Science

2.1 Homesteading (3)

We talked briefly that certain studies postulate that the current human-microbe relationship began with the dawn of agriculture when humans began to actively shape and structure their external ecosystem[i]. So a relationship began that has continued for thousands of years: we are born, inoculated, and select[1] for the microbes that will make our human holobiont their home. Or from the microbial point of view, they find a nutrient rich river valley where they tame the locals, build cities, find jobs that fit their skills, and avoid being murdered by predators.

Selection is a fancy way of saying that the three necessary elements of settlement influence who moves into our guts and what they can do. Selection is a broad terms for various environmental pressures like types of carbohydrate handles that microbes use to attach to the mucus layer, the immune response of our GALT, the microbes already there, the viruses that prey on bacteria, and the foods we eat[2]. Though there is growing evidence that during gestation, maternal forces are active in positioning the mother’s gut microbiota for transfer to her offspring via breast milk[ii], most of the selective elements get laid down after birth[iii].  All are highly modified and rely on initial microbial inoculation, which, in turn, could determine our holobionts’ health for the rest of our lives.

With species diversity, fluctuation in our microbial population, and functional niches all influencing the health of our GI tract, perhaps the best way to understand how to keep our personal holobiont healthy and thriving is to look back at the original colonizers. The microbial populations in the infant gut seem to fluctuate drastically before the introduction of solid foods. They then settle into a relatively stable adult profile by age two. Even though most of the species that seem to thrive in the infant gut disappear, many scientists believe now that the initial microbes matter in later gut shaping.  The settlement of cities like Rome was accomplished in layers as newer inhabitant built on older structures which ultimately influenced the shape of the city. The current inhabitants of Rome today may know little to nothing of the people who built there before (as evidenced by the times when a person discovers that she’s been accidentally parking her Vespa in Nero’s theater), but they are definitely influenced in how they lived based on the layout of the city, the paths of irrigation canals, statues of gods worshiped. Just so, even if they seem to be transient participants in our gut market, our initial microbial inhabitants could possibly have drastic ramifications on our gut health in later life.

[1] Selection is an ecological terms that describes the shifts in genes and species in response to environmental pressures.
[2] Viral presence plays a huge role in selection. We haven’t forgotten about them. However, while we know that viruses have been around us as long as microbes have, their role in shaping and communicating with our human biont is still poorly understood. Viruses are very important to the human holobiont as they are to every holobiont. But this chapter will focus mostly on microbial interactions with our human biont.
[i] Alex Mira, Ravindra Pushker, and Francisco Rodríguez-Valera, “The Neolithic Revolution of Bacterial Genomes,” Trends in Microbiology 14, no. 5 (May 1, 2006): 200–206, doi:10.1016/j.tim.2006.03.001.
[ii] Anne Donnet-Hughes et al., “Potential Role of the Intestinal Microbiota of the Mother in Neonatal Immune Education,” The Proceedings of the Nutrition Society 69, no. 3 (August 2010): 407–15, doi:10.1017/S0029665110001898.
[iii] Song, Dominguez-Bello, and Knight, “How Delivery Mode and Feeding Can Shape the Bacterial Community in the Infant Gut.”
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