Influence of free and immobilized chitosan on a defined human gut microbial ecosystem

•Impact of free/immobilized chitosan on human gut microbiota ecosystem was studied.•Individual gut isolates showed varied susceptibility to free/immobilized chitosan.•Ecosystem structure, viability and function was mainly altered by free chitosan.•Immobilization mitigated the impact of chitosan on microbiota composition.•Chitosan caused a decrease in the ratio of Firmicutes to Bacteroidetes.