Categories: Sanger Science28 June 20216.2 min read

Bacterial Biomes

If you’re asked to think about biodiversity, images of rainforests may be the first that come to mind. These vast green landscapes, teeming with life, are home to thousands of species. Yet the diversity of these ecosystems is matched by much smaller locations, much closer to home. Benches, railings and our own guts are also packed with life. Billions of microbes from thousands of different species live in these environments. Like rainforests, much of the diversity is unexplored and could be a source of new molecules or new knowledge that may be harnessed for health.

Dr Gregorio Iraola is a Group Leader at the Institut Pasteur Montevideo in Uruguay and an International Fellow at the Wellcome Sanger Institute. He is studying bacteria in previously uncharted settings. He was recently involved in a huge international study to map the microbes present in mass transit systems of cities across the world1. Researchers took swabs from subway railings and ticket machines and studied the DNA sequences they found. They uncovered microbes unique to each location as well as a core ‘urban set’ present in almost every city they sampled. Thousands of the species of bacteria and viruses they found are new to science2.

Gregorio’s current research effort is a project called ‘Latinbiota’, in collaboration with the Wellcome Sanger Institute. He leads an international team of researchers who are working to characterise the gut microbes of people living in Uruguay, Mexico, Ecuador, Colombia, Brazil, Argentina and Bolivia.

Essential for our health, the microbes living in our guts are influenced by our diets and environments. The vast majority of studies on gut microbiomes to date have been done in high–income countries in Europe and North America – leaving a massive knowledge gap when it comes to the diversity of organisms that call humans home.

Dr Iraola was interviewed by Alison Cranage, Science Writer at the Wellcome Sanger Institute.


Dr Gregorio Iraola, Microbial Genomics Laboratory, Institut Pasteur Montevideo


Tell us about Latinbiota

Latinbiota is a consortium that aims to uncover and understand the composition and variability of the human microbiome in Latin American populations3. This is because, today, the vast majority of what we know about the human microbiome comes from the study of high-income countries in the Northern hemisphere, mainly the US and European countries.

The main factor shaping the microbiome is diet. And what we eat is strongly determined by the social, economical and cultural aspects of a country. So Latin American countries, most of which are low- and middle-income countries, are going to be different compared to other economies around the world. And so we have our black hole; we don’t know what species or genes are out there.

Why is it important?

Having an overview of microbiome variability in Latin American populations will allow us to better understand the disruptions that are associated with different diseases prevalent in the continent. At the moment, our point of reference for a healthy microbiome comes from populations in other counties.

We are going to be able to focus on specific diseases and conditions that are important for different nations. So for example, some countries are interested in studying what happens to the microbiome during gastric cancer. Others are interested in childhood malnutrition.

I am confident that in the longer term, these data sets will constitute a key resource. For example, they might facilitate the discovery of new biomarkers associated with different diseases. And maybe it will be possible to design new therapies, based on the data we generate.


Microbiome

The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on and in our bodies. The gut microbiome protects us against pathogens, helps our immune system develop, and enables us to digest food to produce energy.

Metagemomics

Also described as environmental genomics, it involves direct extraction of DNA from any environment. The total DNA is then sequenced and analysed.

What have you found?

We’re using metagenomics to sequence the DNA of gut microbiomes from over 600 people across eight countries; Uruguay, Mexico, Chile, Ecuador, Colombia, Brazil, Argentina and Bolivia.

Most of the participants are healthy, and so the first focus was to study normal variability in healthy individuals - to have a reference of high-quality genomes.

We have found new and specific genes in some countries in Latin America that are absent in other populations.

It's not too surprising that when you study a completely new population or a completely new environment, you find new diversity, novel species and previously unknown genes and genetic features and phenotypes.

But in these times of the pandemic, what surprised me the most was the discovery of thousands of new viral species inhabiting our microbiome. Although most of these are viruses that infect bacteria (bacteriophages), this finding shows us the vastly unknown diversity of viruses that exist in nature; and the importance they may have on our health in the future.


Different species of enterobacteria isolated from the urban sewage system of Montevideo, Uruguay. Image Credit: Dr Gregorio Iraola

What are the next steps?

The most challenging thing is the next step. We now know what is there in terms of the species and their genomes, but we want to try to understand why they are there, and the impact they are having. To do that, you need to integrate different fields of knowledge. We need clinical input as well as microbiologists to work together to take this to the next level – whether that’s for developing disease diagnostics or new probiotic therapies.

To complement the genomic analysis of the microbiome, we are also growing the bacteria we find. Having the bacteria in the lab means we can study them further. It is a difficult process – these bacteria usually live in the human gut, in an anaerobic environment. I’ve been lucky to be able to send some of my team to the Sanger Institute to learn anaerobic culturing techniques from our collaborators there.

How has your research changed during the pandemic?

Like so many research institutions, our focus has shifted to COVID-19 over the past 18 months. We set up real-time genomic surveillance to monitor for new coronavirus variants and help in the pandemic response. My laboratory is now working to sequence coronavirus genomes from across Uruguay, and we report our findings to the national Ministry of Health weekly.

We have been able to continue our research on Latinbiota, as the data analysis and bioinformatics work can be done remotely. We are also arranging a virtual meeting of the consortium soon, and I hope everyone is able to continue with their fantastic work, develop local projects, and build this amazing community of researchers.

“As scientists, whatever environment we study, we are well aware that what we know about already is just a small percentage of the diversity that actually exists on Earth.”

Find out more

  • Gregorio is working with Dr Trevor Lawley, a Group Leader at the Sanger Institute, who leads work on the mechanisms that underlie how micro-organisms on mucosal surfaces interact with their host during health and disease.

References