A study of infant nasal microbiome diversity applying cpn60 universal target (UT) as a phylogenetic marker
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Date
2014-01-13
Authors
Peterson, Shelley W.
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Abstract
A protocol was developed to study the nasal microbiome applying a cpn60 universal target (UT) amplicon as a bacterial phylotyping marker using next generation sequencing. The UT can be used to identify organisms in metagenomic samples to the species level. This study aimed to determine the typical composition of anterior nares microbiota for developing infants over time, and to explore diversity of the infant nasal microflora and the relation to microflora observed within their primary caregivers.
Nares swabs were collected from 40 two-week old infants and their primary caregivers over a 1-year period using a single swab in one nare for each subject. These samples were treated to diminish contaminating human DNA, and bacterial template DNA was augmented using a whole-genome linear augmentation procedure. The cpn60 UT target was PCR amplified using degenerate primers and sequenced using high throughput 454/GS FLX pyrosequencing. Reads were quality-filtered and matched to the cpn60 database using an 80% nucleotide identity cutoff. Diversity and metagenomics analyses were performed using mothur v1.27.0 and SIMCA v. 13.
Throughout the first year of life, infant nares microflora increased in diversity. Infants showed differential representation of organisms compared with their primary caregivers. The nares microbiota predominantly belong to the phyla Actinobacteria, Firmicutes, and Proteobacteria. Individuals appear to have only one or two predominating genera; however intra-subject variability was noted. High variability between study subjects and within study subjects over time was also observed.
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Microbiome