title: Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.
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.
authors.affiliation: Department of Viticulture and Enology, University of California, Davis, CA 95616, USA.
authors.forename: Zachery T
authors.initials: ZT
authors.lastname: Lewis
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Bokulich
authors.forename: Karen M
authors.initials: KM
authors.lastname: Kalanetra
authors.forename: Santiago
authors.initials: S
authors.lastname: Ruiz-Moyano
authors.forename: Mark A
authors.initials: MA
authors.lastname: Underwood
authors.forename: David A
authors.initials: DA
authors.lastname: Mills
mesh_terms: D001644:Bifidobacterium / Q000145:classification* / Q000235:genetics; D058448:Biota; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D007223:Infant; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA