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

13 Citations (Scopus)

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

Fingerprint

Restriction Fragment Length Polymorphisms
Bifidobacterium
Feces
Costs and Cost Analysis
Health
Ecology
Population
Gastrointestinal Tract
Breast
Databases
Polymerase Chain Reaction

Keywords

  • Bifidobacteria
  • Gut microbiota
  • Infants
  • NGS
  • TRFLP

ASJC Scopus subject areas

  • Microbiology
  • Infectious Diseases

Cite this

Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. / Lewis, Zachery T.; Bokulich, Nicholas A.; Kalanetra, Karen M.; Ruiz-Moyano, Santiago; Underwood, Mark; Mills, David A.

In: Anaerobe, Vol. 19, No. 1, 02.2013, p. 62-69.

Research output: Contribution to journalArticle

Lewis, Zachery T. ; Bokulich, Nicholas A. ; Kalanetra, Karen M. ; Ruiz-Moyano, Santiago ; Underwood, Mark ; Mills, David A. / Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. In: Anaerobe. 2013 ; Vol. 19, No. 1. pp. 62-69.
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