Enhancing Microbiome Research through Genome-Scale Metabolic Modeling

mSystems, Journal Year: 2021, Volume and Issue: 6(6)

Published: Dec. 14, 2021

Construction and analysis of genome-scale metabolic models (GEMs) is a well-established systems biology approach that can be used to predict growth phenotypes. The ability GEMs produce mechanistic insight into microbial ecological processes makes them appealing tools open range exciting opportunities in microbiome research.

Language: Английский

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Gut Bacteria Regulate the Pathogenesis of Huntington’s Disease in Drosophila Model

Frontiers in Neuroscience, Journal Year: 2022, Volume and Issue: 16

Published: June 2, 2022

Changes in the composition of gut microbiota are implicated pathogenesis several neurodegenerative disorders. Here, we investigated whether bacteria affect progression Huntington's disease (HD) transgenic Drosophila melanogaster (fruit fly) models expressing full-length or N-terminal fragments human mutant huntingtin (HTT) protein. We find that elimination commensal by antibiotics reduces aggregation amyloidogenic HTT and delays development motor defects. Conversely, colonization HD flies with Escherichia coli (E. coli), a known pathobiont links to neurodegeneration other morbidities, accelerates aggregation, aggravates immobility, shortens lifespan. Similar antibiotics, treatment small compounds such as luteolin, flavone, crocin beta-carotenoid, ameliorates phenotypes, promotes survival. Crocin prevents E. alters levels bacteria, which may be linked its protective effects. The opposing effects on defects, survival support involvement gut-brain networks HD.

Language: Английский

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Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re‐Analysis

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT Gut microbiota are fundamental for healthy animal function, but the evidence that host function can be predicted from taxonomy remains equivocal, and natural populations remain understudied compared to laboratory animals. Paired analyses of covariation in parameters powerful approaches characterise host–microbiome relationships mechanistically, especially wild animals also lab models, enabling insight into ecological basis at molecular cellular levels. The fruitfly Drosophila melanogaster is a preeminent model organism, amenable field investigation by ‘omic analyses. Previous work male D. guts analysed paired measurements (A) bacterial diversity abundance, measured 16S amplicon sequencing; (B) gut transcriptome, no signature was detected. Here, we re‐analyse those data comprehensively. We find orthogonal axes microbial genera, which correspond differential expression genes. differentially expressed gene sets were enriched functions including protein translation, mitochondrial respiration, immunity reproduction. Each set had distinct functional signature, suggesting flies exhibit range variation, microbiome variation. These findings lay foundation better connect ecology genetics leading host‐microbiome model.

Language: Английский

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Bioaccumulation and biotransformation of simvastatin in probiotic bacteria: A step towards better understanding of drug-bile acids-microbiome interactions

Frontiers in Pharmacology, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 9, 2023

Introduction: Although pharmacogenetics and pharmacogenomics have been at the forefront of research aimed finding novel personalized therapies, focus has recently extended to potential intestinal microbiota affect drug efficacy. Complex interplay gut with bile acids may significant repercussions on pharmacokinetics. However, far too little attention paid implication in simvastatin response which is characterized by large interindividual variations. The Aim: In order gain more insight into underlying mechanism its contribution assessing clinical outcome, aim our study was examine bioaccumulation biotransformation probiotic bacteria effect vitro conditions. Materials methods: Samples simvastatin, three different were incubated anaerobic conditions 37°C for 24 h. Extracellular intracellular medium samples collected prepared LC-MS analysis predetermined time points (0 min, 15 1 h, 2 4 6 h). concentrations analyzed LC-MS/MS. Potential pathways using a bioinformatics approach correlation experimental assay. Results: During incubation, transported cells leading over time, augmented upon addition after A decrease total level during incubation indicates that partly biotransformed bacterial enzymes. According results analysis, lactone ring most susceptible metabolic changes likely reactions include ester hydrolysis followed hydroxylation. Conclusion: Results reveal might be mechanisms altered bioavailability therapeutic effect. Since this based only selected strains , further in-depth needed elicit completely complex drug-microbiota-bile interactions overall could ultimately lead approaches lipid-lowering therapy.

