival/activation. Dietary supplementation sulfide donor or precursor, methionine, stimulates antitumour immunity suppresses progression. Our findings reveal an unexpected negative interaction between MR, sulfur deficiency further uncover vital role gut microbiota mediating this interaction. study suggests any possible anticancer benefits require careful consideration both system.

Язык: Английский

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Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

Cell, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a restoration strategy comprising diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) randomized controlled feeding trial healthy Canadian adults. The restore diet, despite reducing diversity, enhanced persistence L. reuteri strain from rural Papua New Guinea (PB-W1) redressed several features altered by industrialization. also beneficially microbiota-derived plasma metabolites implicated etiology Considerable cardiometabolic benefits were observed independently administration, which could be accurately predicted baseline diet-responsive features. findings suggest intervention targeted toward restoring can improve host-microbiome interactions likely underpin pathologies, guide recommendations development therapeutic nutritional strategies.

Язык: Английский

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Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction

FEMS Microbiology Reviews, Год журнала: 2023, Номер 47(5)

Опубликована: Сен. 1, 2023

Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is dissimilatory sulfite reductase encoded by genes dsrAB. Based on analysis 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine diversity with potential for sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode energy metabolism. We show: (i) 19 out 23 bacterial 2 4 archaeal phyla harbor uncharacterized SRM, (ii) four including Desulfobacterota to switch between oxidation, (iii) combination as well presence/absence different dsrAB-types, dsrL-types dsrD provides guidance inferred direction further provide an updated dsrAB database > 60% taxonomically resolved, uncultured family-level lineages recommendations existing dsrAB-targeted primers environmental surveys. Our work summarizes insights into ecophysiology newly discovered puts context major recent changes taxonomy, up-to-date framework study a context.

Язык: Английский

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Disease-specific loss of microbial cross-feeding interactions in the human gut

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 20, 2023

Abstract Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us identify rank that significantly affected loss partners in 10 out 11 diseases. When applied Crohn’s disease case-control study, our approach identifies lack species with the ability consume hydrogen sulfide as main distinguishing microbiome feature disease. We propose conceptual framework will help prioritize in-depth analyses, experiments clinical targets, targeting restoration microbial is promising mechanism-informed strategy reconstruct healthy ecosystem.

Язык: Английский

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Diversity and ecology of microbial sulfur metabolism

Nature Reviews Microbiology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 17, 2024

Язык: Английский

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DsrMKJOP is the terminal reductase complex in anaerobic sulfate respiration

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(6)

Опубликована: Янв. 29, 2024

Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical sulfur cycle. In spite of its importance to and carbon cycles, industrial processes, human health, it still not clear how sulfide coupled energy conservation. A central step pathway sulfite by DsrAB reductase, which leads production DsrC-trisulfide. membrane-bound complex, DsrMKJOP, present most organisms that have DsrC, involvement conservation has been inferred from sequence analysis, but precise function was so far determined. Here, we studies revealing DsrMKJOP complex reducer Archaeoglobus fulgidus works as menadiol:DsrC-trisulfide oxidoreductase. Our results reveal close interaction between DsrC-trisulfide show electrons quinone pool reduce consecutively DsrM hemes b , DsrK noncubane [4Fe-4S] 3+/2+ catalytic center, finally with concomitant release sulfide. These clarify role this widespread respiratory membrane support suggestion contributes upon last DSR.

Язык: Английский

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Influence of Gut Microbiota-Mediated Immune Regulation on Response to Chemotherapy

Pharmaceuticals, Год журнала: 2024, Номер 17(5), С. 604 - 604

Опубликована: Май 8, 2024

The involvement of the gut microbiota in anti-cancer treatment has gained increasing attention. Alterations to structure and function bacteria are important factors development cancer as well efficacy chemotherapy. Recent studies have confirmed that related metabolites influence pharmacological activity chemotherapeutic agents through interactions with immune system. This review aims summarize current knowledge how malignant tumor chemotherapy affect microbiota, regulates host response, between response advances strategies for efficiency based on also described. Deciphering complex homeostasis maintained by immunity provides a solid scientific basis bacterial intervention

Язык: Английский

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