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2,000 bacterial species found in human gut by microbiome researchers at EMBL-EBI and Sanger Institute

Researchers have identified almost 2,000 bacterial species living in the human gut.

The human gut contains thousands of species of microbes. Image: Spencer Phillips, EMBL-EBI (7220995)
The human gut contains thousands of species of microbes. Image: Spencer Phillips, EMBL-EBI (7220995)

The work, by scientists at EMBL’s European Bioinformatics Institute and the Wellcome Sanger Institute, both in Hinxton, creates a new genomic blueprint of human gut microbiota.

Studies of our microbiome - the genetic material of trillions of micro-organisms inside us - are accelerating as its importance in human health is uncovered.

Using a range of computational methods, the researchers analysed data on samples from individuals worldwide to identify the species, which have yet to be cultured in the lab.

There are a number of reasons why some microbial species that are part of the gut microbiota have been undiscovered - such as their low abundance in the gut or inability to survive outside it.

Researchers used computational methods to reconstruct the genomes of these bacteria.

Rob Finn, group leader at EMBL-EBI, explained: “Computational methods allow us to understand bacteria that we cannot 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, and after completely removing a few pieces from the mix just to make it that bit harder.

“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.”

But while the study, published in Nature, brings us closer to a comprehensive list of commonly found microbes in the guts of North American and European people, it also highlighted a significant lack of data from other regions of the world.

“We are seeing a lot of the same bacterial species crop up in the data from European and North American populations,” said Dr Finn. “However, 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.”

Alexandre Almeida, postdoctoral fellow at EMBL-EBI and the Wellcome Sanger Institute, said: “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.”

Trevor Lawley Microbiotica. (7221020)
Trevor Lawley Microbiotica. (7221020)

Trevor Lawley, group leader at the Wellcome Sanger Institute, and co-founder of microbiome-based therapeutics company Microbiotica, added: “Research such as this is helping us create a so-called blueprint of the human gut, which in the future could help us understand human health and disease better and could even guide diagnosis and treatment of gastrointestinal diseases.”

Reporting their findings in Nature, the researchers said: “Despite a new wave of culturing efforts, there is still a significant but undetermined degree of unclassified microbial diversity within the gut ecosystem.

“While these unknown community members may have eluded current culturing strategies for a variety of reasons (eg due to lack of nutrients in growth media or their low abundance in the gut), they are likely to perform important biological roles that remain to be discovered. Thus, having access to a comprehensive catalogue of representative genomes and isolates from the intestinal microbiota is essential to gain new mechanistic insights.”

Earlier this month, researchers at Sanger, the EMBL-EBI and Hudson Institute of Medical Research in Australia announced that they had isolated 105 completely new species of bacteria from the human gut after studying faecal samples from 20 people from the UK and Canada.

They successfully grew and DNA sequenced 737 individual bacterial strains, revealing 273 separate bacterial species, including 173 never previously sequenced and 105 never even isolated before.

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