Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities

Zachery T. Lewis, Nicholas A. Bokulich, Karen M. Kalanetra, Santiago Ruiz-Moyano, Mark Underwood, David A. Mills

Research output: Contribution to journalArticle

15 Scopus citations

Abstract

Bifidobacteria are intestinal anaerobes often associated with gut health. Specific bifidobacterial species are particularly common in the gastrointestinal tract of breast-fed infants. Current short read next-generation sequencing approaches to profile fecal microbial ecologies do not discriminate bifidobacteria to the species level. Here we describe a low-cost terminal restriction fragment length polymorphism (TRFLP) procedure to distinguish between the common infant-associated bifidobacterial species. An empirical database of TRF sizes was created from both common reference strains and well-identified isolates from infant feces. Species-specific quantitative PCR validated bifidobacterial-specific TRFLP profiles from infant feces. These results indicate that bifidobacterial-specific TRFLP is a useful method to monitor intestinal bifidobacterial populations from infant fecal samples. When used alongside next generation sequencing methods that detect broader population levels at lower resolution, this high-throughput, low-cost tool can help clarify the role of bifidobacteria in health and disease.

Original languageEnglish (US)
Pages (from-to)62-69
Number of pages8
JournalAnaerobe
Volume19
Issue number1
DOIs
StatePublished - Feb 2013

Keywords

  • Bifidobacteria
  • Gut microbiota
  • Infants
  • NGS
  • TRFLP

ASJC Scopus subject areas

  • Microbiology
  • Infectious Diseases

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