Diversity of bifidobacteria within the infant gut microbiota

Abstract

Background: The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus.

Methods/principal findings: In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed.

Conclusions: In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant's intestine.

Figure 1. Rarefaction curves generated for 16 S rRNA gene sequences obtained from stool samples of infants and faecal samples of mothers.

Panel a represents the rarefaction curves using the Chao index. Panel b displays rarefaction curves using the Shannon index.

Figure 2. Aggregate microbiota composition at phylum level in faecal samples from infants (panel a), mothers (panel b), at order/family level in infants (panel c) and mothers (panel d), and at Bifidobacterium genus level in the same sets of individuals (panels e and f), as indicated.

In panels a and b only major taxonomic groups are shown.

Figure 3. Principal Coordinate Analysis (PCoA) based on the phylotypes identified from different subjects (panel a), different geographical regions (panel b) different mode of delivery (panel c), different age (panel d), and different feeding type (panel e).

Percentages shown along the axes represent the proportion of dissimilarities captured by the axes. Each circle represents the 16 S rRNA gene sequences from each sample, which have different colour and shape according to the subject and the age (infant vs. mother), respectively.

Figure 4. Inter-individual variation in infant stool samples in the proportion of the major microbial phylum/family/species.

The core faecal microbiota of infant subjects at the levels of phylum, family and genus is indicated at the bottom of each inset.

Figure 5. Number of sequences per phylotype for each sample.

The y axis is a neighbour-joining phylogenetic tree containing one representative of each of the OTUs detected in this study; each row represents a different OTU. Increasing darkness of the grayscale corresponds to higher estimated relative abundance. The most conserved OTUs between samples are marked with an arrow. Arrow 1 represents the OTUs corresponding to B. longum, arrow 2 indicates the OTUs of B. pseudocatenulatum, arrow 3 highlights the phylotypes belonging to Streptococcus thermophilus. The boxed area includes those phylotypes belonging to Ruminococcaceae and Clostridiales taxa. The feeding method is indicated for each subject; Br, breast-fed; Bo, bottle fed.

Figure 6. Analysis of species co-occurrence/exclusion.

Panel a represents the C-score distribution for observed and randomized OTU occurrence in each sample. Panel b shows the checkerboard indices for observed and randomized OTU occurrence. Values for the observed distributions are indicated on the X axis.