Our friends or foes?

For many years bacteria or microbes have been associated with threats, diseases and fear, so unsurprisingly, lots of effort has been put into devising ways to eradicate them (antibiotics, disinfectants, hand sanitisers). However, in the last two decades, this approach has dramatically changed as research has shown that apart from pathogenic microbes, there are many that actually help us thrive and we could not survive without them.

This piece focuses on the commensal gut bacteria and its role in our wellbeing and health across lifespan.

57% microbial, 43% human – what does it mean?

If we consider the type of cells we are made of, we are more microbes than human. Until recently, it was assumed that the number of bacteria outnumbered human by 10:1. However, this estimate has been recently revisited by researchers from the Weizmann Institute of Science, and now the most up to date estimate states that we are 43% human, with the ratio of human to bacterial cells closer to 1:1.1

So how did the researchers arrived at the 43% estimate? To calculate the number of bacterial cells in a human body, they used a “reference man”, who is between 20 and 30 years old, of about 70 kg and a height of 170 cm.1 They calculated that his body would consist of about 39 trillion bacterial cells among 30 trillion human cells. So, by doing simple maths, 30x1012/(30+39)x1012 they arrived at 0.435 which stands for 43.5%.

We might be outnumbered by bacterial cells, but unsurprisingly our cells outweigh the bacterial ones, which weight only about 0.2 kg across the whole human body.

Within the human body, microbes reach their highest density in the colon. Compared to the colon, the concentration of bacteria in the stomach and the upper 2/3 of the small intestine (duodenum and jejunum) is much lower.This is due to the relatively low pH of the stomach and the fast flow of the content through the stomach and the small intestine1 and may also explain why probiotic supplements have difficulty travelling through these environments.

The microbes inhabiting our gut are referred to as gut microbiota(microbial community, including bacteria, fungi, viruses etc.) or gut microbiome (this term was originally used to refer to collective genomes harboured by microbes in the gut; however, nowadays ‘microbiome’ is colloquially used as a synonym of ‘microbiota’).2 They are a rich and complex community in which microbes interact with each other and with their host. These interactions have profound implications for human health and disease. Their importance for us becomes more clear when we look at the functions of the gut microbiota.

What does the gut microbiome do for us? 2,3,4

The gut microbiome can:

  • break down food components which we cannot digest by ourselves (such as complex sugars such as oligosaccharides)
  • provide us with some vitamins (such B2, B6, B12, K, folate) which we cannot produce on our own
  • help us manufacture some neurotransmitters (e.g. serotonin)
  • produce short-chain fatty acids which can feed other beneficial bacteria and have anti-cancerogenic role
  • assist in metabolism of bile acids
  • reduce the risk of gut colonization by pathogens (like Salmonella and E. coli)
  • take part in maturation and modulation of the immune system
  • break down toxins and drugs

In return, we provide them with nutrients from the food we consume, and with a relatively stable environment to live in.

A few of the gut microbiome functions mentioned above are important for their interaction with the brain, known as the microbiome-gut-brain axis. The gut microbiome plays an important role in mood, metabolism, cognition, and motor function. Disruptions in the microbiome–gut–brain axis have been associated with a variety of diseases, including anxiety, depression, Multiple Sclerosis (MS), Parkinson’s Disease (PD), and autism.5

Healthy microbiome

Scientists agree that the overall composition and function of the human gut microbiome is important for health. Although there is no checklist for ideal microbes, instead, their diversity is understood as key.

A diverse gut microbiome means that there are numerous microbial species with different functionalities evenly distributed in the community, but at the same time, some of them are functionally related so that they could compensate for activities of species that might go missing. In other words, it is a robust and resilient network of microbes which can take over each others’ work if necessary. Consequently, a diverse gut microbiome is seen as an indicator of a healthy gut.2,6

One could compare the diverse and rich gut microbiome to an orchestra, where several musicians and instruments are needed to play a piece of music. Imagine there are 10 violin players, 15 cellos, 5 flutes, 4 trombones, 3 basses, 1 harp, 1 piano etc. and if one musician is unwell, his task might be taken over by a skilled colleague who can play another instrument, or his absence will go unnoticed if the remaining instruments continue to play. Decreased diversity in the orchestra would mean that in an event where only a pianist and one cello player show up to play a concert, they would not be sufficient to play a symphony on their own.

That is why it is easy to imagine that lower bacterial diversity or impaired balance (i.e. dysbiosis) in the microbial community is not good for our health. It has been observed in people who suffer from irritable bowel syndrome (IBS), obesity, metabolic syndrome, inflammatory bowel disease (IBD), some types of cancer, type 1 diabetes, type 2 diabetes, atopic eczema, coeliac disease, psoriatic arthritis, arterial stiffness and type 2 diabetes.2 Recently, features of gut microbiota dysbiosis has been also reported in autism, depression and Parkinson’s disease.

Symptoms of gut dysbiosis include bloating, gas, diarrhoea, constipation, and weight gain (or difficulty losing weight).

What affects microbiome composition?

There is no such thing as a human gut microbiome signature species composition. Looking at the species level, in the gut of an adult human there could be between 150 to 400 microbial species and the microbiome composition varies dramatically between individuals.6,7

Although each person’s microbiome is unique, it changes over the course of one’s life and may still vary from day to day. In addition, some dramatic changes may occur following an infection, antibiotic treatment and significant changes in diet.  

Despite prominent individual differences in microbiome composition, some common geographic and lifestyle patterns have also been identified. For instance, a Western-style diet (i.e. typical for the U.S.) contributes to the loss of 15-30% of gut microbial species as compared to those living in less industrialized areas. These differences have been attributed mainly to diet (increased fibre and decreased sugar, fat, and meat in non-Western diets has been associated with bacterial richness in the gut), environment and access to healthcare (to medications, including antibiotics).8 In addition, westernization of the gut microbiota has been spotted in recent immigrants from non-Western nations to the U.S. This demonstrates that diet, lifestyle and environment can induce profound and rapid changes to the gut microbiome. It is also an example of how fairly resilient gut microbiota can suddenly be substantially altered.

