title: Early life establishment of site-specific microbial communities in the gut.
abstract: Fecal sampling is widely utilized to define small intestinal tissue-level microbial communities in healthy and diseased newborns. However, this approach may lead to inaccurate assessments of disease or therapeutics in newborns because of the assumption that the taxa in the fecal microbiota are representative of the taxa present throughout the gastrointestinal tract. To assess the stratification of microbes in the newborn gut and to evaluate the probable shortcoming of fecal sampling in place of tissue sampling, we simultaneously compared intestinal mucosa and fecal microbial communities in 15 neonates undergoing intestinal resections. We report three key results. First, when the site of fecal and mucosal samples are further apart, their microbial communities are more distinct, as indicated by low mean Sørensen similarity indices for each patient's fecal and tissue microbiota. Second, two distinct niches (intestinal mucosa and fecal microbiota) are evident by principal component analyses, demonstrating the critical role of sample source in defining microbial composition. Finally, in contrast to adult studies, intestinal bacterial diversity was higher in tissue than in fecal samples. This study represents an unprecedented map of the infant microbiota from intestinal mucosa and establishes discernable biogeography throughout the neonatal gastrointestinal tract. Our results question the reliance on fecal microbiota as a proxy for the developing intestinal microbiota. Additionally, the robust intestinal tissue-level bacterial diversity we detected at these early ages may contribute to the maturation of mucosal immunity.
authors.affiliation: Department of Pediatrics; Vanderbilt University; Nashville, TN USA.
authors.forename: Joann
authors.initials: J
authors.lastname: Romano-Keeler
authors.affiliation: Department of Pediatrics; Vanderbilt University; Nashville, TN USA; Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Moore
authors.affiliation: Genome Technology Center; Stanford University; Palo Alto, CA USA.
authors.forename: Chunlin
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Biological Sciences; Vanderbilt University; Nashville, TN USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Brucker
authors.affiliation: Department of Biostatistics; Vanderbilt University; Nashville, TN USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Fonnesbeck
authors.affiliation: Department of Biostatistics; Vanderbilt University; Nashville, TN USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Slaughter
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
authors.forename: Haijing
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
authors.forename: Danielle P
authors.initials: DP
authors.lastname: Curran
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
authors.forename: Shufang
authors.initials: S
authors.lastname: Meng
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA.
authors.forename: Hernan
authors.initials: H
authors.lastname: Correa
authors.affiliation: Department of Pediatric Surgery; Vanderbilt University; Nashville, TN USA.
authors.forename: Harold N
authors.initials: HN
authors.lastname: Lovvorn
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA; Department of Laboratory Medicine; Memorial Sloan-Kettering Cancer Center; New York, NY USA.
authors.forename: Yi-Wei
authors.initials: YW
authors.lastname: Tang
authors.affiliation: Department of Pathology, Microbiology, and Immunology; Vanderbilt University; Nashville, TN USA; Department of Biological Sciences; Vanderbilt University; Nashville, TN USA.
authors.forename: Seth
authors.initials: S
authors.lastname: Bordenstein
authors.affiliation: Department of Medicine; Division of Genomic Medicine; Vanderbilt University; Nashville, TN USA.
authors.forename: Alfred L
authors.initials: AL
authors.lastname: George
authors.affiliation: Department of Pediatrics; Vanderbilt University; Nashville, TN USA.
authors.forename: Jörn-Hendrik
authors.initials: JH
authors.lastname: Weitkamp
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D007231:Infant, Newborn; D007413:Intestinal Mucosa / Q000382:microbiology
keywords: fecal microbiome; host-microbial interactions; intestinal bacterial diversity; mucosal immunity; neonatal microbiome