Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig

BACKGROUND: The mammalian microbiota plays a key role in host health and disease susceptibility. However, knowledge of the early-age microbiota of pigs is lacking. The purpose of this study was to use high-throughput next-generation sequencing to characterize the fecal and nasal microbiotas of pigs during early life. RESULTS: Ten commercially-raised pigs were randomly enrolled at birth and sampled throughout the first 7 weeks of life. DNA was extracted from fecal and nasal samples and the hypervariable region V4 of the 16S rRNA gene was amplified. The product was sequenced using the Illumina MiSeq platform and 2 × 250 chemistry. Sequencing data was processed and analyzed with the mothur algorithms using an operational taxonomic unit approach. In total, 4.7 million and 5.4 million high-quality sequences were recovered from fecal and nasal samples, respectively. Analysis revealed that these microbiotas contain a very rich and diverse population of bacteria that display a remarkable evolution during the first 7 weeks of life. During this developmental period, a pig was exposed to an average of 1,976 and 6,257 species of bacteria by way of the gastrointestinal and respiratory tracts, respectively. Aging was significantly associated with an increasing measure of richness and diversity as well as with distinct changes to the core microbiota. At 2–3 weeks post-weaning, the rapidly developing microbiotas appeared to reach a developmental milestone as a relative degree of stability was evident. CONCLUSIONS: Pigs are exposed to an incredibly rich and diverse mixture of bacteria during early-life as demonstrated by next-generation sequencing methodology. These findings expand the knowledge of the developing porcine microbiota which is important for understanding susceptibility to disease, particularly for vulnerable neonatal pigs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-015-0512-7) contains supplementary material, which is available to authorized users.