Our gut microbiome ages too.

Updated: Aug 4, 2020

It is fairly well known (in science circles), that Firmicutes, Bacteroidetes, and Actinobacteria are the predominant microbial groups in the gut (Singh, et al. 2017; Kho & Lal, 2018). The figure below shows the taxonomy (Rinninella, et al. 2019). However, as the microbiome is a reflection of our lives (and diet), there are significant changes in the combination and volume of microbes from birth to death.

As babies, we have what’s called commensal microbes which protect us from pathogens along with supporting our immune system. Some commensal bacteria can predisposition us for immune-mediated diseases from birth, e.g. E. coli encourages gliadin (a protein in gluten) to flare the immune system, where Bifidobacteria spp inhibit this (Tlaskalvoa-Hogenova, et al. 2011). We get our commensal microbiome from the vaginal canal during a natural birth, or from the hospital and skin tissues we brush as we are pulled from a cesarean. Microbiome colonisation in infants is also different, depending on whether they were preterm or full term (preterm being less diverse) (Rinninella, et al. 2019). Although, “human milk oligosaccharides (HMOs) related to different mother phenotypes modulate gut microbiota composition in infants” and may be protective (Rinninella, et al. 2019). The mother's microbiome in this case plays an integral role, and would be significant to the predisposing and excitatory factors for the child (Rinninella, et al. 2019). Bifidobacterium are responsible for the fermentation of galactooligosaccharide (GOS), one of the main components of breast milk, so if an infant was struggling to digest breast milk this may be an indication of low levels of Bifidobacterium at that time.

Kho and Lal (2018) report that commensal bacteria such as Bacteroides fragilis, Bifidobacterium infantis, and Firmicutes are crucial in regulating inflammation and tolerance. Building up these particular microbes with prebiotics and specific probiotics may improve the patients symptoms. This is important to achieve their optimal microbiome at a peak age (between 3 and 8 years), before it begins to degrade over time - improving their chances of having a well-positioned microbiome (and therefore a well-maintained immune system, etc.) in the long-term.

During weaning from breastmilk (or formula), the microbiome changes. High-fibre and carbohydrate foods encourage Firmicutes and Prevotella, where high-fibre and animal protein encourage Bacteroidetes (Rinninella, et al. 2019). At one year of age the microbiome composition has Akkermansia muciniphila, Bacteroides, Veillonella, Clostridium coccoides spp., and Clostridium botulinum spp.. By three years old, a child’s microbiome should have a similar diversity and composition to an adult - yet still stabilises with age (Rinninella, et al. 2019).

There is significant variation in Bacteroidetes and Firmicutes between individuals, though the individuals experience less variability over time (Saraswati & Sitaraman, 2015). Any use of antibiotics (generally) reduced bifidobacteria and the Bacteroides-Prevotella group, therefore consistent or recurrent use at any age (though, more so with age) can predispose an individual to infection and increase the chance of a poorly performing microbiome in old age (Saraswati & Sitaraman, 2015).

Belov (2019) seems to suggest that by age 60, the microbiome is less diverse, with less beneficial microbial activity and more enterobacteria (pro-inflammatory bacteria). They generally have a higher volume of proteobacteria, but compared to young adults, have a higher proportion of Bacteroidetes (Aleman & Valenzano, 2019; Saraswati & Sitaraman, 2015). The elderly also likely to have less lactobacilli, Bacteroides/Prevotella and Faecalibacterium prausnitzii, and an increase in the proportion of Ruminococcus, Atopobium, and Enterobacteriaceae (i.e. less protective microbes). This was more associated with “frailty scores” and a general decrease in diversity, diet diversity and increase in inflammatory markers - which is increasingly common (Saraswati & Sitaraman, 2015). The authors particularly note that this negative change in the elderly microbiome was worse for living in care and stay in hospital (Saraswati & Sitaraman, 2015). Interestingly Saraswati & Sitaraman (2015) report that genes involved in aromatic amino acid metabolism and SCFA production may have some control over the microbiome in old age, suggesting that a decreased number of these genes may play a part in a longer life. Therefore, encouraging a strong population of SCFA producing microbes is important in maintaining health.

Reasonably, diet is the largest controllable factor that influences microbiome composition - one which also then impacts the next generation. High fat and high sugar diets generally promote Bacteroides-dominance, and high fibre generally promotes Firmicutes (e.g. Lactobacillus, Bacillus, Clostridium, Enterococcus spp) (Saraswati & Sitaraman, 2015). Largely, diversity of foods also allows diversity in microbes. Even if an individual starts out with a poor microbiome, there is time to build it up before they reach their peak.


Aleman, F. & Valenzano, D. (2019). Microbiome evolution during host aging. PLoS Pathogens. Retrieved from: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007727

Belov, A. (2019). Ageing and the microbiome: what happens when you get older?. Altas Blog. Retrieved from: https://atlasbiomed.com/blog/ageing-and-the-gut-microbiome/#age

Kho, Z. & Lal, S. (2018). The Human Gut Microbiome - A Potential Controller of Wellness and Disease. Frontiers in Microbiology, vol 9. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102370/

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G., Gasbarrini, A. & Mele, M. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, vol 7. Issue 1. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351938/

Saraswati, S. & Sitaraman, R. (2015). Aging and the human gut microbiota - from correlation to causality. Frontiers in Microbiology. Retrieved from: https://www.frontiersin.org/articles/10.3389/fmicb.2014.00764/full

Singh, R., Chang, H., Yan, D., Lee, K., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T., Bhutani, T. & Liao, W. (2017). Influence of diet on the gut microbiome and implication for human health. Journal of Translational Medicine, vol 15. Issue 73. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385025/

Tlaskalvoa-Hogenova, H., Stepankova, R., Kozakova, H., Hudcovic, T., Vannucci, L., Tuckova, L., Rossmann, P., Hrncir, T., Kverka, M., Zakostelska, Z., Klimesova, K., Pribylova, J., Bartova, J., Sanchez, D., Fundova, P., Borovska, D., Srutkova, D., Zidek, Z., Schwarzer, M., Drastich, P. & Funda, D. (2011). The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cellular & Molecular Immunology, vol 8. Issue 2. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4003137/

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