Impacts on the Microbiome

Factors that influence our microbes include:

  • Age
  • Diet
  • Antibiotic use
  • Genetics
  • Physiology

The factors above change the selective environment for gut microbes but they do not change the kind of bacteria – only the amount.



We start with a sterile gut and then accumulate microbes. Babies therefore have low gut microbial diversity and gain more microbes as they meet other people and environments. Their microbes continue to develop as they eat solid foods and explore the world. Microbes become more diverse and stable as we get older. In old age, we lose stability and the composition changes.



Long and short term changes affect our microbes. For instance:

  1. Long-term: those who eat a high carbohydrate diet tend to have lots of Prevotella, whereas those who eat more meat will have more Bacteroides (Wu 2011). Across nations and cultures, if diet falls into a specific category, then so will the microbiota (Yatsunenko et al. 2012)
  1. Short term: (Wu 2011): using a controlled diet for 10 days (low-fat vs high-fat) the observed changes were relatively minor and communities still looked like their original. More extensive diet changes cause increases in some microbes (David et al 2013,Nature)

Diet has one of the largest impacts on the gut microbial community



Antibiotics prevent bacteria from doing things such as: making proteins, dividing, making cell walls and transporting nutrients. They also put holes in cell walls.

Most bacteria die when exposed to antibiotics

Antibiotic resistance is a problem as bacteria evolve to be immune to antibiotics. This makes us vulnerable to pathogens that can’t be stopped.

Antibiotics do not target pathogenic bacteria! They kill all bacteria in their path!

Different antibiotics have different effects and different people experience different effects and may take longer to recover. Some effects can be permanent.

We can counteract these effects by taking probiotics which are live microorganisms. These appear to be helpful in alleviating the symptoms of gastro intestinal disorders, obesity and mood disorders.



When looking at genetic influence, studies have shown mixed results and very subtle changes to microbiota.

Studies have used mono-zygotic twins (same egg and same DNA) as opposed to di-zygotic twins (different egg and different DNA). If mono-zygotic twins have similar microbes then genetics must play a role. The studies have shown conflicting data. Studies also looked at individuals with different genetics in the same environment to see if microbes change to become similar. If they do, then environment is more important, if not then genetics is more important. Mouse studies suggest that environment is more important than genetics but studies show that the presence or absence of a particular gene has a big impact on the relative abundance of microbes – especially for the genera and species, but not the phylum.

The impact of host genetics is not as important as other factors but it does exist



This includes hormone levels, immune system functioning, metabolism etc.



The Human Microbiome Course

What is a Microbe?

The Human Microbiome

How we study the Microbiome Part 1

How we study the Microbiome Part 2

Impacts on the Microbiome

Microbiome and Obesity

The gut microbiota, autoimmune diseases and allergies

Human Microbiota and Gut Disease

Interactions between the Gut Microbiota and Immune System

The Gut-Brain Axis

Useful website articles and links


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