Bacteroides is a genus of opportunistic, anaerobic, gram-negative bacilli. Bacteroides fragilis is the most common species involved in human disease and is part of the normal flora of the large intestine. Infection most commonly occurs when the colon wall is breached and bacteria enter the peritoneal cavity, which can cause intra-abdominal infections and intra-abdominal abscess formation. Management involves antibiotics and abscess drainage.

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Gram negative bacteria classification flowchart

Gram-negative bacteria:
Most bacteria can be classified according to a lab procedure called Gram staining.
Bacteria with cell walls that have a thin layer of peptidoglycan do not retain the crystal violet stain utilized in Gram staining. These bacteria do, however, retain the safranin counterstain and thus appear as pinkish-red on the stain, making them gram negative. These bacteria can be further classified according to morphology (diplococci, curved rods, bacilli, and coccobacilli) and their ability to grow in the presence of oxygen (aerobic versus anaerobic). The bacteria can be more narrowly identified by growing them on specific media (triple sugar iron (TSI) agar) where their enzymes can be identified (urease, oxidase) and their ability to ferment lactose can be tested.
* Stains poorly on Gram stain
** Pleomorphic rod/coccobacillus
*** Require special transport media

Image by Lecturio. License: CC BY-NC-SA 4.0

General Characteristics

Basic features

  • Gram-negative bacilli
  • Pleomorphic: appear as either straight rods or coccobacilli
  • 0.5–0.8 μm in diameter and 1.5–4.5 μm long
  • Anaerobes, although tolerate exposure to oxygen
  • Encapsulated
  • Ferment carbohydrates: 
    • Including complex plant polysaccharides indigestible to the host 
    • Allows for commensal/symbiotic relationship between the bacteria and host
  • Part of indigenous bacterial flora of mucosal surfaces, but opportunistic pathogens
Micrograph of Bacteroides

Micrograph of Bacteroides
Photomicrograph depicts the gram-negative bacterium Bacteroides fragilis.

Image: “3084” by the CDC/ Dr. V.R. Dowell, Jr. License: Public domain.

Virulence factors

  • Adherence to host tissue:
    • Fimbriae: Long, hair-like projections
    • Lipopolysaccharide (LPS):
      • Weakly endotoxic
      • Primary role is adherence to mucosal surfaces
  • Protection from host immune response:
    • Superoxide dismutase and catalase: 
      • Neutralize oxygen radicals created by the immune system 
      • Key for pathogenesis in areas of the body not free from oxygen
    • Capsule: 
      • Protects from complement-mediated phagocytosis 
      • Leads to abscess formation
      • Polysaccharides on the capsule can be altered to evade the host immune response.
    • Conjugative transposons: aid in the transfer of antibiotic resistance genes
  • Destruction of host tissue:
    • Hyaluronidase and chondroitin sulfatase:
      • Destroy brush border enzymes in the intestine
      • Make it harder for the host to absorb nutrients
      • More nutrients available for bacteria
    • Enterotoxin:
      • Destroys tight junctions in the intestinal epithelium
      • Leads to diarrhea
    • Neuraminidase: cleaves polysaccharides, freeing up glucose for bacteria 

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  • Large intestine of humans

Transmission and infection

Transmission and infection from the translocation of bacteria from mucosal surfaces to other tissues may be due to:

  • Blunt trauma
  • Intestinal disease
  • Penetrating wounds
  • Abdominal surgery
  • Ruptured appendix
Pathogenesis of Bacteroides fragilis

Pathogenesis of Bacteroides fragilis
The pathogen contains an antiphagocytic capsule, which adheres to the peritoneal surface. This results in abscess formation. Surgery and trauma accentuate the problem since they disrupt the abscess, allowing for the endogenous spread of the organism into the bloodstream. When this occurs, the pathogen releases degradative enzymes that destroy the host’s cells.

Image by Lecturio. License: CC BY-NC-SA 4.0

Diseases Caused by Bacteroides fragilis

Bacteroides fragilis (B. fragilis) is naturally found in the small intestines as part of the natural flora. B. fragilis is an opportunistic pathogen that rarely infects the gastrointestinal system, more often causing disease when bacteria escape the small intestine. 

