Genomic Diversity and Relatedness of Bifidobacteria Isolated from a Porcine Cecum

Abstract

This study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzyme XbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to represent Bifidobacterium minimum, Bifidobacterium pseudolongum subsp. pseudolongum, and Bifidobacterium pseudolongum subsp. globosum and two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.

Use of pigs as a potential model for research into dietary modulation of the human gut microbiota

“…If they were present, Bifidobacterium spp. in the porcine intestine, such as Bifidobacterium suis, Bifidobacterium globosum or Bifidobacterium pseudolongum, differed from those generally found in the human GIT (70,71) . Nevertheless, the most abundant phylotypes of the pig are the lactic acid-producing bacteria, in particular lactobacilli (22) , in contrast to humans, yet there exists a considerable variation of Lactobacillus spp.…”

Inter-species transplantation of gut microbiota from human to pigs

“…According to the literature, the population of bifidobacteria in pigs was low (o1% total bacteria) or even undetectable (Brown et al, 1997;Leser et al, 2002;Mikkelsen et al, 2003). And the species isolated from porcine samples such as B. suis, B. globosum, B. pseudolongum, B. thermophilum, B. boum and B. choerinum were also different from the species generally found in the human gut (Mikkelsen et al, 2003;Simpson et al, 2003). On the contrary, bifidobacteria-specific amplicons were obtained from all HFA piglet samples and the TGGE patterns of HFA piglets were very similar to that of the human donor, indicating that most of the donor's bifidobacteria species had colonized the intestinal tract of HFA piglets (bands 1-3 and 5; Figure 3a).…”

Laboratory identification of anaerobic bacteria isolated on Clostridium difficile selective medium

“…Total DNA was harvested from a single colony and extracted as described previously [13]. Molecular identification of bacteria by 16S ribosomal DNA sequence analysis was performed using the primers and conditions described by Simpson et al [14]. Sequencing and product purification were performed as described previously [15].…”