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Colorectal Cancer Gut Microbe Clues Bolstered by AI Approach

In Genome Biology, a team from the Tokyo Institute of Technology, Metagen Therapeutics, and elsewhere outlines colorectal cancer (CRC) clusters marked by distinct gut microbial community associations found with an artificial intelligence (AI) approach. The investigators used a Shapley Additive Explanations (SHAP) algorithm and a SHAP-based microbiome analyses tool known as SHAP-MAT to analyze bacterial abundance profiles from five publicly available datasets representing individuals with or without CRC. In the large datasets and in samples from four individuals with CRC, the authors saw that the SHAP strategy could help to focus in on a range of bacteria-based candidate biomarkers that coincided with distinct CRC clusters. "[W]e explored the potential of using explainable AI for gut microbiome-based CRC classification," they write. "We showed that SHAP could be used to obtain more personalized feature importance that can be used to identify potential bacterial biomarkers for CRC.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.