The health benefits of apple bioactive compounds have been extensively reported. However, only few studies have focused on bioactive compounds that are not absorbed and metabolised during gastrointestinal digestion and can induce changes in microbial populations of faeces. We have characterised Braeburn, Fuji, Gala, Golden Delicious, Granny Smith, McIntosh and Red Delicious cultivars and found significant differences for extractable phenolics (1.08-9.2 mg/g) non-extractable proanthocyanidins (3.28-5.7 mg/g), and dietary fibre (20.6-32.2%) among cultivars with Granny Smith having the highest contents. Granny Smith was used after in vitro digestion for fermentation of faeces from diet-induced obese mice. Results showed that relative abundances of Firmicutes, Bacteroidetes, Enterococcus, Enterobacteriaceae, Escherichia coli, and Bifidobacterium in apple cultured faeces tended to resemble the abundance in faeces from lean mice with increased trend in the production of butyric acid. These results suggest that apple non-digestible compounds might help to re-establish a disturbed microbiota balance in obesity. © 2014 Elsevier Ltd. All rights reserved.