Analysis of the microbiota of human milk and baby faeces in Nigeria, using molecular and culture-based approaches

Human breast milk had been traditionally considered sterile. In recent years, studies have suggested that human milk carries bacteria that may help babies build up a beneficial population of bacteria in their gut, which plays a protective role. This research is the first in Nigeria to explore the bacterial diversity in breast milk and compares it with the gut of breastfed babies in addition to looking at the gut microbiota of formula-fed babies. Nigeria is a developing country and owing to its unique characteristics; it becomes important to investigate the presence of these bacteria in breast milk and have coherent data on the type and diversity of the bacteria in breast milk and babies' guts. This may help to build up more awareness about the importance of breastfeeding and its role in the initiation of infant gut microbiota including its importance in the modulation of the infant immune system in addition to other nutritional benefits.

To achieve this goal, pilot research was undertaken in the UK using milk samples from seven mothers and faeces from their breastfed babies to allow for the optimization of the methodology starting from sample collection. The presence of five bacterial genera, including bifidobacteria, lactobacilli, streptococci, staphylococci, and enterococci, in the breast milk and faeces, was investigated using a traditional culture approach followed by species identification by MALDI-TOF Biotyper, as well as a culture-independent method by extracting total microbial DNA from these samples and then using qPCR. Following that, samples of breast milk from 50 breastfeeding mothers in Nigeria, as well as the faeces of their babies, and the faeces of 8 solely formula-fed babies, were collected and analysed using culture technique and 16S ribosomal ribonucleic acid (16S rDNA) NGS sequencing (MiSeq Illumina).

Human milk has a highly personalised microbiota with a lot of inter-individual variabilities, according to the present study. It was revealed that the milk microbiota of mothers from Nigeria is characterised by the high dominance of phylum Firmicutes (61%) mainly represented by the orders Lactobacillales and Bacillales next to the phylum Actinobacteria (26%) largely represented by Micrococcales and Corynebacteriales and then Proteobacteria (10.5%) represented by Caulobacterales and Pseudomonadales. In the faeces of breastfed babies, there was high dominance of members of Actinobacteria (62.6%), Proteobacteria (24%), and Firmicutes (11.6%) represented by bifidobacteria, Escherichia/Shigella as well as streptococci respectively. Within a sample diversity (i.e., alpha diversity) revealed that the milk of Nigerian mothers had higher observed bacterial richness and diversity for a single sample when compared to the gut of breastfed babies. Beta diversity also revealed that human milk and baby faeces had obvious differences, but it is predicted that about 51% of bacteria in baby faeces may have originated from human milk as revealed by source tracker analysis. Furthermore, it was revealed that breastfed babies had lower microbial diversity, but a higher abundance of certain bacteria such as bifidobacteria in their gut compared to formula-fed babies. Faecalibacterium was also exclusively found in the gut of formula-fed babies. The delivery mode revealed an association with gut microbiota, while parity revealed an association with mother’s milk; for example, babies born by C-section had a higher abundance of Klebsiella in their gut compared to babies born naturally via the vagina, while multiparous mothers had a higher abundance of Brevundimonas in their milk.

This study, in addition to providing an overview of the microbiota found in mother's milk and babies' faeces in Nigeria, provides evidence that mothers can transmit bacteria to their breastfed babies via breastmilk; that babies' gut microbial composition varied depending on the type of food they received; and that some maternal or baby factors may influence maternal milk or gut microbiota.