Genetic and transcriptional analysis of human host response to healthy gut microbiota

Allison L. Richards, Michael B. Burns, Adnan Alazizi, Luis B. Barreiro, Roger Pique-Regi, Ran Blekhman, Francesca Luca

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of hostmicrobiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with diseases that have been previously linked to the microbiome, such as obesity and colorectal cancer. In addition, our experimental system allowed us to identify 87 host single nucleotide polymorphisms (SNPs) that show allele-specific expression in 69 genes. Furthermore, for 12 SNPs in 12 different genes, allele-specific expression is conditional on the exposure to the microbiota. Of these 12 genes, 8 have been associated with diseases linked to the gut microbiota, specifically colorectal cancer, obesity, and type 2 diabetes. Our study demonstrates a scalable approach to study host-gut microbiota interactions and can be used to identify putative mechanisms for the interplay between host genetics and the microbiota in health and disease.

Original languageEnglish (US)
Article numbere00067
JournalmSystems
Volume1
Issue number4
DOIs
StatePublished - Jul 1 2016

Bibliographical note

Funding Information:
This work, including the efforts of Ran Blekhman, was funded by The Randy Shaver Cancer Research and Community Fund. This work, including the efforts of Roger Pique-Regi and Francesca Luca, was funded by HHS | NIH | National Institute of General Medical Sciences (NIGMS) (R01GM109215). This work, including the efforts of Ran Blekhman, was funded by American Cancer Society (ACS) (124166-IRG-58-001-55-IRG53).

Keywords

  • Complex traits
  • Gene expression
  • Genetics
  • Host response
  • Hostmicrobiota interaction

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