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Risks of Antibiotic Exposures Early in Life on the Developing Microbiome

2015; Public Library of Science; Volume: 11; Issue: 7 Linguagem: Inglês

10.1371/journal.ppat.1004903

1553-7374

Anjelique Schulfer, Martin J. Blaser,

Infant Nutrition and Health

During birth, a relatively sterile unborn child becomes a newborn coated with microbes on every surface.This collection of bacteria, archaea, viruses, and fungi found in and on the human body is called the microbiota.The collective genomes of the microbiota are considered to be the metagenome, and the totality of the microbiota, metagenome, and their interactions is the microbiome.The microbiota has many critical functions including protection from pathogens, development and maintenance of the immune system, and helping the host access nutrients in food.The gut microbiota has been of particular interest, as perturbations of this community have been linked to disease states including autoimmune disease and neurological disorders.Antibiotics have consistently been shown to change the gut microbiome in humans and animals.We briefly review the importance of the early-life gut microbiome and the risks of disturbing it with antibiotics.Each method used to measure changes in the microbiota and microbiome has advantages and disadvantages.Culturing provides reliable results but is labor intensive and limited in the number of identifiable taxa.16S rRNA gene (16S) sequencing can efficiently identify taxa; however, the results depend on the accuracy of 16S sequence databases.Whole genome sequencing (WGS) is prohibitively expensive for most experiments; however, it can describe both taxa identity and genes available in the community.Predictive metagenomics based on 16S sequencing can estimate genes available in the community, but they are not directly measured.Metabolomics examines which molecules are changing in the bacterial community that could impact the host.These methods are all currently in use and those changes most important for host physiology and susceptibility to disease are not known.