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Published online 9 November 2014
A newly devised computer tool, reported in Bioinformatics1, can automatically identify specific enzyme-coding gene loci in human gut bacteria. Known as polysaccharide utilization loci (PUL), such gene loci encode bacterial enzymes that break down complex dietary sugars in the human gut.
Humans can only digest a handful of dietary sugars such as starch, sucrose and lactose. The other sugars such as xylans, pectins, agaroses and laminarins are broken down by trillions of gut-living bacteria. If the activity of such bateria is disrupted, this impairs nutrition, affecting human health.
To better understand the roles of gut-living bacteria in human health and nutrition, a research team from Centre National de la Recherche Scientifique, France and King Abdulaziz University, Saudi Arabia has developed a computer tool based on the experimental data of PULs from two well-studied human gut bacteria — Bacteroides thetaiotaomicron and Bacteroides ovatus. They applied the tool to probe PULs in 65 species of human gut bacteria and two bacteria from the environment, only by scanning the bacterial genomes.
The researchers identified 3,745 PULs encoding over 7,300 enzymes, such as glycoside hydrolases and polysaccharide lyases.
“This suggests a selection pressure on the bacterial genes that encode enzymes working in concert to degrade complex sugars in gut,” says Bernard Henrissat, a principal investigator of a collaborative research project that aims to analyze the digestive microbiota of humans and animals from the Middle East.