The Genus Bacteroides


The genus Bacteroides has been described over 100 years and comprises a group of small nonmotile, nonsporing, Gram‐negative rods; they are obligate anaerobes and form a major part of the bacterial flora of the human intestinal tract. Poor circumscription of this group has led to the genus accumulating a large and diverse collection of species that only superficially resembles this description but could not be accommodated elsewhere. Based largely on chemotaxonomic and genetic criteria the genus was reclassified (Shah and Collins, 1989) to encompass the type species Bacteroides fragilis and members of the ‘B. fragilis group’. This more restricted definition, spurred on mainly by 16S rRNA (ribosomal ribonucleic acid), has encouraged more in‐depth analysis of the colonic flora and a large number of new species have been described. Full genomes of four species have been completed. Such studies are providing a better basis for elucidating the biological role of specific species within the intestinal tract and their involvement in a variety of physiological and cellular processes.

Keywords: bacteroides; systematics; identification; salient features; biology and pathogenicity

Figure 1.

A phylogenetic tree constructed using neighbour‐joining methods (Thompson et al., ; Van de Peer and De Wachter, ) based on 16S rRNA gene sequences (approximately 1300 bp) from Bacteroides sp. and other closely related genera. Numbers at the nodes indicate percentage bootstrap values of 1000 replicates. GenBank accession numbers for each sequence are given. The separation of Parabacteroides from Bacteroides sensu stricto is clearly shown.

Figure 2.

MALDI‐TOF mass spectral traces of three representative clinical isolates of Bacteroides fragilis isolated at different times. This species is particularly diverse; however, several conserved mass ions are present among isolates. The mass signals shown are considered to represent the same biomarker within the set analytical error margin of 0.08%.

Figure 4.

The deduced three‐dimensional crystal structure of the metalloproteinase encoded by bft. The α‐helices are shown in red, whereas the β‐sheets are in yellow with the arrow tip showing the direction. The blue strands indicate the turns, whereas the green strands depict the amino acid residues which, according to computer predictions, do not fold into secondary structures. Reproduced by permission of Edward Arnold (Publishers) Ltd, from Shah HN, Gharbia SE and Olsen I (2005) Bacteroides, Prevotella and Porphyromonas. In: Borriello AP, Murray PR and Funke G (eds), Topley & Wilson, 10th edn, vol. 2, chap. 75, pp. 1939, figure 75.4, London.

Figure 3.

MALDI‐TOF mass spectral traces of three representative Bacteroides species, B. uniformis, B. vulgatus and B. thetaiotaomicron compared to B. fragilis, the type species of the genus. Despite the high degree of physiological compatibility between species, characteristic mass ions are evident in the spectrum of each.



Akiba M, Nakaoka Y, Kida M et al. (2007) Changes in antimicrobial susceptibility in a population of Salmonella enterica serovar Dublin isolated from cattle in Japan from 1976 to 2005. Journal of Antimicrobial Chemotherapy 60: 1235–1242.

Almeida FS, Nakano V and Avila‐Campos MJ (2007) Occurrence of enterotoxigenic and nonenterotoxigenic Bacteroides fragilis in calves and evaluation of their antimicrobial susceptibility. FEMS Microbiology Letters 272: 15–21.

Appelbaum PC, Spangler SK and Jacobs MR (1993) Susceptibility of 539 Gram‐positive and Gram‐negative anaerobes to new agents, including RP59500, biapenem, trospectomycin and piperacillin/tazobactam. Journal of Antimicrobial Chemotherapy 32: 223–231.

Arzese AR, Tomasetig L and Botta GA (2000) Detection of tetQ and ermF antibiotic resistance genes in Prevotella and Porphyromonas isolates from clinical specimens and resident microbiota of humans. Journal of Antimicrobial Chemotherapy 45: 577–582.

Bakir MA, Sakamoto M, Kitahara M, Matsumoto M and Benno Y (2006a) Bacteroides dorei sp. nov., isolated from human faeces. International Journal of Systematic Evolutionary Microbiology 56: 1639–1643.

Bakir MA, Kitahara M, Sakamoto M, Matsumoto M and Benno Y (2006b) Bacteroides finegoldii sp. nov., isolated from human faeces. International Journal of Systematic Evolutionary Microbiology 56: 931–935.

Bakir MA, Kitahara M, Sakamoto M, Matsumoto M and Benno Y (2006c) Bacteroides intestinalis sp. nov., isolated from human faeces. International Journal of Systematic Evolutionary Microbiology 56: 151–154.

Brook I (1989) Pathogenicity of the Bacteroides fragilis group. Annals of Clinical and Laboratory Science 19: 360–376.

De A, Varaiya A and Mathur M (2002) Anaerobes in pleuropulmonary infections. Indian Journal of Medical Microbiology 20: 150–152.

