Almost simultaneously as the skills of aerobes and anaerobes dictating niches and stratification, the second necessary step of successful colonization occurs as the infant begins pumping nutrient energy into the gut ecosystem. We know what we eat matters for both the adult and infant microbiota, and scientists are working hard at figuring out exactly why. One lucky premature infant received a full microbial sequencing as the child moved in and out of the NICU ^[i].  Some of the most observable and drastic changes occurred when the child switched from a diet of breast milk to intravenous feeding to formula feeding: the microbial population^[1] as well as activated microbial genes radically shifted each time the child changed diet, external environment, and went off and on antibiotics.

This study tells us one thing: while mode of initial inoculation matters, diet also matters just as much. But it still doesn’t let us know if a certain diet is better than another. Just as there isn’t a solid population consensus on what exactly lives in our adult guts, there is also confusion on the infant’s gut as well. Until the more stable adult microbiota becomes fully established, the infant gut is subject to dramatic fluctuations and shifts that seem to leave the tiny human biont relatively unscathed.  There are many things that baffle researchers, for example C. difficile, a normally pathogenic microbe in adults, appears to be common in many healthy infant guts. Further, despite many respected researchers’ maintaining that species diversity is fundamental to adult gut health^[2], the gut of a breastfed infant lacks the overall microbial diversity of its formula fed counterpart; however, a group of breastfed infants did prove to be more diverse within the particular genus Bifidobacterium^[3] than formula fed infants^[ii].  While these studies do not show that breastfeeding is the clear better way of feeding your infant, they do show that breast milk has measurable effects on our gut ecosystem.

^[1] Also present in this child’s gut were phage and plasmids.

^[2] We’ll discuss more about species diversity and its ecological implications later. There is an intriguing counter argument to the diversity argument which claims that species diversity in the gut is not a valuable indicator of metabolic health; rather, we need to examine functional diversity (which types of energy a microbial community processes and what products do they make from that energy) rather than species diversity. So instead of who lives in our gut ecosystem, the more interesting question would be what do they do.

^[3] Diversity in a genus means there were a variety of species that all fall under the Bifidobacterium genus.

^[i] Michael J. Morowitz et al., “Strain-Resolved Community Genomic Analysis of Gut Microbial Colonization in a Premature Infant,” Proceedings of the National Academy of Sciences, December 29, 2010, doi:10.1073/pnas.1010992108.

^[ii] Laure C Roger and Anne L McCartney, “Longitudinal Investigation of the Faecal Microbiota of Healthy Full-Term Infants Using Fluorescence in Situ Hybridization and Denaturing Gradient Gel Electrophoresis,” Microbiology (Reading, England) 156, no. Pt 11 (November 2010): 3317–28, doi:10.1099/mic.0.041913-0; Laure C Roger et al., “Examination of Faecal Bifidobacterium Populations in Breast- and Formula-Fed Infants during the First 18 Months of Life,” Microbiology (Reading, England) 156, no. Pt 11 (November 2010): 3329–41, doi:10.1099/mic.0.043224-0.