Language: Английский

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The complex world of kefir: Structural insights and symbiotic relationships

Comprehensive Reviews in Food Science and Food Safety, Journal Year: 2024, Volume and Issue: 23(4)

Published: June 7, 2024

Abstract Kefir milk, known for its high nutritional value and health benefits, is traditionally produced by fermenting milk with kefir grains. These grains are a complex symbiotic community of lactic acid bacteria, acetic yeasts, other microorganisms. However, the intricate coexistence mechanisms within these microbial colonies remain mystery, posing challenges in predicting their biological functional traits. This uncertainty often leads to variability milk's quality safety. review delves into unique structural characteristics grains, particularly distinctive hollow structure. We propose hypotheses on formation, which appears be influenced aggregation behaviors members alliances. In systematic colonization process driven metabolite release, orchestrating spatiotemporal rearrangement ecological niches. place special emphasis dynamic changes community. Spatially, we observe variations species morphology distribution across different locations grain Temporally, highlights succession patterns community, shedding light evolving interactions.Furthermore, explore underpinning formation stable composition. The interplay cooperative competitive microorganisms ensures balance, contributing community's richness stability. foster diversity stability, whereas bolster mutualistic symbiosis. By deepening our understanding communities, can pave way future advancements development diversification starter cultures food fermentation processes.

Language: Английский

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Microbiome modeling: a beginner's guide

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: June 19, 2024

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, biotechnological applications interact with each other, their environment, hosts via ecological interactions. Our understanding microbiomes is still limited hampered by complexity. A concept improving this systems biology, which focuses on the holistic description biological utilizing experimental computational methods. An important set such methods are metaomics analyze output lists molecular features. These data integrated, interpreted, compiled into microbiome models, to predict, optimize, control behavior. There exists a gap between microbiologists modelers/bioinformaticians, stemming from lack interdisciplinary knowledge. This knowledge hinders establishment models analysis. review aims bridge tailored for microbiologists, researchers new modeling, bioinformaticians. To achieve goal, it provides an overview starting fundamental microbiomes, methods, common modeling formalisms, how facilitate control. It concludes guidelines repositories modeling. Each section entry-level information, example applications, references, serving as valuable resource comprehending navigating complex landscape research

Language: Английский

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Microbiome Modeling: A Beginner’s Guide

Published: Jan. 10, 2024

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, biotechnological applications interact with themselves, their environment, hosts via metabolites signaling molecules. Our understanding microbiomes is still limited hampered by complexity. A concept improving this systems biology, which focuses on the holistic description biological utilizing experimental computational methods. An important set such methods are metaomics analyze output lists molecular features. These data integrated, interpreted, compiled into microbiome models, to predict, optimize, control behavior. There exists a gap between microbiologists modelers/bioinformaticians, stemming from lack interdisciplinary knowledge. This knowledge hinders establishment models analysis. review aims bridge tailored for microbiologists, researchers new modeling, bioinformaticians. To achieve goal, it provides an overview starting fundamental microbiomes, metagenomics methods, modeling formalisms. Furthermore, explains model building, examples prediction, optimization, control. It concludes guidelines, software, repositories modeling. Each section entry-level information, serving as valuable resource comprehending navigating complex landscape research

Language: Английский

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Insect Lipid Metabolism in the Presence of Symbiotic and Pathogenic Viruses and Bacteria

Advances in experimental medicine and biology, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

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Succinate: A microbial product that modulates Drosophila nutritional physiology

Insect Science, Journal Year: 2021, Volume and Issue: 29(1), P. 315 - 318

Published: Feb. 24, 2021

Fig. S1. Effect of succinate (A) and fumarate (B) on Drosophila nutritional indices survival. S2. food intake (A,B) (C,D) supplemented diets. S3. Among-trial variation in for female male flies fed control diet without metabolite added. Please note: The publisher is not responsible the content or functionality any supporting information supplied by authors. Any queries (other than missing content) should be directed to corresponding author article.

Language: Английский

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A Functional Analysis of the Purine Salvage Pathway in Acetobacter fabarum

Journal of Bacteriology, Journal Year: 2022, Volume and Issue: 204(7)

Published: June 13, 2022

Acetobacter species are a major component of the gut microbiome fruit fly Drosophila melanogaster, widely used model organism. While range studies have illuminated impacts on their hosts, less is known about how association with host bacteria. A previous study identified that purine salvage locus was commonly found in associated Drosophila. In this study, we sought to verify functions predicted genes fabarum DsW_054 and test hypothesis these bacteria can utilize metabolites as sole source nitrogen. Targeted gene deletion complementation experiments confirmed encoding xanthine dehydrogenase (xdhB), urate hydroxylase (urhA), allantoinase (puuE) were required for growth respective substrates Utilization by significant because substrate nitrogenous waste product Drosophila, its accumulation excretory system detrimental both flies humans. The potential significance our findings homeostasis health discussed, implications interactions among microbiota members, which differ capacity IMPORTANCEAcetobacter flies, including melanogaster. We evaluated function bacterium Our results identify three urate, product. utilization other may play role survival environment. Future research into microbial metabolism lead therapies

Language: Английский

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