title: High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin.
abstract: The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.
authors.affiliation: Teagasc Food Research Centre, Fermoy, Cork, Ireland.
authors.forename: Fiona
authors.initials: F
authors.lastname: Fouhy
authors.forename: Caitriona M
authors.initials: CM
authors.lastname: Guinane
authors.forename: Seamus
authors.initials: S
authors.lastname: Hussey
authors.forename: Rebecca
authors.initials: R
authors.lastname: Wall
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Ryan
authors.forename: Eugene M
authors.initials: EM
authors.lastname: Dempsey
authors.forename: Brendan
authors.initials: B
authors.lastname: Murphy
authors.forename: R Paul
authors.initials: RP
authors.lastname: Ross
authors.forename: Gerald F
authors.initials: GF
authors.lastname: Fitzgerald
authors.forename: Catherine
authors.initials: C
authors.lastname: Stanton
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
mesh_terms: D039903:Actinobacteria / Q000187:drug effects* / Q000235:genetics; D000667:Ampicillin / Q000009:adverse effects; D000900:Anti-Bacterial Agents / Q000009:adverse effects; D001644:Bifidobacterium / Q000187:drug effects* / Q000235:genetics; D015169:Colony Count, Microbial; D017931:DNA Primers; D005243:Feces / Q000382:microbiology; D005260:Female; D041981:Gastrointestinal Tract / Q000187:drug effects / Q000382:microbiology*; D005839:Gentamicins / Q000009:adverse effects; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D007263:Infusions, Parenteral; D007778:Lactobacillus / Q000187:drug effects* / Q000235:genetics; D008297:Male; D054892:Metagenome / Q000187:drug effects*; D016133:Polymerase Chain Reaction; D020560:Proteobacteria / Q000187:drug effects* / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D020127:Recovery of Function / Q000502:physiology
chemical_list: D000900:Anti-Bacterial Agents; D017931:DNA Primers; D005839:Gentamicins; D012336:RNA, Ribosomal, 16S; D000667:Ampicillin