Mapping the microbes in your mouth

Posted on February 18, 2016   by Anand Jagatia

Scientists from the Forsyth Institute have managed to visualise communities of bacteria in the human mouth, showing their spatial organisation for the first time in “microbial maps”. The maps could help scientists understand the interactions between different oral bacteria and their potential role in disease. We spoke to lead author Dr Gary Borisy about the research published in PNAS this month.

If you run your tongue across the surface of your teeth, you’re actually licking an elaborate community of microbes all living together on the enamel. Tasty, right? This community, known as dental plaque, is made up of many species of bacteria that interact with each other in complex ways, and begins to form just a few minutes after brushing. Left unchecked, these bacteria can cause tooth decay, tooth loss and gum disease.

The build-up of dental plaque is thought to happen as a succession of different bacteria, with each new species laying the foundations for another to flourish. First, proteins in your saliva bind together in a film called dental pellicle. This provides a surface for the first wave of bacterial settlers to adhere to, and these bacteria in turn offer a substrate for a second set of colonisers. Each new species creates a different environment of nutrients, receptors and oxygen that favours the next.

Now, for the first time, scientists from the Forsyth Institute have been able to visualise these communities of bacteria to see the kind of structures they form and the different species involved. Using a novel imaging technique, they produced maps which show the spatial relationships between different bacteria in the mouth.

“Structure underlies function. We wanted to look not only at what species were present, but see what was next to what,” says Dr Gary Borisy, the study’s lead author. “Only then can we hope to understand how they interact.”

The researchers found that certain structures, which they call ‘hedgehogs’ and ‘cauliflowers’ because of how they look, could be consistently found on the surface of people’s teeth. Hedgehogs are made up of Corynebacterium filaments, with small bunches of Streptococcusat the ends, along with certain other species. Cauliflowers are plaques formed of bacteria like Lautropia, Streptococcus and Veillonella.

“These ‘hedgehogs’ were actually first observed 120 years ago, although scientists didn’t know what species they were made of,” Gary says. “They were called ‘ears of grain’, but then they seem to have been forgotten.”

Before now, scientists have used DNA sequencing to analyse the different microbes in the mouth. While this gives you a good sense of the complexity of the community, it tells you nothing about the spatial relationships between different species. This new study sheds light on the “biogeography” of this microbial environment, which exists on a microscopic scale, and is influenced by the physical properties of the tooth surface and concentration gradients of nutrients and oxygen.

Using data from the Human Microbiome Project, the scientists identified the species, families and genera of bacteria important in dental plaque. They then created a set of 10 fluorescent probes which were able to hybridise with the DNA of these different groups. The probes that bound to different taxa could be imaged using a spectral fluorescence microscope, showing which species of bacteria were present.

The team used the maps to produce a new hypothetical model of plaque formation. A biofilm of Streptococcus and Actinomyces forms on the tooth, which Corynebacteriumfilaments then bind to, creating a kind of scaffolding for other species to grow. Streptococcus bacteria, found at the tips of these filaments, thrive in the oxygen rich environment at the surface of the community. In turn they create a micro-environment that is rich in CO₂ and lactate, but low in oxygen, which is perfect for other bacteria that begin growing in the middle layers of the biofilm.

“The spatial structure provides a framework for understanding the metabolism and interaction between members of the bacterial community,” says Gary. “The fact that the members of the community are not only different species, but that each species is from a different genus and even from a different family, implies deep evolutionary roots.”

The research combines the huge quantity of data on the oral microbiome with the spatial precision of fluorescence imaging. But this technique is not just restricted to teeth – bacterial communities anywhere, from human skin to medical instruments, could be visualised in this way.

“Simply put, we are mapping microbiomes. It seems basic, but imagine how we would manage in real life without maps or GPS. We’d be lost,” says Gary. “Knowledge of the map will provide a deeper understanding of microbiomes and bring closer the possibility of precision engineering it to maintain health or prevent disease.”

Mark Welch, J., Rossetti, B., Rieken, C., Dewhirst, F., & Borisy, G. (2016). Biogeography of a human oral microbiome at the micron scale Proceedings of the National Academy of Sciences, 113 (6) DOI: 10.1073/pnas.1522149113