In previous articles related to autoimmune diseases (Is Bread Certain Death?, Autoimmune Diseases - Prevalence and Role of the Major Histocompatibility Complex, and Gender Differences in Autoimmune Diseases), I have touched upon the role of the microbiome in disease initiation and progression.

Rob Knight's Ted Talk from 2015 provides fascinating insights on the microbiome and how this influences human health: How our microbes make us what we are

A central theme of this video is the succession of microbes that normally develop in the human gut and which can be perturbed by various interventions (e.g. C-section at birth, use of antibiotics). Diet clearly may also play a critical role in altering the microbial community:

Hadrich, D. Microbiome research is becoming the key to better understanding health and nutrition. Front. Genet. 9: 212 (2018)

Nagpal, R., Shively, C.A., Appt, S.A., Register, T.C., Michalson, K.T., Vitolins, M.Z., Yadav, H. Gut microbiome composition in non-human primates consuming a Western or Mediterranean diet. Front. Nutr. 5: 28 (2018)

Sonnenburg, J.L, Bäckhed, F. Diet-microbiota interactions as moderators of human metabolism. Nature 535: 56-64 (2016)

David, L.A., Maurice, C.F., Carmody, R.N., Gootenberg, D.B., Button, J.E., Wolfe, B.E., Ling, A.V., Devlin, A.S., Varma, Y., Fischbach, M.A., Biddinger, S.B., Dutton, R.J., Turnbaugh, P.J. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-563 (2014)

However, progress in understanding the regulation of this complex microbial community in the gut, and how the microbes interact with one another, has been hindered by a lack of a suitable in vitro model.

Escherichia coli, one of the many species of bacteria present in the human gut. Image Source:

Very recently a protocol has been developed for studying the dynamic gut microbiome succession in a synthetic human gut microbiome community:

Venturelli, O.S., Carr, A.C., Fisher, G., Hsu, R.H., Lau, R., Bowen, B.P., Hromada, S., Northen, T., Arkin, A.P. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol. Syst. Biol. 14: e8157 (2018)
"Analysis of microbial interactions in a synthetic human gut microbiome community shows that pairwise microbial interactions are major drivers of multi-species community dynamics. The study reveals ecological drivers, metabolite hub species and ecologically sensitive organisms in the network."

The above article by Venturelli et al (2018) is accompanied by a commentary/editorial by Abreu et al. (2018):

Abreu, C., Lopez, A.O., Gore, J. Pairing off: a bottom-up approach to the human gut microbiome. Mol. Syst. Biol. 14: e8425 (2018)
"Analyses of how the gut microbiome develops and evolves through interspecies competition and cooperation have been lacking. In their recent work, Venturelli et al (2018) build a synthetic gut bacterial community and predict its dynamics with a simple network of pairwise interactions."

This in vitro innovation has potential to assist in understanding the mechanisms contributing to gut microbiome dysbiosis and development of autoimmune diseases.