Teaching computers to recognize sick guts--machine learning and the microbiome

A new proof-of-concept study by researchers from the University of California San Diego succeeded in training computers to "learn" what a healthy versus an unhealthy gut microbiome looks like based on its genetic makeup. Since this can be done by genetically sequencing fecal samples, the research suggests there is great promise for new diagnostic tools that are, unlike blood draws, non-invasive. As recent advances in scientific understanding of Parkinson's disease and cancer immunotherapy have shown, our gut microbiomes – the trillions of bacteria, viruses and other microbes that live within us – are emerging as one of the richest untapped sources of insight into human health. The problem is these microbes live in a very dense ecology of up to 1 billion micobes per gram of stool. Imagine the challenge of trying to specify all the different animals and plants in a complex ecology like a rain forest or coral reef – and then imagine trying to do this in the gut microbiome, where each creature is microscopic and identified by its DNA sequence.