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Intestinal Bacteria Mapped Using Artificial Intelligence

100 BILLION bacteria, approximately, live in our intestines. Medical researchers have so far struggled to study these bacteria in their natural environment but now a team at the University of Copenhagen, Copenhagen, Denmark, have developed a method, using faeces and artificial intelligence (AI), to map these intestinal bacteria.

There are around 500–1,000 species of bacteria in our intestines, and these are thought to play a role in diseases such as diabetes, obesity, and inflammatory bowel disease. Assoc Prof Simon Rasmussen, co-leader of the study, highlighted the problem that research has faced in this area: “The presence of bacteria is vital to the immune system, and this is true not least of intestinal bacteria. But the problem is that it is very difficult to study intestinal bacteria in their natural environment, which they often deeply depend on in order to survive.”
Therefore, the team had the idea of studying faeces instead as it contains traces of the bacteria that metabolised food in the stomach and intestines. The team then needed to reconstruct the DNA profiles of these bacteria to identify them, which was the motivation behind their AI technique, named variational autoencoders for metagenomic binning (VAMB).

Assoc Prof Rasmussen explained: “If we are able to reconstruct their DNA, it will give us an idea of the types of bacteria we are dealing with, what they are capable of, and what they actually do. It is not the complete picture, but it is a huge step forward.”

The VAMB programme can be run on standard hardware and is free for other researchers to use, as the team hope it may be applied to other microbiology disciplines.