CSUN microbiologists reveal how a taste for milk lets this bacterium make its home in our guts

We aren’t born with our gut microbiome, but we do acquire it very early in life — so early that the community of bacteria in our digestive tract is probably heavily influenced by the nutrients available in human milk. A new paper by CSUN microbiologists identifies the specific genes that enable one genus of gut-associated bacteria to take advantage of milk sugars, and settle in for a symbiosis that can last a lifetime.

Akkermansia bacteria are beneficial members of the gut microbial community, where they digest mucin produced by gut epithelial cells. However, Akkermansia can also grow on the complex sugars, or oligosaccharides, found in human milk, breaking them down into forms that stimulate mucin production and which may aid in milk digestion by their host. Work by the lab of CSUN Associate Professor of Biology Gilberto Flores has identified a strain of Akkermansia biwaensis that grows particularly efficiently on human milk oligosaccharides, and may carry unique genetic coding to break them down. This ability would help A. biwaensis establish in the guts of breastfeeding infants as one of the first members of their developing microbiomes.

In the new paper, lead author and CSUN Biology Master’s alumnus Loren Padilla worked with postdoctoral researcher Ashwana Fricker, recent BSci graduate Estefani Luna, as well as Flores and collaborators at UC San Diego and Duke University School of Medicine to identify Akkermansia genes that could explain its taste for milk. They compared the DNA sequence, gene expression, and metabolic products of A. biwaensis to related A. muciniphila, which is markedly less efficient in growth on milk sugars. Two genes located close together in the A. biwaensis genome turned out to be actively expressed while digesting milk oligosaccharides, and absent from the A. muciniphila genome. The purified protein product of one of these genes proved to degrade a target oligosaccharide in vitro; and a strain of A. muciniphila engineered to express the other gene showed growth on milk oligosaccharides comparable to A. biwaensis. This experimental evidence confirms the two genes account for A. biwaensis‘s capacity to use milk sugars — and let it establish in infants’ guts.

The full paper is available Open Access on the Journal of Bacteriology website.