Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Javdan, Bahar; Lopez, Jaime G.; Chankhamjon, Pranatchareeya; Lee, Ying Chiang J.; Hull, Raphaella; Wu, Qihao; Wang, Xiaojuan; Chatterjee, Seema; Donia, Mohamed S.

doi:10.1016/j.cell.2020.05.001

Cited by 283 publications

(298 citation statements)

References 91 publications

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“…Proteins are metabolized by gut microbes into small metabolites, such as short-chain fatty acids (SCFAs), neurotransmitters, and organic acids, that have physiological effects both locally and systemically ( 83 – 87 ). A plethora of widely consumed dietary and nondietary constituents, such as emulsifiers ( 88 – 90 ), nonnutritive sweeteners ( 91 – 96 ), trehalose ( 97 ), probiotics ( 98 – 101 ), omega-3 fatty acids ( 102 ), and medications ( 103 – 105 ), were shown to feature considerable microbiome-mediated health impacts and are a subject of intensive research that is beyond the scope of this review.…”

Section: Nutrition-microbiome Cross Talkmentioning

confidence: 99%

The Gut Microbiome and Individual-Specific Responses to Diet

2020

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Nutritional content and timing are increasingly appreciated to constitute important human variables collectively impacting all aspects of human physiology and disease. However, person-specific mechanisms driving nutritional impacts on the human host remain incompletely understood, while current dietary recommendations remain empirical and nonpersonalized. Precision nutrition aims to harness individualized bodies of data, including the human gut microbiome, in predicting person-specific physiological responses (such as glycemic responses) to food.

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Section: Nutrition-microbiome Cross Talkmentioning

confidence: 99%

The Gut Microbiome and Individual-Specific Responses to Diet

2020

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“…As more functional microbiome datasets become publicly available, one could organize microbe-sets by their shared experimental conditions or treatment. For instance, one approach is to collect microbes with differential abundance after drug treatment to compile a microbe-set library for drugs 40,41 . Microbe sets can also be constructed as fuzzy sets, where the membership between a microbe-set and individual microbe can be partial.…”

Section: Discussionmentioning

confidence: 99%

Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data

Kou¹,

Xu²,

Zhu³

et al. 2020

Sci Rep

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The commensal microbiome is known to influence a variety of host phenotypes. Microbiome profiling followed by differential abundance analysis has been established as an effective approach to study the mechanisms of host-microbiome interactions. However, it is challenging to interpret the collective functions of the resultant microbe-sets due to the lack of well-organized functional characterization of commensal microbiome. We developed microbe-set enrichment analysis (MSEA) to enable the functional interpretation of microbe-sets by examining the statistical significance of their overlaps with annotated groups of microbes that share common attributes such as biological function or phylogenetic similarity. We then constructed microbe-set libraries by query PubMed to find microbe-mammalian gene associations and disease associations by parsing the Disbiome database. To demonstrate the utility of our novel MSEA methodology, we carried out three case studies using publicly available curated knowledge resource and microbiome profiling datasets focusing on human diseases. We found MSEA not only yields consistent findings with the original studies, but also recovers insights about disease mechanisms that are supported by the literature. Overall, MSEA is a useful knowledge-based computational approach to interpret the functions of microbes, which can be integrated with microbiome profiling pipelines to help reveal the underlying mechanism of host-microbiome interactions.

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“…1). There are 108,506 prokaryote genomes that are associated with human (Chromosome(1,539), Complete (8,179), Contig(57,034), Scaffold(41,754) ) ( Fig. 1a).…”

Section: Ncbi Prokaryotes Genome Databasesmentioning

confidence: 99%

“…Further, its disorder is a potential risk factor of various chronic diseases such as type 2 diabetes, gastrointestinal cancer, and brain disorders [4][5][6]. Furthermore, the gut microbiota is one of the crucial factors which in uence drug effectiveness owing to its effects on drug metabolism [7,8]. Despite decades of researches, the composition of the gut microbiota remains unidenti ed.…”

Section: Introductionmentioning

confidence: 99%

Recovery of Human Gut Microbiota Genomes Substantially With Third-generation Sequencing

Li¹,

Jin²,

Pan³

et al. 2020

Preprint

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BackgroundHuman gut microbiota modulates normal physiological functions, such as the maintenance of barrier homeostasis and the modulation of metabolism, and various chronic diseases including type 2 diabetes and gastrointestinal cancer. Despite decades of researches, the composition of the gut microbiota remains unexplored and unidentified. ResultsHere we established an effective extraction method to obtain high-quality gut microbiota genomic DNA and detected the samples with third-generation sequencing technology. We acquired a quite big data form each sample and assembled many reliable contigs. Not only enormous unknown genes, but also several new bacteria subspecies or species were identified. ConclusionsThis work provides a novel and reliable framework to recover gut microbiota genomes substantially, facilitating the understanding of the roles of the microbiome that underlie in human health and disease.

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Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Cited by 283 publications

References 91 publications

The Gut Microbiome and Individual-Specific Responses to Diet

The Gut Microbiome and Individual-Specific Responses to Diet

Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data

Recovery of Human Gut Microbiota Genomes Substantially With Third-generation Sequencing

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