Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications

Gastroenterology, Journal Year: 2022, Volume and Issue: 164(2), P. 272 - 288

Published: Sept. 23, 2022

Background & AimsWe investigate interrelationships between gut microbes, metabolites, and cytokines that characterize COVID-19 its complications, we validate the results with follow-up, Japanese 4D (Disease, Drug, Diet, Daily Life) microbiome cohort, non-Japanese data sets.MethodsWe performed shotgun metagenomic sequencing metabolomics on stools cytokine measurements plasma from 112 hospitalized patients SARS-CoV-2 infection non–COVID-19 control individuals matched by important confounders.ResultsMultiple correlations were found COVID-19–related microbes (eg, oral short-chain fatty acid producers) metabolites branched-chain aromatic amino acids, carbohydrates, neurotransmitters, vitamin B6). Both also linked to inflammatory dynamics interferon γ, λ3, interleukin 6, CXCL-9, CXCL-10). Such detected highly in severe disease pneumonia; moderately high D-dimer level, kidney dysfunction, liver dysfunction groups; but rarely diarrhea group. We confirmed concordances of altered spermidine, putrescine, B6) their corresponding microbial functional genes. Results metabolomic alterations cross-sectional set partly concordant those follow-up set. Microbial signatures for distinct diabetes, bowel disease, proton-pump inhibitors overlapping rheumatoid arthritis. Random forest classifier models using microbiomes can predict disease. The showed moderate concordance Hong Kong Japan.ConclusionsMultiomics analysis revealed multiple microbe-metabolite-cytokine COVID-19related complications few gastrointestinal suggesting microbiota-mediated immune responses organ sites. Our underscore existence a gut-lung axis COVID-19. sets. confounders. Multiple Japan. Multiomics

Language: Английский

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The global human gut microbiome: genes, lifestyles, and diet

Trends in Molecular Medicine, Journal Year: 2023, Volume and Issue: 29(10), P. 789 - 801

Published: July 27, 2023

Language: Английский

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A metagenomic catalog of the early-life human gut virome

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 29, 2024

Early-life human gut microbiome is a pivotal driver of homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish Early-Life Gut Virome (ELGV), catalog 160,478 non-redundant DNA RNA sequences from 8130 virus-like particles (VLPs) enriched or bulk metagenomes in first three years life. By clustering, 82,141 species are identified, 68.3% which absent existing databases built mainly adults, 64 8 based on VLPs-enriched metagenomes, respectively, exhibit potentials biomarkers to distinguish infants adults. With largest longitudinal population profiled by either metagenomic sequencing, track inherent instability temporal development early-life virome, identify differential viruses associated with multiple clinical factors. The mother-infant shared virome interactions between bacteriome early life further expanded. Together, ELGV provides most comprehensive complete blueprint facilitating discovery pediatric disease-virome associations future.

Language: Английский

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Examining the healthy human microbiome concept

Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 23, 2024

Language: Английский

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Signals triggering prophage induction in the gut microbiota

Molecular Microbiology, Journal Year: 2022, Volume and Issue: 118(5), P. 494 - 502

Published: Sept. 27, 2022

Compared to bacteria of the gut microbiota, bacteriophages are still poorly characterised, and their physiological importance is far less known. Temperate phages probably a major actor in gut, as it estimated that 80% intestinal lysogens, meaning they carrying prophages. In addition, prophage induction rates higher than vitro. However, studies on signals leading have essentially focused genotoxic agents with poor relevance for this environment. review, we sum up recent findings about able trigger gut. Three categories at play: those originating from interactions between microbes, human or animal host physiology external intakes. These results highlight diversity factors influencing start unveil ways by which microbiota composition may be modulated.

Language: Английский

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Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy

Gut Microbes, Journal Year: 2023, Volume and Issue: 15(1)

Published: June 22, 2023

Although changes in gut microbiome have been associated with the development of T2D and its complications, role virome remains largely unknown. Here, we characterized alterations complications diabetic nephropathy (DN) by metagenomic sequencing fecal viral-like particles. Compared controls, subjects, especially those DN, had significantly lower viral richness diversity. 81 species were identified to be altered including a decrease some phages (e.g. Flavobacterium phage Cellulophaga phaga). DN subjects depleted 12 species, Bacteroides phage, Anoxybacillus virus Brevibacillus enriched 2 (Shigella Xylella phage). Multiple functions, particularly lysing host bacteria, markedly reduced DN. Strong viral-bacterial interactions healthy controls disrupted both Moreover, combined use bacterial markers achieved powerful diagnostic performance for AUC 99.03% 98.19%, respectively. Our results suggest that complication are significant diversity, specific loss multiple disruption correlations. The potential

Language: Английский

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Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 15, 2024

As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting in metagenomic data not trivial. In past few years, many bioinformatic identification tools have been developed this task, making it challenging to choose right tools, parameters, and cutoffs. all these measure different biological signals, use algorithms training reference databases, imperative conduct an independent benchmarking give users objective guidance.

Language: Английский

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Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

The microbiota in individual habitats differ both relative composition and absolute abundance. While sequencing approaches determine the abundances of taxa genes, they do not provide information on their abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from abundance data. Applying our prediction model large-scale metagenomic dataset (n = 34,539), demonstrated that load is major determinant gut microbiome variation associated with numerous host factors, including age, diet, medication. We further found for several diseases, changes load, rather than disease condition itself, more strongly explained alterations patients' microbiome. Adjusting this effect substantially reduced statistical significance majority disease-associated species. Our analysis reveals confounder studies, highlighting its importance understanding health disease.

Language: Английский

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The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

Viruses, Journal Year: 2023, Volume and Issue: 15(1), P. 173 - 173

Published: Jan. 6, 2023

Virome research is a rapidly growing area in the microbiome field that increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of virota. In this review, we describe must be considered to accurately report virome composition and current knowledge on health IBD. First, description shows strong biases related wetlab (e.g., VLP enrichment) bioinformatics approaches (viral identification classification). Second, IBD patients show consistent viral imbalances characterized by high relative abundance phages belonging Caudovirales low Microviridae. Simultaneously, sporadic contraction CrAss-like potential expansion lysogenic intestinal are observed. Finally, despite numerous studies have conducted diversity analysis, it difficult draw firm conclusions due biases. Overall, present many environmental factors influence virome, its consensus IBD, contributing hypothesis called “positive feedback loop” may play role pathophysiology

Language: Английский

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Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products

Microorganisms, Journal Year: 2023, Volume and Issue: 11(8), P. 1899 - 1899

Published: July 27, 2023

Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial therapeutic applications. The human skin an ecological niche which harbours a rich compositional microbiome stemming from multifactorial interactions between host microbiota facilitated by exploitable effector compounds. Advances in understanding microbial colonisation mechanisms alongside species strain have revealed novel chemical displays applicative potential. Studies elucidating organismal interfaces concomitant central processes biology begun to unravel potential wealth molecules can exploited for their proposed functions. A variety skin-microbiome-derived display applications, ranging antioncogenic agents relevant cancer therapy treatment strategies antimicrobial-resistant bacterial fungal infections. Considerable opportunities emerged translation personal care products, such as topical mitigate various conditions acne eczema. Adjacent compound developments focused on cosmetic applications reducing ageing its associated changes properties microbiome. contains applications; however, considerable work required vitro findings vivo models ensure translatability.

Language: Английский

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