High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin
Author
Fouhy, Fiona
Guinane, Caitriona M.
Hussey, Seamus
Wall, Rebecca
Ryan, C. Anthony
Dempsey, Eugene
Murphy, Brendan
Ross, R Paul
Fitzgerald, Gerald F
STANTON, CATHERINE

Cotter, Paul D.
Keyword
AntibioticsInfant
Gut microbiota
High-throughput sequencing
Ampicillin
Gentamycin
Bifidobacterium
Date
04/09/2012
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Fouhy, Fiona et al. High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin. Antimicrob. Agents Chemother., November 2012 vol. 56 no. 11: 5811-5820. doi: 10.1128/AAC.00789-12Abstract
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.Funder
Irish Research Council for Science, Engineering and Technology; Teagasc Walsh Fellowship Programme; Science Foundation IrelandGrant Number
SFI/11/PI/1137ae974a485f413a2113503eed53cd6c53
http://dx.doi.org/10.1128/AAC.00789-12