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Understanding the Organization, Composition & Functions of the Intestinal Microbiota

The Laboratory for Interdisciplinary Microbiome Research combines high throughput culturing and phenotyping methods with next-generation sequencing approaches to investigate the function of the human microbiome. The lab was one of the first to demonstrate that the human gut microbiome is readily cultured and that culturing reveals a greater microbial diversity (and metabolomic potential) than culture independent methods alone1.  The lab has generated a large collection of sequenced human microbiome isolates (>4000) and has established methods for targeted culturing of specific bacterial taxa. The lab has expertise in applying and improving next-generation sequencing approaches to characterize the microbiome with extensive expertise in bacterial profiling (16S), metagenomics and whole genome sequencing2.  The lab manages microbiome analysis for 2 large national cohorts3 and many smaller studies.  These methods and resources are being used for bioprospecting the microbiome4 to find novel biologics and live biotherapeutics to improve health across the life course, and to treat gut associated diseases.

Michael Surette:

Lab Website:

  1. Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med. 2016 Jul 1;8(1):72. PMID: 27363992;
  2. Derakhshani H, Bernier SP, Marko VA, Surette MG. Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. BMC Genomics. 2020 Jul 29;21(1):519. PMID: 32727443.
  3. Mann E, Shekarriz S, Surette MG. Human Gut Metagenomes Encode Diverse GH156 Sialidases. Appl Environ Microbiol. 2022 Dec 13;88(23):e0175522. PMID: 363943277.
  4. Moayyedi P, MacQueen G, Bernstein CN, Vanner S, Bercik P, Madsen KL, Surette M, Rioux JD, Dieleman LA, Verdú E, de Souza RJ, Otley A, Targownik L, Lavis J, Cunningham J, Marshall DA, Zelinsky S, Fernandes A. IMAGINE Network’s Mind And Gut Interactions Cohort (MAGIC) Study: a protocol for a prospective observational multicentre cohort study in inflammatory bowel disease and irritable bowel syndrome. BMJ Open. 2020 Oct 21;10(10):e041733 PMID: 33087380.