Microbe map

In a museum world first, visitors have truly become part of the exhibition by sharing their microbial DNA fingerprint—at the same time contributing to medical research.

The microbe map installation created for Gut Feelings (on display March 2019–August 2020, Melbourne Museum) has revealed the secrets of Victorians’ microbiomes, offering a new understanding about the microbes that live in our mouths—aka the gut entrance—and how they vary with different lifestyles and diets.

Melbourne Museum, the University of Melbourne and the Peter Doherty Institute for Infection and Immunity created this joint research project.

Using the map

  • Zoom: use the mouse wheel / pinch-to-zoom gesture (mobile)
  • Pan: left-click + hold the mouse and drag / move finger across map (mobile)
  • Rotate: right-click + hold the mouse and drag
  • Hover over / touch (mobile) a suburb for details
  • Purple indicates higher diversity, height indicates sample size

About the State of Our Microbes: Victorian Oral Microbiome and Lifestyle Study

Having a rich and diverse community of microbes is good for us, but how do our lifestyles affect this mix? Does who we live with influence our microbial richness? Eating well and spending time in nature might be beneficial for obtaining a diverse microbiome, but what about owning a pet? Or drinking tea vs. coffee? Or even where we live?

To investigate these questions and others, we have created a digital microbe map of Victoria, by taking a sample from one end of the gut: the mouth. Visitors were invited to donate a microbe-containing spit sample, and fill out a survey about the food they ate, their pets, sleeping habits and more.

Researchers from the University of Melbourne and the Peter Doherty Institute for Infection and Immunity whisked the tiny tubes of saliva away for microbial DNA sequencing. They then profiled and compared the community of creatures living in the mouths of Victorians. All results were de-identified for privacy. No individual results were given to participants, as this was not a health diagnostic project, but rather a study on the microbiomes of people within a community.

1,450 adults and children took part in the study, and the dynamic microbe map has been on display at the entrance of Gut Feelings throughout the project—growing with new data that reveals the microbial diversity of participants from across Victoria. 

Microbes, including bacteria, affect people's physical and mental health via immune, hormone and nerve pathways. Generally, the higher the microbe diversity the better! Think of it like a tiny balanced ecosystem.

We found that:

  • Microbe proportions are carb-sensitive
    High carbohydrate intakes, such as added sugar and refined flours, were associated with lower microbe diversity in participants’ saliva. 88% of adults reported not eating the recommended five serves of vegetables a day, and 30% reported eating one or fewer serves a day. Indicating that Victorians should be eating more fruit and vegetables to increase the health of their microbes!
  • Antibiotics decrease bacterial diversity
    The results show a drop in microbe diversity in participants who had recently taken antibiotics—as we would hope for even in this age of superbugs.
  • We aren’t so special
    At first glance of these preliminary results the common bacterial phyla (such as the Proteobacteria and Firmicutes) and genera (Neiseseria, Haemophilus) are broadly the same in Victorians as those seen in the mouths of people in other parts of the world. Could an ideal human microbiome exist?
  • Your flatmates matter
    There was a trend towards higher microbe diversity when participants shared their home with one person or more. Further sampling may give the researchers a statistically significant result.
  • Victorians have varied microbe fingerprints
    While broad human patterns exist, the balance of microbes in an individual differs so much you could refer to it as a fingerprint. The results show that postcodes varied in average microbe diversity, but the more samples received the more differences started to average out. Interestingly, the anticipated pattern of higher microbe diversity in country vs. city was not there—however the highest scorer, our ‘super spitter’, did come from the country.
  • We can’t be pigeonholed by one variable
    As for the questions of whether microbes differ between dog owners and cat owners? And coffee and tea drinkers? Northsiders and southsiders? The huge data sets need more analysis before the researchers can say for sure. Your lifestyle interplay with microbes is complex and looking at a single factor—like your coffee habits—either doesn’t have a huge effect or isn’t enough to single you out in our current results.

Meet your microbes...

Neisseria

Are detected in our mouths from birth. They are found in humans across the globe, including isolated communities that have little contact with the outside world.

