September 2012

How human milk nurtures the gut microbiome

Cover of the September 2012 issue of the journal Molecular & Cellular Proteomics

Breastfeeding is a major influence on the makeup of a baby’s gut microbiome, because human milk has been shaped by evolution to nourish and protect infants. “Notably milk guides the development of the infant gut microbiota, in particular enriching for certain Bifidobacterium species,” explains David Mills at the University of California, Davis.

Bifidobacteria are symbiotic bacteria in the human colon. In a recent paper in Molecular & Cellular Proteomics, Mills and colleagues analyzed how bifidobacteria digested N-glycans from complex milk glycoproteins (1). Babies can’t digest these N-glycans, so the study, says Mills, is the first “to explain how these glycoproteins might serve as growth substrates for bifidobacterial enrichment.”

To break down N-glycans, Mills and colleagues established that the bifidobacteria had special endoglycosidases. The most interesting enzyme was EndoBI-1, the endoglycosidase from a particular bacterium called Bifidiobacterium infantis that is predominant in the infant gut microbiome. EndoBI-1 “was amazingly unique in its ability to cleave any type of N-linked glycan away from the corresponding protein,” says Mills, adding that the finding strengthened the argument that B. infantis “evolved in concert with mammals and lactation.”

Furthermore, the researchers discovered that EndoBI-1 is heat stable. “This feature, combined with the ability to cleave any type of N-linked glycoprotein, potentially makes this enzyme a very useful tool in proteomics and pharmaceutical research,” notes Mills. He adds that because bifidobacteria are eaten as probiotics, EndoBI-1 could have “a slew of applications in food processing as well.”

  1. 1. Garrido, D., et al. Mol. Cell. Proteomics (2012) DOI 10.1074/mcp.M112.018119.


Raj_MukhopadhyayRajendrani Mukhopadhyay ( is the senior science writer for ASBMB Today and the technical editor for The Journal of Biological Chemistry. Follow her on Twitter at

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