Here, we report for the first time the bacterial and fungal microbiota dynamics during early childhood. In conducting a direct comparison between bacterial and fungal gut communities, we demonstrated how the two follow very distinct developmental trajectories, having contrasting associations with the mother’s microbiota. We also found a previously unreported and surprising compositional change in maternal stool microbiotas during the postpartum period.
We found undetectable levels of fungi in a large subset of stool samples from children and mothers in a rural African setting. This finding is consistent with a previous study in Norway, an urban high-resource setting18. We additionally confirmed that the samples with undetectable fungi, including those from the youngest age groups, contained readily amplifiable bacterial genes providing further evidence that the lack of detectable fungi in these samples reflected their absence or extremely low abundance, rather than sample processing artefacts. However, lysis methods that successfully lysed bacteria may have failed to lyse fungal cells. Interestingly, most breastmilk samples were positive for fungi, especially those from 4 weeks postpartum, while we did not detect fungi in half of the corresponding breastfeeding infants.
As in our study, increasing bacterial4, 6, and unchanging fungal19, 20 richness and diversity during infancy were previously reported, but never together in the same study. However, the timing of increases in bacterial richness and diversity in our study differed from those in other studies in both high- and low-resource regions. In our Ghanaian cohort, richness and diversity remained stable over the first year of life and dramatically increased thereafter. In studies of American and European cohorts, alpha diversity steadily increased from birth to two years6 or 3 months to 5 years4, respectively. Numbers of observed OTUs increased steadily from birth to 3 years among Amerindian and Malawian infants1, and from birth to two years in an Indian setting33. The distinct timing in our study may reflect lifestyles, diet or an environment unique to this study cohort in Ghana.
The bacterial succession we observed, with sequential dominance by E. coli, Bifidobacterium, and Prevotella, as well as sequential high abundance of Staphylococcus,Streptococcus,Bacteroides, and Faecalibacterium, was consistent with previous studies of newborn and adult microbiotas4, 32. The Bacteroidetes phylum in older children and adults is typically dominated by either Bacteroides or Prevotella1, 34, 35. Prevotella was dominant in adults in rural Ghana, as demonstrated among the one month post-partum women in our study. We found that Bacteroides was abundant in the Ghanaian infants prior to 1 year, after which, Prevotella colonized the children and became dominant. The ability of Bacteroides species to utilize human milk oligosaccharides (HMOs)36as well as diet-derived polysaccharides37 as an energy source, is thought to contribute to their unique ability to persist in both infant and adult guts. However, Prevotella appears to outcompete Bacteroides in adults with a fiber-rich diet 38. This transition occurs early in life in this Ghanaian population, probably associated changes to the child’s diet at this time.
We found dominance of the gut fungal microbiota of some children by Candida sp., as has been found in some17, 20 but not other16, 19 studies, where additional fungal taxa, such as Aspergillus and Penicillium, featured prominently. We also detected an early increase in the relative abundance of Malassezia that was not seen in other studies of newborns17, 18. Given the high relative abundance of this taxon in breastmilk in our study and another21, and evidence of its’ transmission from mother to newborn39, absence of this taxon in other studies is puzzling but may reflect regional differences in maternal breastmilk fungal microbiotas, which have not been well-studied.
We were surprised to find substantial differences between the gut bacterial microbiotas of mothers 1 week versus 4 weeks postpartum. These dramatic differences were not due to cross-contamination between maternal and infant samples, as mothers in both groups were sampled using the same protocol and time points, and samples from both groups were processed simultaneously. Given the cross-sectional study design, we cannot definitively conclude that the microbiota changed in these women over this time. However, both the 3-month recruitment window and the greater microbiota similarity of mothers and their infants 1 week postpartum imply that such a change is the most likely interpretation of the data. Studies of the stool microbiota during pregnancy have yielded mixed results, with some studies showing no change in community composition during pregnancy40, 41 and others showing substantial shifts42, 43. The latter two studies showed an increase in Proteobacteria during pregnancy, which is consistent dominance of Proteobacteria that we observed 1 week postpartum. However, our finding of a low relative abundance of Prevotella 1 week postpartum is novel, and was one of the greatest differences we observed in the postpartum period. One week postpartum, we also observed a high relative abundance of Faecalibacterium, associated with decreased inflammation and protection from inflammatory bowel diseases44, and Blautia, negatively associated with type 1 diabetes45 and gestational diabetes melittus (GDM) without prescribed dietary intervention 43. Together, our findings suggest that differences in maternal microbiota around the time of birth reflect both increases in taxa common to newborns (Escherichia) and decreases in taxa absent in newborns (Prevotella), as well as increases in abundance of taxa not abundant in infants but with potential health benefits to the mother (Faecaibacterim and Blautia).
We did not identify fungal taxa that were differentially abundant in the gut microbiota 1 week versus 4 weeks postpartum. We also did not identify many commonly shared fungal OTUs between pairs. In contrast to the bacterial gut microbiota, the fungal gut microbiota of mothers does not appear to be substantially affected by postpartum time and does not appear to strongly influence colonization of the infant’s gut.
We found that common skin taxa dominated breastmilk bacterial (Streptococcus, Staphylococcus) and fungal (Malasezzia) communities, as previously shown11, 21, 46, 47. When dominant in a mother’s breastmilk, OTUs of these taxa tended to be present at lower relative abundance in her infant’s gut microbiota, consistent with the breastmilk being a source for these organisms colonizing the infant gut. However, it is important to note that detection of their DNA in breastmilk and feces does not demonstrate that these OTUs colonize, or even survive these two environments. Further investigation is required to determine if these skin taxa have any function in breastmilk or the gut. OTUs of common gut taxa (Bifidobacterium, Bacteroides, Lactobacillus and Rothia) were also frequently shared between a mother’s breastmilk and her infant’s gut microbiota, as previously reported46. However, the gut commensals tended to have higher relative abundance in the gut than the breastmilk, suggesting that the infant’s (or mother’s) gut was a source for these organisms colonizing the breastmilk. Overall, our study identifies strong and novel associations between the microbiotas of breastmilk and the infant gut, particularly in the case of bacteria versus fungi.
With its cross-sectional design, this study cannot definitively prove that differences among age groups represent microbiota changes over time; although, such changes are the most compelling interpretation of the results. Sample size, a lack of data on infant and mother health, and on mode of delivery, limited the analysis to effects of age and not other host factors that also may have influenced the microbiotas.