Haemophilus

Some species help to convert the nitrate in the vegetables we eat, like celery and spinach, into nitric oxide that helps us maintain healthy blood pressure. Others, such as Haemophilus influenzae can cause infection and bacterial meningitis if they get beyond the mouth.

Veillonella

May help protect teeth against tooth decay, as they consume the acids made by other bacteria from dietary sugar, like Streptococcus and Actinomyces.

Prevotella

Increase in number during pregnancy, and are part of a microbial shift that occurs in pregnancy.

Actinomyces

Like Streptococcus and Leptotrichia, some Actinomyces species convert the sugar and some other carbohydrates we eat into acids. Some species convert the sugar we eat into long chains of sugar molecules to eat later, and this is what can leave the furry feeling in our mouths after eating sugary foods.

Leptotrichia

Prefer to live on teeth, so aren’t detected in our mouths until our teeth start to grow. Like Streptococcus, Leptotrichia species consume sugar and convert it into tooth enamel eating acids.

Fusobacterium

Can produce hydrogen sulphide, which in high amounts cause bad breath.

Streptococcus

Acid producing species in the genera Streptococcus, Leptotrichia and Actinomyces can also make the mouth a less welcoming place for other kinds of bacteria when sugar intake is high. This could explain why we see a lower diversity of bacteria in our mouths when sugar intake is high.

What does this mean for Victorians?

  • What you eat matters! Not just because of weight management and nutrition but because it clearly impacts your microbiome. Having a diverse array of microbes in your mouth/gut is important because they play important roles in not only your oral health, but your health overall, by interacting with your immune, nervous, and hormonal systems.
  • Just like any community, the interactions between microbes and their human hosts are many and complex. Projects like this help paint the picture of what the human oral microbiome looks like, and how it varies.
  • The human microbiome is dynamic. These results are a snapshot in time, and reflect visitors mouths at the time of their saliva sample only. It’s a first glimpse into the microbiomes of everyday Victorians.

What is its significance?

Before now, we never knew much about Victorians’ microbe mix or ‘microbiome’.

As the links between microbes and our mental and physical health become clearer, having an idea of what a baseline population looks like is very important.

The world is still wondering if there is an ultimate human microbiome, or if we are all so unique that what’s good for me might not be good for you. This study is helping to answer these big questions.

The exhibition continues to build public awareness so we can all make informed lifestyle choices. Perhaps more veg? More time outdoors? More time relaxing?
 

Dr Johanna Simkin, the curator of Gut Feelings said:

‘What makes this project so great is involving our museum visitors in this first ever glimpse into Victoria’s microbes. They get to come on the journey with us as results trickle through—the visitors’ microbes become a part of the exhibition. It’s a real first.

‘The project was born when the Northside hipster in me wondered how I’d compare to a Southsider, or someone in rural Victoria. The scientist in me wondered if Melburnians might have their own unique microbe fingerprint, considering that Melbourne is the world capital for food allergies.

‘We want to empower visitors to consider how their everyday lifestyle choices impact their microbes. Melbourne Museum’s showcased results don’t focus on things you can’t change—like whether you were born by caesarean or breastfed. Instead we went a bit lighter—does having a dog impact your microbe mix? What are you eating? We know you can improve your microbiome in as little as 24 hours just by eating well’.
 

Andre Mu, University of Melbourne Postdoctoral Fellow and lead microbiome researcher, Doherty Institute, said:

‘This is a fantastic ‘citizen science’ project looking at the microbiome of Victorians; a project that we, at Doherty Applied Microbial Genomics, are extending to include many other ecosystems such as the gut, skin, and the environment. This work will help drive microbiome sciences across Melbourne, and indeed Australia.’
 

Julian Simmons, Senior Research Fellow and Study Chief Investigator, the University of Melbourne said:

‘This study provided a unique opportunity to engage with the community in citizen science, both questioning, learning and educating. There is huge public interest in the role bacteria play in our health, yet common misunderstandings and so much more to discover. The best things you can do for your microbes are eat less sugar and refined flours, eat more vegetables and fruit, and regularly brush your teeth and floss.’
 

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