D'Elia JN and Salyers AA (1996) Contribution of a neopullulanase, a pullulanase, and an alpha‐glucosidase to growth of Bacteroides thetaiotaomicron on starch. Journal of Bacteriology 178: 7173–7179.

Edmiston CE Jr, Krepel CJ, Seabrook GR and Jochimsen WG (2002) Anaerobic infections in the surgical patient; microbial etiology and therapy. Clinical Infectious Diseases 35: S112–S118.

Fenner L, Roux V, Mallet MN and Raoult D (2005) Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn. International Journal of Systematic Evolutionary Microbiology 55: 1335–1337.

Fletcher HM and Macrina FL (1991) Molecular survey of clindamycin and tetracycline resistance determinants in Bacteroides species. Antimicrobial Agents Chemotherapy 35: 2415–2418.

Franco AA (2004) The Bacteroides fragilis pathogenicity island is contained in a putative novel conjugative transposon. Journal of Bacteriology 186: 6077–6092.

Holdeman LV, Good IJ and Moore WEC (1976) Human fecal flora; variation in bacterial composition within individuals and a possible effect of emotional stress. Applied and Environmental Microbiology 31: 359–375.

Hong PY, Wu JH and Liu WT (2008) Relative abundance of Bacteroides spp; in stools and wastewaters as determined by hierarchical oligonucleotide primer extension. Applied and Environmental Microbiology 74: 2882–2893.

Keys CJ, Dare DJ, Sutton H et al. (2004) Compilation of a MALDI‐TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases. Infection Genetics and Evolution 4: 221–242.

Kitahara M, Sakamoto M, Ike M, Sakata S and Benno Y (2005) Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov. isolated from human faeces. International Journal of Systematic Evolutionary Microbiology 55: 2143–2147.

Kling JJ, Wright RL, Moncrief JS and Wilkins TD (1997) Cloning and characterization of the gene for the metalloprotease enterotoxin of Bacteroides fragilis. FEMS Microbiology Letters 146: 279–284.

Kuwahara T, Yamashita A, Hirakawa H et al. (2004) Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proceedings of the National Acadamy of Science of the USA 101: 14919–14924.

Lan PT, Sakamoto M, Sakata S and Benno Y (2006) Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. International Journal of Systematic Evolutionary Microbiology 56: 2853–2859.

Macy JM (1979) The biology of gastrointestinal Bacteroides. Annual Review of Microbiology 33: 561–594.

McBain AJ and MacFarlane GT (1998) Ecological and physiological studies on large intestinal bacteria in relation to production of hydrolytic and reductive enzymes involved in formation of genotoxic metabolites. Journal of Medical Microbiology 47: 407–416.

Miyagawa E, Azuma R, Suto T and Yano I (1979) Occurrence of free ceramides in Bacteroides fragilis NCTC 9343. The Journal of Biochemistry 86: 311–320.

Miyamoto Y and Itoh K (2000) Bacteroides acidifaciens sp. nov., isolated from the caecum of mice. International Journal of Systematic Evolutionary Microbiology 50: 145–148.

Nakano V, Gomes DA, Arantes RM, Nicoli JR and Avila‐Campos MJ (2006) Evaluation of the pathogenicity of the Bacteroides fragilis toxin gene subtypes in gnotobiotic mice. Current Microbiology 53: 113–117.

Paavonen J, Valtonen VV and Kasper DL (1981) Serological evidence for the role of Bacteroides fragilis and Enterobacteriaceae in the pathogenesis of acute pelvic inflammatory disease. Lancet 1 8215: 293–295.

Rasmussen BA, Bush K and Tally FP (1997) Antimicrobial resistance in anaerobes. Clinical Infectious Diseases 24(suppl 1): S110–S120.

Rudek W and Haque RU (1976) Extracellular enzymes of the genus Bacteroides. Journal of Clinical Microbiology 4: 458–460.

Salyers AA and Shoemaker NB (1992) Chromosomal gene transfer elements of the Bacteroides group. European Journal of Clinical Microbiology and Infectious Diseases 11: 1032–1038.

Salyers AA and Shoemaker NB (1995) Conjugative transposons; the force behind the spread of antibiotic resistance genes. Anaerobe 1: 143–150.

Schmidt AS, Bruun MS, Dalsgaard I and Larsen JL (2001) Incidence, distribution, and spread of tetracycline resistance determinants and integron‐associated antibiotic resistance genes among motile aeromonads from a fish farming environment. Applied and Environmental Microbiology 67: 5675–5682.

Shah HN (1991) The genus Bacteroides and related taxa. In: Balows A, Trüper HG, Dworkin M, Harder W and Schleifer KH (eds) The Prokaryotes, 2nd edn, pp. 3593–3607. New York: Springer.

