Gut Health as We Age – The Microbiome Through the Life Course

The gut microbiome is a community of microorganisms that live in the gastrointestinal tract. This microbiome is unique to each of us, even in the case of genetically identical twins. Throughout our lives, the gut microbiome fluctuates. As we reach old age, our microflora experiences large shifts similar to those seen in infancy. Interestingly, these two life stages are when we are the most vulnerable to disease. These findings suggest that our microbiota and health develop and age as a team, and build a case for why many refer to our microbiome as an extension of self.

Why is our gut microbiome important?

The colonization of the human microbiome begins immediately after birth.1,2 The gut microbiome has co-evolved with humans and represents the largest concentration of microorganisms in the human body.2 It is often referred to as the second genome, because it contains a large array of genetic information. Gut health is so important in fact, that human breastmilk has been “designed” with a function to feed desired bacteria and shape the intestinal microbiota of infants.1,3

Our gut microbiome, which consists of trillions of bacteria, viruses, fungi, archaea and some unicellular eukaryotes, not only enables us to extract nutrients from foods that we cannot digest ourselves, but is also in constant ‘chatter’ with our own cells.2 Because of these inhabitants, we ourselves have lost the ability to produce thousands of metabolites, so there is no wonder that our health is affected significantly by the communities in our gut.4 Our relationship is symbiotic, meaning that it benefits both, the host and the commensals.

The correct composition and functionality our microbiome is essential for maintaining a ‘healthy status’.2 It is difficult to state what exact microbial composition is deemed ‘healthy’ because there is huge inter-individual variability. However, certain shifts in microbial composition have been linked to several pathologies.5,6

Early life1,3,7

Upon birth, beneficial bacteria colonize the gut (Fig. 1). The mode of delivery (vaginal or C-section) and mode of feeding (breast or bottle feeding) have an effect on the microbiome development. Both modes are related to the rate of microbial colonization; vaginal delivery transfers maternal vaginal bacteria to the new-born, whilst breastmilk contains its own microbiota, signalling molecules and human milk oligosaccharides which feed beneficial microbes. It is known that the rate at which the gut microbiota is established affects future health.

Fig 1. Graph taken from Dogra et al. (2015) on PubMed. Modified – graph only party shown. “(…) schematic diagram representing a simplified view of the progression of the infant fecal microbiota across the first year of life, incorporating Stages (A–D)”. Stage D represents a more adult-like microbiota.3

It is known that a healthy microbiome prevents the adhesion of pathogenic bacteria by literally using up all the space. Beneficial bacteria also produce secondary metabolites, like the short chain fatty acids (SCFAs) that inhibit the growth of pathogens. SCFAs also enhance host immunity having a localised as well as a systematic (whole body) effect.

“Our gut composition is largely unstable in the first years of life. From an initial low diversity and complexity, the intestinal microbiota evolves until reaching a diverse, complex, and stable population about the age of 3 y”.8


In healthy adults, the phylum Firmicutes and Bacteroidetes represent 80-90% of the total gut microbiome. Despite inter-individual variation, the genera Bacteroides, Provotella and Ruminococcus are most dominant. Adult microbiota is associated with long term dietary patterns as well as short term diets. Whilst it is considered relatively stable, alterations do occur due to stress, antibiotics use, diet and lifestyle. We know that gut microorganism diversity is beneficial, because many pathologies are linked to the reduction of such.

Advanced age2,8-10

“Our microbiota undergoes the most prominent deviations during infancy and old age and, interestingly, our immune health is also in its weakest and most unstable state during these two critical stages of life, indicating that our microbiota and health develop and age hand-in-hand”.5 As we age, the opposite of infant gut colonization (Fig. 1) occurs and the microbiota becomes unstable again. Bacterial diversity can drop and there is a shift in dominant species – generally fewer members of the phylum Firmicutes and Actinobactera and more Proteobacteria. These changes in the bacterial communities also result in fewer SCFA-producers and hence less SCFAs. These changes happen gradually and at different rates in different people. Whilst changes in microbial composition are common and do not necessarily predict illness, in elderly subjects specifically, altered microbiota has been linked to several illnesses (Fig. 2), such as infections, bowel disorders and hypertension.

Fig 2. Graph taken from Nagpal et al., 2018) on PubMed. “The two-way connection between human gut microbiome and host aging, and the potential underlying and/or associated elements”.5


  1. Bode, L. 2012. Human milk oligosaccharides: every baby needs a sugar mama. 22(9), pp.1147-1162.
  2. Zapata, H.J. and Quagliarello, V.J. 2015. The microbiota and microbiome in aging: potential implications in health and age-related diseases. Journal of the American Geriatrics Society. 63(4), pp.776-781.
  3. Dogra, S., Sakwinska, O., Soh, S.-E., Ngom-Bru, C., Brück, W.M., Berger, B., Brüssow, H., Karnani, N., Lee, Y.S., Yap, F., Chong, Y.-S., Godfrey, K.M. and Holbrook, J.D. 2015. Rate of establishing the gut microbiota in infancy has consequences for future health. Gut microbes. 6(5), pp.321-325.
  4. British Nutrition Foundation. 2020. Personalised Nutrition: Listen to your gut.[Online]. [Accessed 4April 2020]. Available from:
  5. Nagpal, R., Mainali, R., Ahmadi, S., Wang, S., Singh, R., Kavanagh, K., Kitzman, D.W., Kushugulova, A., Marotta, F. and Yadav, H. 2018. Gut microbiome and aging: Physiological and mechanistic insights. Nutrition and healthy aging. 4(4), pp.267-285.
  6. Tuohy, K.M., Fava, F. and Viola, R. 2014. ‘The way to a man’s heart is through his gut microbiota’ – dietary pro- and prebiotics for the management of cardiovascular risk. Proceedings of the Nutrition Society. 73(2), pp.172-185.
  7. Childs, C. 2020. Immunity Webinar Series, Part 2: Gut Health & Immunity through the Lifecourse. [Online]. [Accessed 20 May 2020] Available from:
  8. Salazar, N., Valdés-Varela, L., González, S., Gueimonde, M. and de Los Reyes-Gavilán, C.G. 2017. Nutrition and the gut microbiome in the elderly. Gut microbes. 8(2), pp.82-97.
  9. Askarova, S., Umbayev, B., Masoud, A.-R., Kaiyrlykyzy, A., Safarova, Y., Tsoy, A., Olzhayev, F. and Kushugulova, A. 2020. The Links Between the Gut Microbiome, Aging, Modern Lifestyle and Alzheimer’s Disease. Frontiers in cellular and infection microbiology. 10, pp.104-104.
  10. Xu, C., Zhu, H. and Qiu, P. 2019. Aging progression of human gut microbiota. BMC Microbiology. 19(1), p236.
Rusne Z

Rusne Z.

Rusne is a United Kingdom-based writer passionate about nutrition as treatment and prevention of illness. She is currently completing her Bachelor in Food Science and Nutrition at the University of Leeds, and has Research & Development experience in the reformulation of sugary soft drinks.

Apart from her studies, Rusne particularly enjoys cooking, travelling and exploring independent coffee shops.

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