ConditionCharacteristicsInfection type
Intra-abdominalIntra-abdominal infection
  • Most common form of infection
  • Takes place when the intestinal wall is breached
  • Polymicrobial infection
  • Usually seen with abscess formation
  • Cause of perforation is usually not the bacterium (may be surgery, trauma, or cancer).
Perforated appendicitis
  • Spontaneous rupture of the appendix due to an infection
  • Polymicrobial infection
GastrointestinalInflammatory diarrhea
  • Seen only with forms of Bacteroides that secrete enterotoxins
  • Destroys tight junctions in the intestinal epithelium
  • Leads to the loss of water into the stool and diarrhea
GynecologicPelvic infections
  • Mucopurulent infection of the cervix or uterus
  • Rare
  • Usually seen with concomitant Bartholin’s gland abscess
Fallopian tube and ovarian abscesses
  • Rare, because Bacteroides is not usually part of the normal genitourinary flora
Skin and soft tissueDiabetic foot infection
  • Poor peripheral circulation and decreased sensation of the extremities puts patients with diabetes at risk of developing infected wounds on their feet.
  • Polymicrobial infections favoring anaerobic agents
Animal bite infections
  • Bacteroides is rarely found in human bite infections but has been seen with dog bites.
BrainMeningitis and brain abscess
  • Rarely seen in healthy patients
  • Commonly seen when there is a communication between the brain and peritoneum (i.e. a ventriculoperitoneal shunt)
  • Dissemination of the pathogen through the bloodstream
  • Common in the elderly
  • Seen in patients who are immunocompromised and have a compromised gastrointestinal mucosa
  • Rare in children

Diagnosis and Management


  • History:
    • Predisposing factors: 
      • Recent abdominal surgery
      • Trauma 
      • Malignancy
      • Immunocompromised state
    • Known history of Bacteroides infections
  • Physical exam:
    • Presence of pyogenic abscesses
    • Foul smell is often associated with anaerobic infections.
  • Laboratory testing:
    • Appropriate tissue samples must be utilized to culture Bacteroides:
      • Blood cultures and fine-needle aspirates of infectious material
      • Requires an anaerobic environment to propagate
    • Defining laboratory characteristics:
      • Isolated as a single agent, but usually seen with other anaerobes
      • Gram –
      • Grows on blood agar and Bacteroides-bile-esculin (BBE) agar 
      • Kanamycin, vancomycin, and colistin-resistant 
      • Grows in 20% bile
      • Catalase producing
      • Variably indole positive


  • Prevention:
    • Planned prophylactic antibiotics for abdominal surgeries
    • Antibiotic therapy if contamination from the colon is suspected
  • Treatment:
    • When present, the drainage of abscesses is the primary form of treatment
    • Given the polymicrobial nature of most infections, antibiotic therapy should be directed to multiple anaerobes:
      • Antibiotic of choice for all anaerobic infections is metronidazole.
      • Effective antibiotics include: piperacillin/tazobactam, meropenem 
      • Resistant to penicillin due to the production of beta-lactamase
      • Moxifloxacin previously utilized; now, resistance reported in up to 57% of cases


  1. Wexler, H.M. (2007). Bacteroides: The good, the bad, and the nitty-gritty. Clinical microbiology reviews, 20(4), 593–621.
  2. Moncrief, J.S., Obiso, R. Jr., et al. (1995). The enterotoxin of Bacteroides fragilis is a metalloprotease. Infect Immun. 63(1), 175–81.
  3. Franco, A.A. (2004). The Bacteroides fragilis pathogenicity island is contained in a putative novel conjugative transposon. J Bacteriol, 186(18), 6077–92.
  4. Takesue, Y., Kusachi, S., et al. (2018). Antimicrobial susceptibility of common pathogens isolated from postoperative intra-abdominal infections in Japan. J Infect Chemother, 24(5), 330–340.
  5. Snydman, D.R., Jacobus, N.V., et al. (2010). Lessons learned from the anaerobe survey: Historical perspective and review of the most recent data (2005–2007). Clin Infect Dis. 50 Suppl(1), S26–33.

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