The infant gut microbiota plays a critical role in early life growth and derives mainly from maternal gut and breast milk. This study aimed to analyze the differences in the gut microbiota, namely
Bifidobacterium and
Lactobacillus communities at species level among breast milk as well as maternal and infant feces at different time points after delivery. Fifty-one mother–infant pairs from Indonesia were recruited, and the breast milk and maternal and infant feces were collected and analyzed by high throughput sequencing (16S rRNA,
Bifidobacterium groEL and
Lactobacillus groEL genes). PCoA results showed bacterial composition was different among breast milk and maternal and infant feces within the first two years. The abundance of
Bifidobacterium and
Bacteroides were significantly higher in infant feces compared to their maternal feces from birth to two years of age, and maternal breast milk within six months after birth (
p < 0.05), whereas the abundance of
Blautia,
Prevotella, and
Faecalibacterium was higher in maternal feces compared to that in breast milk within six months and infant feces within one year after birth, respectively (
p < 0.05). The relative abundances of
Bacteroides and
Lactobacillus was higher and lower in infant feces compared to that in maternal feces only between one and two years of age, respectively (
p < 0.05). For
Bifidobacterium community at species level,
B. adolescentis, B. ruminantium, B. longum subsp. infantis, B. bifidum, and
B. pseudolongum were identified in all samples. However, the profile of
Bifidobacterium was different between maternal and infant feces at different ages. The relative abundances of
B. adolescentis and
B. ruminantium were higher in maternal feces compared to those in infant feces from birth to one year of age (
p < 0.05), while the relative abundances of
B. longum subsp.
infantis and
B. bifidum were higher in infant feces compared to those in maternal feces beyond three months, and the relative abundance of
B. pseudolongum was only higher in infant feces between three and six months (
p < 0.05). For
Lactobacillus community,
L. paragasseri showed higher relative abundance in infant feces when the infant was younger than one year of age (
p < 0.05). This study showed bacterial composition at the genus level and
Bifidobacterium and
Lactobacillus communities at the species level were stage specific in maternal breast milk as well as and maternal and infant feces.
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