Background Recent studies have described the bifidobacterial composition of neonates at a species level; however, with advancing technologies we can gain insight into the diversity of the bifidobacterial microbiota residing within the infant gut.

Objective To compare species and strain diversity of culturable bifidobacterial populations in faecal samples obtained from healthy term infants on three different feeding regimes.

Study design In total, 51 healthy term infants were recruited for this study and divided equally into three different groups (n=17) based on their feeding regime during the first 4 weeks of life. Culturable bifidobacterial populations were analysed at week 1, week 4 and 6 months of age. Isolates were characterised to species level by 16s rRNA-internally transcribed spacer (ITS) gene sequence analysis and to strain level by pulsed field gel electrophoresis (PFGE).

Results In total,173 bifidobacterial strains were detected across all three groups from 2295 isolates, 42% (72 of 173) of which were detected in the prebiotic-fed group, followed by 30% (52 of 173) and 28% (49 of 173) in the breastfed and non-prebiotic-fed groups, respectively. Surprisingly, only two of the 51 infants harboured an identical bifidobacterial strain which was not present in the other 49 infants. Prebiotic supplementation in the early neonatal period increased the prevalence of Bifidobacterium longum in infants, in addition to promoting strain diversity. B. longum was the dominant species recovered from all three groups during the first 6 months of life, followed by Bifidobacterium breve and Bifidobacterium bifidum.

Conclusions This study reveals a hitherto unknown level of diversity at the strain level among bifidobacteria isolated from different infants and the influence prebiotic formula feeding has on the bifidobacterial population.