There is controversy over previous findings that a high ratio of Firmicutes to Bacteriodetes helps obese animals harvest energy from the diet. To further investigate the relationship between microbial composition and energy harvest, microbial adaptation to diet and time should be considered. In this study, lean and obese rats were successfully induced with low-fat and high-fat diets. An 8-week high soyabean fibre (HSF)-containing diet was then fed to investigate the interaction between the diet and the rats’ gut microbiota, as well as their influence on rats’ growth. Rats’ body weight (BW) was recorded weekly; their plasma lipids and their gut microbiota at week 11, 15 and 19 were analysed. After the consumption of the HSF diet, BW of lean rats increased significantly (P<0·05), but no significant alteration in BW was found in obese rats. The average content of plasma cholesterol was lowered and that of TAG was upgraded in both the groups when fed the HSF diet. There was no significant difference observed at each period between lean and obese rats. In the group of lean rats, the diversity of gut microbiota was elevated strongly (P<0·01), and bacteria from phylum Firmicutes and Bacteroidetes were both increased largely (P<0·01); however, the bacterial diversity and composition in obese rats were less altered after the HSF diet control. In conclusion, the increased Firmicutes and Bacteriodetes might relate to lean rats’ higher BW gain; ‘obese microbiota’ could not help the hosts harvest more energy from the HSF diet.