Dietary fiber and slow carbohydrates can have differential beneficial effects on gut microbial composition and metabolism. Insoluble substrates such as RS cannot be used in continuous simulation systems and we tested an in vitro batch fermentation system for possible prebiotic effects using waxy maize starch granules, pectin‐rich potato fiber, and potato lintner starch tested with human fresh fecal microbiota spiked with the probiotic Lactobacillus acidophilus NCFM. Microbial quantification by real‐time polymerase chain‐reaction (qRT‐PCR) revealed that Bacteroidetes was specifically suppressed by each insoluble carbohydrate resulting in a clear decrease in the ratio of Bacteroidetes and Firmicutes. Notably, all carbohydrates tested appeared to block the formation of the potentially harmful branched chain fatty acids (BCFA) fermentation products, but supported lactobacilli growth and increase in lactic acid production. Potato lintner starch had the greatest effect. Insoluble carbohydrates also suppressed production of SCFAs as compared to the control medium. Importantly, potato lintner starch most efficiently suppressed the ratio between the Bacteroidetes and Firmicutes and suppressed growth of bifidobacteria, Enterobactericeae and Faecalibacterium prausnizii. Degradative resistance of the lintner starch were linked to these effects. Problems using continuous fermentation systems for insoluble prebiotics and interpretation of batch fermentation data are discussed.