Dataset Information

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

ABSTRACT: 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.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.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.

SUBMITTER: Slifierz MJ

PROVIDER: S-EPMC4578254 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Slifierz Mackenzie Jonathan MJ Friendship Robert M RM Weese J Scott JS

BMC microbiology 20150921 1

<h4>Background</h4>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.<h4>Results</h4>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 a ...[more]

PMID: 26391877

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Project description:The biological succession that occurs during the first year of life in the gut of infants in Western countries is broadly predictable in terms of the increasing complexity of the composition of microbiotas. Less information is available about microbiotas in Asian countries, where environmental, nutritional, and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n?=?204) and New Zealand (NZ) (n?=?74) infants 6 to 7?months and 12?months of age. Comparisons were made by analysis of 16S rRNA gene sequences and derivation of community diversity metrics, relative abundances of bacterial families, enterotypes, and cooccurrence correlation networks. Abundances of Bifidobacterium longum subsp. infantis and B. longum subsp. longum were determined by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater for NZ infants. B. longum subsp. infantis dominated the microbiotas of Indonesian children, whereas B. longum subsp. longum was dominant in NZ children. Network analysis showed that the niche model (in which trophic adaptation results in preferential colonization) of the assemblage of microbiotas was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiotas of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries, and they point to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.IMPORTANCE This study addresses the microbiology of a natural ecosystem (the infant bowel) for children in a rural setting in Indonesia and in an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of nutrition and environment on the development of the gut microbiota and for determining the long-term effects of microbiological events in early life on human health and well-being.

Project description:BackgroundThe majority of chicken microbiota studies have used the ceca as a sampling site due to the specific role of ceca in chicken productivity, health and wellbeing. However, sampling from ceca and other gastrointestinal tract sections requires the bird to be sacrificed. In contrast, fecal sampling does not require sacrifice and thus allows the same bird to be sampled repeatedly over time. This is a more meaningful and preferred way of sampling as the same animals can be monitored and tracked for temporal studies. The commonly used practice of selecting a subset of birds at each time-point for sacrifice and sampling introduces added variability due to the known animal to animal variation in microbiota.ResultsCecal samples and fecal samples via cloacal swab were collected from 163 birds across 3 replicate trials. DNA was extracted and 16S rRNA gene sequences amplified and pyrosequenced to determine and compare the phylogenetic profile of the microbiota within each sample. The fecal and cecal samples were investigated to determine to what extent the microbiota found in fecal samples represented the microbiota of the ceca. It was found that 88.55% of all operational taxonomic units (OTUs), containing 99.25% of all sequences, were shared between the two sample types, with OTUs unique for each sample type found to be very rare. There was a positive correlation between cecal and fecal abundance in the shared sequences, however the two communities differed significantly in community structure, represented as either alpha or beta diversity. The microbial populations present within the paired ceca of individual birds were also compared and shown to be similar.ConclusionsFecal sample analysis captures a large percentage of the microbial diversity present in the ceca. However, the qualitative similarities in OTU presence are not a good representation of the proportions of OTUs within the microbiota from each sampling site. The fecal microbiota is qualitatively similar to cecal microbiota but quantitatively different. Fecal samples can be effectively used to detect some shifts and responses of cecal microbiota.

Dataset Information

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

Publications

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

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