Jong Pyo Chae

Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines

This study examined the fecal bacterial diversity of 15-weekold pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Proteomic and transcriptional analysis of Lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR.

Lactobacillus johnsonii PF01 has been reported to be highly resistant to bile, a key property of probiotic microorganisms. Here, we examine the nature of the bile-salt tolerance of L. johnsonii PF01. Growth inhibition and surface morphology and physiology aberrations were observed after overnight exposure to bile stress. Quantitative proteomic profiles using iTRAQ-LC-MS/MS technology identified 8307 peptides from both untreated PF01 cells and those exposed to 0.1%, 0.2%, and 0.3% bile salts. Some 215 proteins exhibited changed levels in response to bile stress; of these, levels of 94 peptides increased while those of 121 decreased. These were classified into the following categories: stress responses, cell division, transcription, translation, nucleotide metabolism, carbohydrate transport and metabolism, cell wall biosynthesis, and amino acid biosynthesis, and 16 of unidentified function. Analysis of the mRNA expression of selected genes by quantitative reverse transcriptase-PCR verified the proteomic data. Both proteomic and mRNA data provided evidence for increased phosphotransferase activity and cell wall biosynthesis. In addition, three bile salt hydrolases were significantly upregulated by bile exposure. These findings provide a basis for future evaluations of the tolerance of potential probiotic strains toward the various gastrointestinal challenges, including bile stress.

Genome Sequence of Lactobacillus mucosae LM1, Isolated from Piglet Feces

Lactobacillus mucosae LM1, isolated from stool samples of a healthy piglet, displays good in vitro mucin adhesion and antimicrobial activity against pathogenic bacteria. To elucidate its antimicrobial effects and to find its epithelial cell and mucin adhesion genes, the genomic sequence of L. mucosae LM1 was investigated.

Molecular cloning, characterization and comparison of bile salt hydrolases from Lactobacillus johnsonii PF01

To clone, characterize and compare the bile salt hydrolase (BSH) genes of Lactobacillus johnsonii PF01.

Genome Sequence of Lactobacillus johnsonii PF01, Isolated from Piglet Feces

Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of L. johnsonii PF01.

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

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation

The microbial communities in the pig gut perform a variety of beneficial functions. Along with host genetics and diet, farm management practices are an important aspect of agricultural animal production that could influence gut microbial diversity. In this study, we used barcoded pyrosequencing of the V1–V3 regions of the 16S ribosomal RNA (rRNA) genes to characterise the faecal microbiome of three common commercial purebred pig lines (Duroc, Landrace and Yorkshire) before and after cohabitation. The diversity of faecal microbiota was characterised by employing phylogenetic, distance-based and multivariate-clustering approaches. Bacterial diversity tended to become more uniform after mixing of the litters. Age-related shifts were also observed at various taxonomic levels, with an increase in the proportion of the phylum Firmicutes and a decrease in Bacteroidetes over time, regardless of the purebred group. Cohabitation had a detectable effect on the microbial shift among purebred pigs. We identified the bacterial genus Parasutterella as having utility in discriminating pigs according to time. Similarly, Dialister and Bacteroides can be used to differentiate the purebred lines used. The microbial communities of the three purebred pigs became more similar after cohabitation, but retained a certain degree of breed specificity, with the microbiota of Landrace and Yorkshire remaining distinct from that of their distant relative, Duroc.

Effects of Bacillus subtilis CSL2 on the composition and functional diversity of the faecal microbiota of broiler chickens challenged with Salmonella Gallinarum

BackgroundThe chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with Bacillus subtilis CSL2 were evaluated in broilers challenged and unchallenged with Salmonella Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed.ResultsThe Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period. A total of 718,204 sequences from broiler chickens were recorded and analysed. At the phylum level, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial taxa. In Salmonella-infected chickens (SC), Bacteroidetes were more highly abundant compared to control (NC) and Bacillus-treated (BT) chickens. At the genus level, in the NC and BT groups, Lactobacillus was present at high abundance, and the abundance of Turicibacter, unclassified Enterobacteriaceae, and Bacteroides increased in SC broilers. Furthermore, taxon-independent analysis showed that the SC and BT groups were compositionally distinct at the end of the 24-h period. Further analysis of functional properties showed that B. subtilis CSL2 administration increased gut-associated energy supply mechanisms (i.e. carbohydrate transport and metabolism) to maintain a stable microbiota and protect gut integrity.ConclusionsThis study demonstrated that S. Gallinarum infection and B. subtilis CSL2 supplementation in the diet of broiler chickens influenced the diversity, composition, and functional diversity of the faecal microbiota. Moreover, the findings offer significant insights to understand potential mechanisms of Salmonella infection and the mode of action of probiotics in broiler chickens.

Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing

Demand for the development of non‐antibiotic growth promoters in animal production has increased in recent years. This report compared the faecal microbiota of weaned piglets under the administration of a basal diet (CON) or that containing prebiotic lactulose (LAC), probiotic Enterococcus faecium NCIMB 11181 (PRO) or their synbiotic combination (SYN). At the phylum level, the Firmicutes to Bacteroidetes ratio increased in the treatment groups compared with the CON group, and the lowest proportion of Proteobacteria was observed in the LAC group. At the family level, Enterobacteriaceae decreased in all treatments; more than a 10‐fold reduction was observed in the LAC (0.99%) group compared with the CON group. At the genus level, the highest Oscillibacter proportion was detected in PRO, the highest Clostridium in LAC and the highest Lactobacillus in SYN; the abundance of Escherichia was lowest in the LAC group. Clustering in the discriminant analysis of principal components revealed distinct separation of the feeding groups (CON, LAC, PRO and SYN), showing different microbial compositions according to different feed additives or their combination. These results suggest that individual materials and their combination have unique actions and independent mechanisms for changes in the distal gut microbiota.

Isolation of Bacillus amyloliquefaciens ATC6 Producing Acidic Cellulase

Se Hyung Lee, Jong Pyo Chae, Min Jeong Kim and Dae-Kyung Kang*Department of Animal Resources Science, College of Bio-Resources Science, Dankook UniversityABSTRACTA bacterium producing acidic cellulase was isolated from pig feces. The isolate, ATC6 strain, was found to be Gram-positive, non-motile, catalase-positive, and spore-forming stain. Under an electron microscope, the cells were observed to be rod-shaped. The isolate was identified as Bacillus amyloliquefaciens ATC6 on the basis of morphological and biochemical properties as well as 16S rRNA gene sequences. Optimum pH and temperature for the cellulase activity of the culture supernatant of B. amyloliquefaciens ATC6 were found to be pH 4.5 and 55, respectively. More than 80% of its maximum activity was maintained at pH 4.0. The cellulase activity was maintained at temperatures ranging from 35 to 55after 2 h incubation at pH 4.5, whereas its activity decreased rapidly at 65.(Key words :Enzyme, Acidic cellulase, Bacillus amyloliquefaciens)