Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore–forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.

Bacteroides species are normally mutualistic, making up the most substantial portion of the mammalian gastrointestinal microbiota, where they play a fundamental role in processing of complex molecules to simpler ones in the host intestine. As many as 10¹⁰–10¹¹ cells per gram of human feces have been reported. They can use simple sugars when available; however, the main sources of energy for Bacteroides species in the gut are complex host-derived and plant glycans. 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.

One of the most important clinically is Bacteroides fragilis.

The former Bacteroides melaninogenicus was reclassified and split into Prevotella melaninogenica and Prevotella intermedia.

Bacteroides species also benefit their host by excluding potential pathogens from colonizing the gut. 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.^{[page needed]} Although Bacteroides species are anaerobic, they are transiently aerotolerant and thus can survive in the abdominal cavity.

In general, Bacteroides are resistant to a wide variety of antibiotics—β-lactams, aminoglycosides, and recently many species have acquired resistance to erythromycin and tetracycline. This high level of antibiotic resistance has prompted concerns that Bacteroides species may become a reservoir for resistance in other, more highly pathogenic bacterial strains. It has been often considered susceptible to clindamycin, but recent evidence demonstrated an increasing trend in clindamycin resistance rates (up to 33%).

In cases where Bacteroides can move outside the gut due to gastrointestinal tract rupture or intestinal surgery, Bacteroides can infect several parts of the human body. Bacteroides can enter the central nervous system by penetrating the blood brain barrier through the olfactory and trigeminal cranial nerves and can cause meningitis and brain abscesses. Bacteroides has also been isolated from abscesses in the neck and lungs. Some Bacteroides species are associated with Crohn's disease, appendicitis and inflammatory bowel disease. Bacteroides species play multiple roles within the human gut microbiome.

An alternative fecal indicator organism, Bacteroides, has been suggested because they make up a significant portion of the fecal bacterial population, have a high degree of host specificity that reflects differences in the digestive system of the host animal 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. One study has measured the amount of Bacteroides by using qPCR to quantify the host-specific 16S rRNA genetic marker. This technique allows quantification of genetic markers that are specific to the host of the bacteria Bacteroides and allow detection of recent contamination. A recent report found temperature plays a major role in the amount of time the bacteria will persist in the environment, the life span increases with colder temperatures (0–4 °C).