Assessment of fecal bacterial diversity among healthy piglets during the weaning transition

Abstract

The high level of genetic diversity in the microflora of the gastrointestinal tract has the potential to provide numerous beneficial functions to the host. Thus it is now acknowledged that the complexity in animal functioning is linked to the interacting microbiome in the gut. Despite the importance of gut microbiome, there is a lack of information concerning the microbial communities in the pig gut during the weaning transition. This study describes the fecal microbial shifts of healthy piglets during the weaning transition using barcoded pyrosequencing of the prokaryotic 16S rRNA gene. Fecal samples were obtained from 15 piglets during the pre-weaning period (fourth week after birth) and post-weaning (sixth week after birth) and were subjected to community genomic DNA extraction for pyrosequencing analysis. As the piglets underwent the weaning transition a trend toward increased bacterial diversity was observed, based on species abundance as measured by the Shannon-Weaver index. Firmicutes (54.0%) and Bacteroidetes (59.6%) were the most dominant phyla during pre-weaning and post-weaning, respectively. During the weaning transition a distinct shift from Bacteroides to Prevotella as the most abundant genus was observed. Additionally, we detected a number of abundant gut bacterial species that have not been reported previously. Clostridium rectum, C. clostridioforme, C. lactatifermentans and Butyricimonas virosa were uniquely detected prior to weaning while Roseburia cecicola and Blautia wexlerae were detected during the post-weaning period only.

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

“…We also identified bacterial OTUs (95% identity) corresponding to core bacteria that may play a key role in maintaining the metabolism of the gut in Duroc pigs (Kim et al, 2011; Pajarillo et al, 2014a, b). Bacterial genera, including Prevotella , Succinivibrio , Ruminococcus , Roseburia , and Clostridium , as well as unclassified OTUs (95% identity), including DQ905034_g, EU843283_g, EF404137_g, EF404362_g, and EF602759_g (Supplementary Tables 2 and 3), were identified as the possible core fecal microbiome in Duroc because these bacteria were present in all adult Duroc pig fecal samples ( n = 17) regardless of their abundance in each individual.…”

“…Raw sequence reads from each fecal sample were analyzed as described previously (Pajarillo et al, 2014a, b). Briefly, demultiplexing and removal of the barcodes were performed for all sequence reads.…”

“…However, the results were limited to organisms with high copy numbers, including Firmicutes, Bacteroidetes, methanogens, and sulfate-reducing bacteria; thus, the ability to characterize the overall microbial composition was limited. High-throughput pyrosequencing methods have enabled researchers to generate a massive amount of data for community analyses to describe the effect of weaning (Pajarillo et al, 2014b), age (Kim et al, 2011), diet (Lu et al, 2013), and antibiotics (Kim et al, 2012) on the swine gut microbiome. Here, we describe the fecal bacterial diversity among Duroc pigs using 16S rRNA gene pyrosequencing and suggest core members of the microbial community, as well as uncultivable members of the adult Duroc gut microbiota.…”

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets

“…Bacteroidetes increased in both yeast fed groups, but not significantly in group without probiotic feeding. In early-weaned piglets, other studies have shown that Firmicutes were most abundant in pre-weaning piglets, but shifted gradually to Bacteroidetes after weaning (Upadrasta et al, 2013; Pajarillo et al, 2014). The results in this study may suggest that Duan-Nai-An sped up the shift and adapted piglets more quickly to the weaned situation.…”

“…Among them, interestingly, Bacteroides was more abundant in both yeast probiotics fed piglets. Previous reports have established Bacteroides species as some the early colonizers of pig gut (Poroyko et al, 2010; Lu et al, 2014; Mach et al, 2015), and considered them to be clinically important anaerobes in relation to gastrointestinal well-being (Pajarillo et al, 2014). Among the 13 significantly more abundant taxa in Duan-Nai-An fed piglets, Enterococcus strains have been commercialized as probiotics, and could prevent the colonization and stabilization of microbiota unfavorable to the host by competing for adhesion sites in the epithelial cells with pathogens (Araujo and Ferreira, 2013).…”