Microbes across lifespan

There are many other factors which affect the diversity and stability of the gut microbiome one of them is age. Although during adulthood the gut microbiome is relatively stable, there are two periods in life when it undergoes a myriad of changes - early life and senescence.9

Levels of Bifodobacteria over a lifespan - Bimuno

Reproduced from https://www.frontiersin.org/articles/10.3389/fmicb.2016.01204/

Early life as an important beginning of gut colonisation

Our gut starts to get colonized at birth, with the bacteria resembling that of the mother’s vagina (if born vaginally), or that of her skin (if born by C-section). From birth to around 3 years of age gut microbiota diversity increases, and its composition starts to look like that of an adult. The process of establishing the gut microbiota is affected not only by the mode of delivery (vaginal vs C-section) but also gestational age, type of feeding (breast milk vs formula feeding), antibiotic usage, timing of the introduction of solid foods and cessation of milk feeding.10

Early gut colonization, between infancy and weaning, plays an important role in adequate maturation and modulation of the infant’s immune system, and thereby affecting protection against infections and the likelihood of allergy and/or atopy.11

Studies show that in addition to reducing the risk of obesity, chronic diseases, such as diabetes and IBD, breastfeeding confers protection against respiratory, gastrointestinal tract infections and allergies. This indicates that just diet makes a big difference to infant health.

During the first year of life, human breast milk promotes a gut microbiome dominated by species of Bifidobacterium. Various components of human breast milk contribute to these effects, with Human Milk Oligosaccharides (which an infant cannot digest itself) having a prebiotic role, feeding beneficial microbes such as bifidobacteria, one of the most abundant bacteria in breast-fed infants.

Formula-fed infants have a different gut microbiota composition, with lower levels of Bifidobacterium as compared to breast-fed infants.9

Recently, researchers demonstrated that the gut microbiome of infants born by C-section and breast-fed, with time becomes comparable to those born vaginally.10 This again demonstrates how the diet has impact on the gut microbiota.

Gut microbiome diversity decreases with age

The elderly have a different gut microbiome profile compared to healthy younger adults. Generally, their gut microbiome diversity is decreased, and the overall composition is changed, with reduced levels of commensals such as bifidobacteria and lactobacilli, and increased levels of opportunistic bacteria.9

These changes could be attributed to several features of ageing, such as changed lifestyle and dietary schedule, decreased mobility, weakened immune strength, reduced intestinal and overall functionality, recurrent infections, hospitalizations, and use of medications. On the other hand, decreased gut microbiota diversity is associated with increased inflammation, which is a risk factor for many age-related diseases, including Alzheimer’s disease.

Given that gut microbiome diversity is currently perceived as one of key factors for longevity and healthy ageing, maintaining a healthy gut microbiome may lead to a reduced incidence of disease and contribute to longevity.9

How to maintain a healthy, diverse gut microbiome? – Focus on the diet

Diet emerges as one of the most important factors affecting the gut microbiome and at the same time appears as one of the “easiest” to take control of. There are fairly simple steps one can take to improve or maintain a healthy gut microbiome.

On one hand, there are foods and diets proven to reduce microbiome diversity: artificial sweeteners such as sucralose, aspartame, and saccharin; emulsifiers such as polysorbate-80 and carboxymethyl cellulose; antiseptics such as potassium sorbate and sodium benzoate; restrictive diets such as gluten-free.2

On the other hand, the gut bacteria have their food preferences, and these foods produce predictable shifts in the existing gut bacterial community. First of all, eating a varied, balanced diet is likely to lead to an equally diverse microbiome. If focusing on specific gut microbiome favourites, eating a diet rich in prebiotics (fibre)polyphenols and omega-3 fatty acids is key for a healthy microbiome as it has been shown that these nourish the good gut bacteria.12


  • 1 Sender R., Fuchs S. and Milo R. (2016) Revised estimates for the number of human and bacteria cells in the body. PLOS Biol 14(8):e1002533.
  • 2 Valdes AM, Walter J, Segal E, Spector TD. (2018) Role of the gut microbiota in nutrition and health. BMJ;361:k2179.
  • 3 LeBlanc JG et al. (2013) Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol.;24(2):160-8.
  • 4 Cani P (2018) Human gut microbiome: hopes, threats and promises. Gut; 67:1716–1725. 5 Knight R, Callewaert C, Marotz C, et al. (2017)
  • The microbiome and human biology. Annu Rev Genomics Hum Genet; 18:65–86.
  • 6 Lloyd-Price J, Abu-Ali G, Huttenhower C. (2016) The healthy human microbiome. Genome Med.;8:51.
  • 7 Davenport ER et al. (2017) The human microbiome in evolution. BMC Biology 15:127.
  • 8 Vangay P, Johnson AJ, Ward TL et al. (2018). US immigration westernizes the human gut microbiome. Cell 175, 962–972.
  • 9 Nagpal R, Mainali R, Ahmadi S, et al. (2018) Gut microbiome and aging: Physiological and mechanistic insights. Nutr Healthy Aging. 4(4):267-285.
  • 10 Hill CJ, Lynch DB, Murphy K et al. (2017) Evolution of get microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome. 5:4.
  • 11 Tanaka M, Nakayama J (2017) Development of the gut microbiota in infancy and its impact on health in later life. Allergology International 66: 515-522.
  • 12 Lockyer S, Stanner S (2019) Prebiotics – an added benefit of some fibre types. Nutrition Bulletin 43:1-18.

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