Bacteroides species are normally mutualistic, making up the most substantial portion of the mammalian gastrointestinal microbiota,[4] where they play a fundamental role in processing of complex molecules to simpler ones in the host intestine.

[9] Studies indicate that long-term diet is strongly associated with the gut microbiome composition—those who eat a higher proportion of protein and animal fats have predominantly Bacteroides bacteria, while for those who consume more carbohydrates or fiber the Prevotella species dominate.

Some species (B. fragilis, for example) are opportunistic human pathogens, causing infections of the peritoneal cavity, gastrointestinal surgery, and appendicitis via abscess formation, inhibiting phagocytosis, and inactivating beta-lactam antibiotics.

[5] An alternative fecal indicator organism, Bacteroides, has been suggested because they make up a significant portion of the fecal bacterial population,[3] have a high degree of host specificity that reflects differences in the digestive system of the host animal[21] Over the past decade, real-time polymerase chain reaction (PCR) methods have been used to detect the presence of various microbial pathogens through the amplification of specific DNA sequences without culturing bacteria.

"[24] Another study showed a 5.6-times higher risk of osteoporosis fractures in the low Bacteroides group of Japanese postmenopausal women.

[25] Members of the Bacillota and Bacteroidota phyla make up a majority of the bacterial species in the human intestinal microbiota (the "gut microbiome").

[26] Bacteroides species' main source of energy is fermentation of a wide range of sugar derivatives from plant material.

[citation needed] Bacteroides are symbiont colonizers of their host intestinal niche and serve several physiological functions, some of which can be beneficial while others are detrimental.

Bacteroides participate in the regulation of the intestinal micro-environment and carbohydrate metabolism with the capacity to adapt to the host environment by hydrolyzing bile salts.