Metagenomic Analysis of Bacterial Microbiota in Breast Milk

There are still many unknowns about the exact bacterial composition of breast milk, and the theoretical and real risks represented by its microbiota. In addition to determining the Total Aerobic Flora (TAF) and the Staphylococcus aureus presence, the most commonly isolated enterobacterales species identified by agar culture by the Prevention and Infection Control department are also among those potentially found in diagnostic samples: Enterobacter cloacae, Klebsiella pneumoniae, Klebsiella aerogenes, Klebsiella oxytoca and Escherichia coli. However, it is not yet known whether these are identical strains or not. It is therefore legitimate to ask whether there are any differences between the strains present in the microbiota of breast milk and those responsible for newborn infections.

Conventional methods for enumerating and identifying the bacteria making up the milk microbiota are not standardized, which makes it difficult to draw up a precise, multicentric inventory of its composition. It is therefore impossible to know whether exceeding a threshold value defined by expert consensus represents a real danger for newborns who must receive breast milk.

At the Centre National de Recherche en Génomique Humaine (CNRGH), a metagenomic sequencing approach makes it possible to study the microbiota using two complementary methodologies. Either by sequencing the genomes of organisms (bacteria, viruses, fungi, etc.) present in the environment to be analyzed (shotgun metagenomics), or by sequencing one or more genes specific to each bacterial species (targeted metagenomics). The gene that codes for 16S ribosomal RNA (rRNA) has sequence regions common to different bacterial species, as well as variable regions that can be used to distinguish the bacteria present in a sample.

A comparison of the composition of the bacterial microbiota in breast milk using conventional agar culture methods and metagenomic analysis methods would enable us to make progress in understanding its potential involvement in infectious pathologies in premature infants. It is in this scientific and medical context that a collaborative project was initiated for the first time between the departments of Neonatal Medicine and Intensive Care and of Prevention and Infection Control, and the CNRGH. This was a pilot study with the aim of perpetuating this collaboration, which combines scientific knowledge of the metagenome with the CNRGH's high-performance technological tools, as well as potential applications in the medical environment in the CHSF's care departments.