Exploring the diversity of the bifidobacterial population in the human intestinal tract - PubMed (original) (raw)
. 2009 Mar;75(6):1534-45.
doi: 10.1128/AEM.02216-08. Epub 2009 Jan 23.
Elena Foroni, Paola Pizzetti, Vanessa Giubellini, Angela Ribbera, Paolo Merusi, Patrizio Cagnasso, Barbara Bizzarri, Gian Luigi de'Angelis, Fergus Shanahan, Douwe van Sinderen, Marco Ventura
Affiliations
- PMID: 19168652
- PMCID: PMC2655441
- DOI: 10.1128/AEM.02216-08
Exploring the diversity of the bifidobacterial population in the human intestinal tract
Francesca Turroni et al. Appl Environ Microbiol. 2009 Mar.
Abstract
Although the health-promoting roles of bifidobacteria are widely accepted, the diversity of bifidobacteria among the human intestinal microbiota is still poorly understood. We performed a census of bifidobacterial populations from human intestinal mucosal and fecal samples by plating them on selective medium, coupled with molecular analysis of selected rRNA gene sequences (16S rRNA gene and internally transcribed spacer [ITS] 16S-23S spacer sequences) of isolated colonies. A total of 900 isolates were collected, of which 704 were shown to belong to bifidobacteria. Analyses showed that the culturable bifidobacterial population from intestinal and fecal samples include six main phylogenetic taxa, i.e., Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Bifidobacterium pseudolongum, Bifidobacterium breve, and Bifidobacterium bifidum, and two species mostly detected in fecal samples, i.e., Bifidobacterium dentium and Bifidobacterium animalis subp. lactis. Analysis of bifidobacterial distribution based on age of the subject revealed that certain identified bifidobacterial species were exclusively present in the adult human gut microbiota whereas others were found to be widely distributed. We encountered significant intersubject variability and composition differences between fecal and mucosa-adherent bifidobacterial communities. In contrast, a modest diversification of bifidobacterial populations was noticed between different intestinal regions within the same individual (intrasubject variability). Notably, a small number of bifidobacterial isolates were shown to display a wide ecological distribution, thus suggesting that they possess a broad colonization capacity.
Figures
FIG. 1.
Phylogenetic tree of the genus Bifidobacterium, computed on the basis of 16S rRNA gene sequences (a), ITS sequences (b), or concatenated sequences of the 16S rRNA gene and ITS (c). Bar scales indicate phylogenetic distances. Bootstrap values are reported for a total of 1,000 replicates. Trees were calculated by the neighbor-joining method as implemented in the neighbor module of PHYLIP. The trees were rooted using Nocardia farcinica. Shaded blocks indicate the different bifidobacterial phylogenetic clusters (53).
FIG. 2.
Relative abundances of bifidobacteria isolated from intestinal mucosa and fecal samples. Panel a shows the phylogenetic distribution of the bifidobacterial isolates among the different bifidobacterial species based on the combined human intestinal and fecal 16S rRNA gene-ITS sequence data set. The angle where each triangle joins the tree represents the relative abundance of sequences, and the lengths of the two adjacent sides indicate the range of branching depths with that clade. The numbers indicated in parentheses indicate the number of isolates obtained for each species. Panel b indicates the percentage and the total number of bifidobacterial isolates identified in this study from different environments (intestine versus feces) and from different subjects (adult versus infant).
FIG. 3.
DPCoA analysis for colonic mucosa (a), colonic mucosal sites alone (b), or for mucosa and stool (c). In panel a, the Rao dissimilarity values captured by each axis are represented by the histogram, where each histogram represents a Rao dissimilarity value. In panels b and c, percentages shown along the axes indicate the proportion of total Rao dissimilarity captured by that axis. Ellipses indicate the distribution of bifidobacterial strain per sample, except in panel c, where all mucosal samples and fecal samples are represented by one ellipse.
FIG. 4.
(a) Distribution of bifidobacterial isolates that were found to be widely distributed among different subjects. The y axis of this panel is a neighbor-joining phylogenetic tree containing all the 32 bifidobacterial isolates that were found to be present more than one time in different individuals from this study. Each column is labeled by subject and sample (C, colonoscopic mucosa; F, fecal sample). The presence of the strain is indicated by a black box. (b) ERIC-PCR patterns of different bifidobacterial strains. The sets of strains displaying the same ITS sequences are clustered. Strains used are indicated above each lane. Lane M, 1-kb DNA ladder (Gibco BRL).
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