Which species should be present in a healthy gut microbiome?

Author:Dr Paula Smith-Brown (APD, PhD)

August 2021



Are there any species a healthy microbiome must contain?

Over the last decade the use of high throughput technology for sequencing the gut microbiome has led to a revolution in our understanding of the role of the gut microbiome in human health and disease. These technologies have now advanced to the stage where it has become cost effective enough to allow healthcare professionals to measure their patient’s microbiome using the gold standard approach, known as shotgun metagenomics. This unprecedented comprehensive view of your patient’s microbiome provides much information to guide patient care but can also lead to many questions about what we should expect to see and what exactly makes a microbiome healthy.

Metagenomic sequencing works by ‘reading’ all the DNA in a faecal sample which allows the whole genome of microorganisms to be captured. In practice the benefit of measuring the whole genome is that it allows the accurate identification of all species within a sample, but the real clinical advantage is that it also reveals which microbes contain the genes required to perform important functions, providing information on the microbiome’s functional potential. Read on to find out how this complete understanding of the microbiome’s functional potential and the species providing these functions can contribute to improved patient outcomes.


So, are there species that are considered ‘healthy’ and which ones are they?

When looking at a patient’s Insight™ report you might be hoping to see well known beneficial species. These might be common probiotic species or species identified in the scientific literature as being associated with health. The widespread use of Bifidobacterium species within probiotic supplements might make you reasonably assume these species are essential for a healthy microbiome. But in fact, there are no particular bacterial species that are essential for health and not one of the 4500 species identified by Microba has been found in everyone. Bifidobacterium species are found at high levels in the breastfed infant’s gut but tend to decrease in abundance as we age with around 1 in 4 samples within Microba’s own database containing no detectable levels of Bifidobacterium. So, don’t worry if you don’t see Bifidobacterium species in your patient’s Insight™ report, there are plenty of other beneficial microbes to look for!


Then, which species are associated with good health in the scientific literature?

Some species of bacteria are well studied and have lots of scientific papers supporting their health associations. In the Insight™ report, these are highlighted in the ‘Species of Interest’ section which can be filtered to show the species which have been linked to ‘good health’ or ‘poor health’. It is important to remember that most research to date simply shows associations between the levels of these species and a particular health condition so it cannot be assumed that having these species necessarily makes someone more or less likely to suffer from that health condition. Nonetheless, accurately identifying which species your patient’s microbiome contains can be an important piece of the puzzle in designing interventions for optimal outcomes. For example, research has shown that patients whose microbiome contains the ‘dream team’ of both Ruminococcus_E_bromii and Agathobacter rectalis (previously known as Eubacterium rectale) are most likely to benefit from increasing resistant starch intake in terms of stimulating butyrate production. Another example of a ‘species of interest’ is Akkermansia muciniphila which has been associated with improved metabolic health.


What about the species not reported in the scientific literature?

Although the scientific literature is rapidly advancing our understanding of the role of particular species within the microbiome there still remains much to learn about the majority of the species within the human gut microbiome. This means that most of the species within your patient’s microbiome will not have had much scientific research published about them. This could be because they were discovered more recently or are less frequent inhabitants of the human gut microbiome, but this does not mean that they are not important on your patient’s microbiome. The benefit of metagenomics is that even if a species has not been reported in the scientific literature, you can make informed assessments on the impact the species is having in your patient by looking at the fuel sources it is able to use and the metabolites it can produce. This information is provided for each species identified in your patient’s Insight™ report, helping you identify which species are making an important contribution to their gut microbiome health.


Changing our clinical focus to microbiome function over species

While understanding which species your patient’s microbiome contains is an important part of overall microbiome assessment, the real value in the use of metagenomic sequencing is the ability to quantify the microbiome’s overall capacity to perform certain functions.

A healthy microbiome should contain lots of species with the ability to perform functions which are associated with good health. For example, the ability to degrade fibre and generate short-chain fatty acids (SCFAs), such as butyrate and propionate. This should be balanced with lower numbers of species with the capacity to perform functions which have been associated with poor health, such as the ability to degrade protein or mucins and generate pro-inflammatory metabolites, such as hexa-LPS, trimethylamine or hydrogen sulphide. Many different species contain the genes to perform these functions and generally the overall balance is more important than the exact species performing the function.

To put it simply, it doesn’t really matter which species does the job, what matters is how many species are doing the job. For example, Faecalibacterium prausnitzii is a common resident of the human gut that has gained significant attention for its metabolic and anti-inflammatory properties, but just because some patient’s microbiomes do not contain this butyrate-producing species, it does not necessarily mean that their microbiome as a whole does not have good capacity to produce butyrate. In this example, assessing the whole microbiome’s capacity to produce butyrate and accurately identifying which species are providing this function is more clinically relevant to that patient than identifying whether they have a handful of well-studied butyrate-producing species or not.



Insight™ gut microbiome analysis uses metagenomic sequencing to accurately identify all the species within your patient’s gut microbiome and provides an assessment of the balance of species within the microbiome which can perform beneficial or detrimental functions. There are no species that a healthy microbiome must contain, but accurately identifying which species a microbiome contains and the functions that they can perform can provide a comprehensive assessment of microbiome health.


About the author



Dr Paula Smith-Brown (APD, PhD)

Paula is the Clinical Science Lead and Accredited Practising Dietitian for Insight™ at Microba. Paula was awarded her PhD from the University of Queensland in 2017 which explored the association between diet, gut microbiota and body composition in children and has over 10 years of clinical experience.