Feces and algorithms: Artificial Intelligence to map our intestinal bacteria

The intestines and their bacteria are sometimes called our 'second brain', but studying these bacteria in their natural environment is difficult. Now researchers have developed a method that uses artificial intelligence to map intestinal bacteria using feces. The researchers thus hope to gain more knowledge of the role played by these bacteria in various diseases. 

University of Copenhagen researchers have developed a ground-breaking technique that can help us unravel some of the mysteries of the human intestinal bacteria. Aside from working together with the immune system in a vital cooperation, imbalance in the intestinal bacteria composition is the cause of chronic disease of the alimentary tract of which 50,000 Danes suffer.

Faeces contain remains of the bacteria that have helped metabolise the food in the stomach and intestines and thus offer unique insight into an otherwise inaccessible environment. So far technology has only allowed researchers to read fragments of the bacteria's' DNA -- which is equivalent to doing a puzzle with only a fraction of the pieces.

For example, if you want to know how polluted soil has affected the microorganisms, you could use the new method to analyse a soil sample from the area in question. The same applies to lakes and watercourses located close to a factory or similar. Or, as Simon Rasmussen points out, if there are bacteria present, they can be now be identified.

See: Jakob Nybo Nissen, Joachim Johansen, Rosa Lundbye Allesøe, Casper Kaae Sønderby, Jose Juan Almagro Armenteros, Christopher Heje Grønbech, Lars Juhl Jensen, Henrik Bjørn Nielsen, Thomas Nordahl Petersen, Ole Winther, Simon Rasmussen. Improved metagenome binning and assembly using deep variational autoencoders. Nature Biotechnology, 2021; DOI: 10.1038/s41587-020-00777-4

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)