Development of the gut microbiota in southern Indian infants from birth to 6 months: a molecular analysis

Abstract

Acquisition of the gastrointestinal microbiota at birth may have long-term health impacts. We longitudinally characterised major microbial communities in the faeces of a cohort of infants using molecular methods. Faecal samples were prospectively obtained at several time points after birth from eighty-three infants. Real-time PCR using SYBR green and primers targeted at 16S rRNA gene sequences were used to quantify Bifidobacterium, Lactobacillus acidophilus group, Bacteroides-Prevotella group, Enterobacteriaceae, Enterococcus, Clostridium coccoides-Eubacterium rectale group, Clostridium leptum group and Staphylococcus. Microbial community abundance was expressed relative to amplification of sequences conserved universally for domain bacteria. Faecal copy number of 16S rRNA genes increased non-significantly from a mean of 4·1 × 10(9)/g on day 1 to 1·1 × 10(10)/g on day 4. All microbial communities were detected from day 1 after birth. Enterobacteriaceae and lactobacilli predominated on day 1, while bifidobacteria and staphylocci increased on day 4. Bacteroides-Prevotella and C. coccoides-E. rectale increased by day 180. C. leptum was detected in half of the cohort at birth and in a slightly larger percentage by 6 months. Caesarean section was associated with delayed colonisation by several bacterial communities. Higher socio-economic status was associated with more abundant lactobacilli and Bacteroides-Prevotella at 90 and 180 d. Supplemental feeding was associated with a reduction in Enterobacteriaceae. Microbial colonisation of the gut was well established on the first day of birth, and relative abundance of microbial communities was influenced by mode of delivery, socio-economic status and supplemental feeding. These findings may have relevance to infant nutrition and growth.

Keywords: 16S rRNA gene; Bacteroides–Prevotella; Bifidobacterium; Clostridium; Ct, threshold cycle; Faeces; Lactobacillus.

Fig. 1.

Total bacterial count in faeces estimated using real-time PCR amplification of universal 16S rDNA sequences conserved for domain bacteria. Quantification was done with reference to an external standard of plasmid DNA copies. Values are means, with standard errors represented by vertical bars. None of the values was statistically significantly different from the others.

Fig. 2.

Abundance of specific microbial communities in the faeces of neonates followed longitudinally at 6 months. Data were acquired by real-time PCR targeting specific sequences of the 16S rRNA gene and are expressed as relative difference in comparison with amplification of the ‘universal’ Bacteria domain sequence. Values are means, with standard errors represented by vertical bars. ^a,bMean values with unlike letters were significantly different (P < 0·05; repeated measures ANOVA with post hoc Tukey's test).

Fig. 3.

Association of mode of delivery (normal vaginal delivery (); lower segment Caesarean section ()) and faecal microbial colonisation. Values are means, with standard errors represented by vertical bars. P values shown were calculated using the Student's t test with Welch's correction.

Fig. 4.

Association of socio-economic status and microbial colonisation. Based on the socio-economic score, mothers were classified into three equal groups, with the lowest tertile being represented as Lo_ and the highest tertile as Hi_. Values are means, with standard errors represented by vertical bars. P values shown were calculated using Student's t test with Welch's correction. The other microbial communities tested did not significantly differ between low and high socio-economic groups (data not shown).