Mapping the human gut: Researchers identify 2,000 gut microbes

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12 Feb 2019 --- Researchers at the European Molecular Biology Laboratory's (EMBL) European Bioinformatics Institute (EBI) and the Wellcome Sanger Institute have identified almost 2,000 gut bacterial species, using a range of computational methods. Since the findings are mostly based on European and Northern American samples the researchers are highlighting the need for more data from other regions of the world.

The study results, published in the journal Nature, are the basis for the formation of a comprehensive list of commonly found microbes in the gut. 

“By having a larger ‘map’ of the bacterial species found in the gut, we can analyze individual microbiomes much more accurately. We now need to determine among these thousands of species, which ones are more important for health,” Alexandre Almeida, Postdoctoral Fellow at EMBL-EBI and the Wellcome Sanger Institute, tells NutritionInsight.

“If we eventually find that some of these unknown bacteria contribute to a healthy gut we might think about nutritional strategies or therapies that promote the growth and stability of these organisms,” he adds.

Despite the continuously emerging research on the gut microbiome, researchers are still working on identifying the individual microbial species hosted in the gut and their role in human health. 

Click to EnlargeEMBL-EBI researchers and collaborators used computational tools to identify almost 2,000 previously unknown gut bacteria species. Image Credit: Spencer Phillips/EMBL-EBI Earlier this month, another study from EMBL and the Wellcome Sanger Institute, featuring some of the same researchers, isolated more than 100 previously unknown species of bacteria from healthy people’s intestines. The involved researchers created what they say is the most “comprehensive public database of human health-associated intestinal bacteria to date.” It could provide a wealth of information on treating different disorders, as well as a diverse range of potential probiotics. The new study is a computational one, building on the knowledge of the previous one. 

“The first study described the isolation and laboratory culturing of 100 novel gut bacteria. In this work, we used that first study as a basis to determine, using computational methods alone, how many bacterial species are still left to be discovered in the lab,” says Almeida.

Geographical limitations 
According to the researchers, a lot of the same bacterial species crop up in the data from European and North American populations. But there is limited data on the gut bacteria found in other parts of the world. The researchers note how the composition of gut bacteria differs around the world and how important it is for the samples studied to reflect this diversity.

“The few South American and African datasets we had access to for this study revealed significant diversity not present in the former populations. This suggests that collecting data from underrepresented populations is essential if we want to achieve a truly comprehensive picture of the composition of the human gut,” explains Rob Finn, Group Leader at EMBL-EBI. 

Almeida mentions that previous studies have found that what we eat and the environment around us have a bigger role than genetics in determining the composition of the gut microbiota but further research is necessary on the matter.

“In our study, we did not have enough data to determine this, but we speculate that the differences between the European/North American populations and the African/South American ones are influenced by many factors, one of the most important ones being differences in diet,” he explains.

“However, we definitely need much more data from these underrepresented populations to really understand the reasons behind the differences we are seeing. Our analysis revealed that many more undiscovered bacteria are still present in regions such as Africa, Asia and South America, so greater efforts are needed in these regions to create a complete global map of gut intestinal bacteria,” Almeida notes.

Identifying bacteria via computational methods
Microbial species that are part of the gut have remained unknown until now, due to being found in low concentrations in the gut or having the inability to survive outside of it. This time, the researchers used computational methods in order to reconstruct the genomes of the bacteria. This allowed them to understand bacteria that they could not yet culture in the lab. 

“Using metagenomics to reconstruct bacterial genomes is a bit like reconstructing hundreds of puzzles after mixing all the pieces together, without knowing what the final image is meant to look like,” says Finn. 

“Researchers are now at a stage where they can use a range of computational tools to complement and sometimes guide lab work, in order to uncover new insights into the human gut,” he adds.

Click to EnlargeGenomic blueprint of the gut microbiota
According to Almeida, computational methods allow us to get an idea of the many bacterial species that live in the human gut, how they evolved and what kind of roles they may play within their microbial community.

“In this study, we leveraged the most comprehensive public databases of gastrointestinal bacteria to identify bacterial species that have not been seen before. The analysis methods we used are highly reproducible and can be applied to larger, more diverse datasets in the future, enabling further discovery,” he adds.

Trevor Lawley, Group Leader at the Wellcome Sanger Institute, says that this sort of research can help create a so-called blueprint of the human gut, which could, in turn, offer a better understanding of human health and disease and could even “guide diagnosis and treatment of gastrointestinal diseases.”

“Our work provides the means to perform future studies in much greater detail. IBS and other gut-related diseases are very complex, so it is important to have as much information about the gut microbiota as possible to inform experimental studies trying to find novel treatments for these diseases,” Almeida concludes.

By Kristiana Lalou

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