Shah HN and Collins MD (1989) Proposal to restrict the genus Bacteroides to Bacteroides fragilis and closely related species. International Journal of Systematic Bacteriology 39: 85–97.

Shah HN, Keys C, Gharbia SE et al. (2000) The application of MALDI‐TOF mass spectrometry to profile the surface of intact bacterial cells. Microbial Ecology in Health and Disease 12: 241–246.

Shah HN, Keys CJ, Schmid O and Gharbia SE (2002) Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and proteomics; a new era in anaerobic microbiology. Clinical Infectious Diseases 1; 35(suppl 1): S58–S64.

Shapiro ME, Kasper DL, Zaleznik DF et al. (1986) Cellular control of abscess formation; role of T cells in the regulation of abscesses formed in response to Bacteroides fragilis. Journal of Immunology 137: 341–346.

Simon GL, Klempner MS, Kasper DL and Gorbach SL (1982) Alterations in opsonophagocytic killing by neutrophils of Bacteroides fragilis associated with animal and laboratory passage; effect of capsular polysaccharide. Journal of Infectious Diseases 145: 72–77.

Smith CJ (1987) Nucleotide sequence analysis of Tn4551; use of ermFS operon fusions to detect promoter activity in Bacteroides fragilis. Journal of Bacteriology 169: 4589–4596.

Song YL, Liu CX, McTeaque M and Finegold SM (2004) ‘Bacteroides nordii’ sp. nov. and ‘Bacteroides salyersae’ sp. nov. isolated from clinical specimens of human intestinal origin. Journal of Clinical Microbiology 42: 5565–5570.

Speer BS, Shoemaker NB and Salyers AA (1992) Bacterial resistance to tetracycline; mechanisms, transfer, and clinical significance. Clinical Microbiology Reviews 5: 387–399.

Teng LJ, Hsueh PR, Tsai JC et al. (2002) High incidence of cefoxitin and clindamycin resistance among anaerobes in Taiwan. Antimicrobial Agents and Chemotherapy 46: 2908–2913.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG (1997) The ClustalX windows interface; flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876–4882.

Tzianabos AO, Onderdonk AB, Smith RS and Kasper DL (1994) Structure–function relationships for polysaccharide induced intraabdominal abscesses. Infection and Immunity 62: 3590–3593.

Van de Peer Y and DeWachter R (1994) TREECON for Windows; a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Computar Applications in the Biosciences 10: 569–570.

Whitehead TR, Cotta MA, Collins MD, Falsen E and Lawson PA (2005) Bacteroides coprosuis sp. nov., isolated from swine‐manure storage pits. International Journal of Systematic Evolutionary Microbiology 55: 2515–2518.

Whittle G, Whitehead TR, Hamburger N et al. (2003) Identification of a new ribosomal protection ype of tetracycline resistance gene, tet(36), from Swine manure pits. Applied and Environmental Microbiology 69: 4151–4158.

Wybo I, Pierard D, Verschraegen I et al. (2007) Third Belgian multicentre survey of antibiotic susceptibility of anaerobic bacteria. Journal of Antimicrobial Chemotherapy 59: 132–139.

Xu J, Bjursell MK, Himrod J et al. (2003) A genomic view of the human‐Bacteroides thetaiotaomicron symbiosis. Science 5615: 2074–2076.

Xu J, Mahowald MA, Ley RE et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology 5(7): 1574–1586.

Yamamoto I, Saito H and Ishimoto M (1987) Regulation of synthesis and reversible inactivation in vivo of dual coenzyme‐specific glutamate dehydrogenase in Bacteroides fragilis. Journal of General Microbiology 133: 2773–2780.

Further Reading

Duerden BI and Drasar BS (1991) Anaerobes in Human Disease. London: Edward Arnold.

Finegold SM and Lance George W (1989) Anaerobic Infections in Humans. New York: Academic Press.

Gharbia SE, Williams JC, Andrews DMA and Shah HN (1995) Genomic clusters and codon usage in relation to gene expression in Gram‐negative anaerobes. Anaerobe 1: 239–262.

Salyers AA (1984) Bacteroides of the human lower intestinal tract. Annual Review of Microbiology 38: 293–313.

Shah HN, Gharbia SE and Duerden BI (1998) The genera Porphyromonas, Prevotella and Bacteroides. In: Balows A and Duerden BI (eds) Topley Wilson's Microbiology and Microbial Infections, vol. 2, Systematic Bacteriology, 9th edn, vol. 58, pp. 1305–1330. London: Arnold.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Shah, Haroun N, Jacinto, Rogério C, Ahmod, Nadia, Langham, Sally, Gharbia, Saheer E, Kallow, Wibke, and Welker, Martin(Dec 2008) The Genus Bacteroides. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000450.pub2]