Analysis of gut microbiota–An ever changing landscape

Michael J. Sadowsky, Christopher Staley, Cheryl Heiner, Richard Hall, Colleen R. Kelly, Lawrence Brandt, Alexander Khoruts

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.

Original languageEnglish (US)
Pages (from-to)268-275
Number of pages8
JournalGut Microbes
Volume8
Issue number3
DOIs
StatePublished - May 4 2017

Keywords

  • Clostridium difficile
  • PacBio
  • SMRT sequencing
  • fecal microbial transplant
  • gut microbiota
  • next-generation sequencing

ASJC Scopus subject areas

  • Microbiology
  • Gastroenterology
  • Microbiology (medical)
  • Infectious Diseases

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  • Cite this

    Sadowsky, M. J., Staley, C., Heiner, C., Hall, R., Kelly, C. R., Brandt, L., & Khoruts, A. (2017). Analysis of gut microbiota–An ever changing landscape. Gut Microbes, 8(3), 268-275. https://doi.org/10.1080/19490976.2016.1277313