Roles of human colonic bacteria in pectin utilization and associated cross-feeding networks revealed using synthetic co-cultures

Dietary fibre is a crucial component of healthy diets via its action on the human gut microbiota, but fibre intake is well below current international dietary guidelines at the population level. Pectin is a fibre constituent in fruit and vegetables that has the promise to promote a healthy and diverse microbiota. It is a highly complex molecule, and its composition differs between plants. Here, we assessed the ability of a panel of 23 human gut bacteria to ferment pectins extracted from different plants based on their genome carriage of carbohydrate-active enzymes (CAZymes) and their growth in pure culture on several mono-, oligo- and polysaccharides, as well as pectins from different plant sources. Growth behaviour was overall in good agreement with CAZyme carriage, and the results were used to design synthetic co-culture communities with different combinations of pectin degraders, pectin cross-feeders and background strains not expected to play a major role in pectin degradation. For pectin degraders, Lachnospira eligens DSM 3376 outcompeted Phocaeicola vulgatus DSM 1447 and Segatella copri DSM 18205, which appeared to act more as a cross-feeder in the presence of L. eligens DSM 3376. Between the cross-feeders, Roseburia intestinalis M50/1 likely utilized breakdown products from the pectin backbone and side chains, whereas Faecalibacterium duncaniae A2-165 grew better in co-culture on homogalacturonan-rich pectins. Our work will help to explain individual-specific responses to pectin intake based on microbiota compositional variation and contribute to the design of personalized dietary strategies to optimize the microbiota.