Testing number twos: the leading tech in gut microbiome analysis

Author: Dr Ken McGrath and Hayley Parcell

20 August 2019 Education News

What can modern stool tests tell you about your health?

Stool testing. It’s something most of us are aware of, some of us understand, and few want to talk about. Yet stool tests in many cases are lifesaving, and some of the more modern tests can provide detailed insights into what’s going on in an individual’s gut. So how do we understand the different types of tests, why they’re important and exactly what they can show us?

I sat down with Dr Ken McGrath, Technology Liaison Manager for Brisbane-based gut health specialists, Microba to find out more.

Dr McGrath explained that there had been a change in perception about the microorganisms that live in and on us – the human microbiome.

“In the past, the perception of our gut bacteria was that the only good bug was a dead bug, and that’s what many traditional stool tests were really looking for – the bad bugs,” he said.

“However, over the past several years, what we’ve seen is a new way of thinking about the gut microbiome – the community of bacteria living in a person’s gut – and how essential these microbes are for each and every one of us to remain healthy.”

Exploration of the gut microbiome over the past decade has identified strong associations with various disease states both inside and outside of the gut – indicating the gut microbiome could be a contributing factor in many diseases.

“We’ve seen the gut microbiome associated with neuro-degenerative diseases such as Parkinson’s, mental health disorders such as anxiety and depression, cardiovascular diseases, inflammatory diseases such as Crohn’s or ulcerative colitis, and metabolic diseases,” Dr McGrath said.

“In the future, the goal is to be able to gain insight into what came first – disease state or microbiome changes – and whether the gut microbiome can be used to diagnose, recognise markers earlier or develop therapeutics.”

How does your microbiome influence health and what functions does it impact? Discover the microbiome.

What are the different tests available?

What exactly are the different test types and what do they look at?

“The different kinds of stool tests either look at human-produced compounds, specific bacteria and parasites, or profile the entire microbiome living in the gastrointestinal tract to see what organisms are living there and what they might be doing,” Dr McGrath said.

“The tests that look at human-produced compounds detect blood in stool or inflammation markers such as the calprotectin protein.

“Examples of these tests are the National Bowel Cancer Screening Program and tests for Inflammatory Bowel Disease (IBD).

“The specific bacteria and parasites tests include pathogen screening via multiplex polymerase chain reaction (PCR) – which detect specific organisms such as E.coli, Salmonella and Campylobacter. You can also look for parasites like worms, Giardia and other cysts using microscopy.”

How do they test the entire gut microbiome?

Dr McGrath explained that there were two previously popular ways – cell culture and 16S rRNA gene sequencing.

“Cell culture is where a scientist will grow bacterial colonies on a plate, and this is typically only able to look at less than five per cent of organisms in a sample.

“16S rRNA gene sequencing looks at a small piece of the genome and tries to predict the bacteria present based on the 16S ribosomal gene. It’s better at providing a comprehensive overview of the microbiome than culture methods, but it still limits the number and types of organisms you can see, is unable to provide species-level identification, and cannot provide information on what the bacteria is capable of doing.”

The most efficient and detailed way to look at the entire microbiome is through metagenomic analysis, which analyses the DNA of all the microorganisms in a sample. This is the type of analysis that Microba uses in their Brisbane laboratory.

Advanced metagenomic analysis

“Metagenomics analyses the entire genome, meaning that it looks at all of the DNA from the organisms in a sample.

“This analysis provides species-level resolution and most importantly, can identify the functional genes present.”

Microba is currently the only company providing metagenomic gut microbiome sequencing to general consumers in Australia and uses world-leading analysis technology. The gut microbiome consists of a community of many hundreds of different microorganisms, and metagenomics works by breaking down the genomes (DNA) of these microbes into small fragments and then sequencing the DNA fragments.

Once these small pieces of DNA are sequenced, they are like individual pieces of a puzzle that need to be fit back together to build the original picture of the individual microorganisms. Microba is one of the world leaders in fitting these “puzzle pieces” back together to form the genome of a microorganism. Having the complete genome picture of a microorganism lets you identify that microbe to the species and even strain level and tells you what the microbes are able to do. Microba’s metagenomic sequencing is also not limited to bacterial species; it can provide high-resolution identification of the microorganisms present above 0.05%, including bacteria, archaea, fungi and protists.

“Because we have access to most of the genome, we can “see” the functional potential of that microbe, including its growth requirements and the metabolites it can produce or consume.”

What does this mean?

There are many stool tests out there that look at different aspects of your gut health by looking for different information. Tests such as the Bowel Cancer Screening Test and searching for parasites are important, and if you are sent one of these tests in the mail, or asked by your Doctor to undertake these, you definitely should do the test!

What can you access with a Microba Insight™ test? Find out here.

But when it comes to exploring your own gut microbiome to gain more understanding of how well the microbes are performing important jobs, and which bacterial species are living in there, metagenomic sequencing is the best method available. Tests such as Microba’s Insight™ provide you with detailed information such as which bacterial species are living in your gut, what they are doing, what foods they need as fuel and how they may be connected to other areas of your body and health. This allows you to take control of your gut health and empower yourself with personalised insights that may assist you with dietary or lifestyle changes to improve your overall health. You can also work with a Microba-informed health care practitioner to further delve into your report and access their expertise on ways to improve your overall health into the future.


Dr Ken McGrath is the Technology Liaison Manager with Microba. He has a PhD in Molecular Pathology from the University of Queensland, with a research background in microbial community genomics, including human and environmental microbiomes and metagenomics analysis. Ken has also been a part of several international microbiome research projects.

This microbiome test is not intended to be used to diagnose or treat medical conditions. A full disclaimer is available here