Browse > Article
http://dx.doi.org/10.15324/kjcls.2022.54.4.239

Update on the Taxonomy of Clinically Important Anaerobic Bacteria  

Myungsook, Kim (Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine)
Publication Information
Korean Journal of Clinical Laboratory Science / v.54, no.4, 2022 , pp. 239-248 More about this Journal
Abstract
The taxonomy of bacteria in the field of clinical microbiology is in a state of constant flux. A large-scale revamping of the classification and nomenclature of anaerobic bacteria has taken place over the past few decades, mainly due to advances in molecular techniques such as 16S rRNA and whole genome sequencing (WGS). New genera and species have been added, and existing genera and species have been reclassified or renamed. A major role of the clinical microbiological laboratories (CMLs) is the accurate identification (ID) and appropriate antimicrobial susceptibility testing (AST) for clinically important bacteria, and rapid reporting and communication of the same to the clinician. Taxonomic changes in anaerobic bacteria could potentially affect the choice of appropriate antimicrobial agents and the antimicrobial breakpoints to use. Furthermore, current taxonomy is important to prevent treatment failures of emerging pathogenic anaerobes with antimicrobial resistance. Therefore, CMLs should periodically update themselves on the changes in the taxonomy of anaerobic bacteria and suitably inform clinicians of these changes for optimum patient care. This article presents an update on the taxonomy of clinically important anaerobic bacteria, together with the previous names or synonyms. This taxonomy update can help guide antimicrobial therapy for anaerobic bacterial infections and prevent treatment failure and can be a useful tool for both CMLs and clinicians.
Keywords
Anaerobic bacteria; Taxonomic change; Update;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Ulger-Toprak N, Liu C, Summanen PH, Finegold SM. Murdochiella asaccharolytica gen. nov., sp. nov., a Gram-stain-positive, anaerobic coccus isolated from human wound specimens. Int J Syst Evol Microbiol. 2010;60:1013-1016. https://doi.org/10.1099/ijs.0.015909-0   DOI
2 Yassin AF, Sproer C, Pukall R, Sylvester M, Siering C, Schumann P. Dissection of the genus Actinobaculum: Reclassification of Actinobaculum schaalii Lawson et al. 1997 and Actinobaculum urinale Hall et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended descriptions of the genus Actinobaculum and Actinobaculum suis; and re-examination of the culture deposited as Actinobaculum massiliense CCUG 47753T ( = DSM 19118T), revealing that it does not represent a strain of this species. Int J Syst Evol Microbiol. 2015;65:615-624. https://doi.org/10.1099/ijs.0.069294-0   DOI
3 Lawson PA, Falsen E, Akervall E, Vandamme P, Collins MD. Characterization of some Actinomyces-like isolates from human clinical specimens: reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and description of Actinobaculum schaalii sp. nov. Int J Syst Bacteriol. 1997;47: 899-903. https://doi.org/10.1099/00207713-47-3-899   DOI
4 Mattarelli P, Bonaparte C, Pot B, Biavati B. Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. nov. Int J Syst Evol Microbiol. 2008;58:767-772. https://doi.org/10.1099/ijs.0.65319-0   DOI
5 Kageyama A, Benno Y, Nakase T. Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov. Int J Syst Bacteriol. 1999;49:557-565. https://doi.org/10.1099/00207713-49-2-557   DOI
6 Wurdemann D, Tindall BJ, Pukall R, Lunsdorf H, Strompl C, Namuth T, et al. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol. 2009;59:1405-1415. https://doi.org/10.1099/ijs.0.005900-0   DOI
7 Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol. 2016;66:1009-1016. https://doi.org/10.1099/ijsem.0.000824   DOI
8 Allen-Vercoe E, Daigneault M, White A, Panaccione R, Duncan SH, Flint HJ, et al. Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976. Anaerobe. 2012;18(5):523-529. https://doi.org/10.1016/j.anaerobe.2012.09.002   DOI
9 Taras D, Simmering R, Collins MD, Lawson PA, Blaut M. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2002;52:423-428. https://doi.org/10.1099/00207713-52-2-423   DOI
10 Lawson PA, Citron DM, Tyrrell KL, Finegold SM. Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prevot 1938. Anaerobe. 2016;40:95-99. https://doi.org/10.1016/j.anaerobe.2016.06.008   DOI
11 Gerritsen J, Fuentes S, Grievink W, van Niftrik L, Tindall BJ, Timmerman HM, et al. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov. Int J Syst Evol Microbiol. 2014;64: 1600-1616. https://doi.org/10.1099/ijs.0.059543-0   DOI
12 Haapasalo M. Black-pigmented gram-negative anaerobes in endodontic infections. FEMS Immunol Med Microbiol. 1993;6:213-217. https://doi.org/10.1111/j.1574-695X.1993.tb00329.x   DOI
13 Sasi Jyothsna TS, Tushar L, Sasikala C, Ramana CV. Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii. Int J Syst Evol Microbiol. 2016;66:1268-1274. https://doi.org/10.1099/ijsem.0.000874   DOI
14 Alauzet C, Mory F, Carlier JP, Marchandin H, Jumas-Bilak E, Lozniewski A. Prevotella nanceiensis sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol. 2007;57:2216-2220. https://doi.org/10.1099/ijs.0.65173-0   DOI
15 Willems A, Collins MD. 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapsalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. Nov. Int J Syst Bacteriol. 1995;45:832-826. https://doi.org/10.1099/00207713-45-4-832   DOI
16 Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y, Ohkuma M. Porphyromonas pasteri sp. nov., isolated from human saliva. Int J Syst Evol Microbiol. 2015;65:2511-2515. https://doi.org/10.1099/ijs.0.000294   DOI
17 Kawamura Y, Kuwabara S, Kania SA, Kato H, Hamagishi M, Fujiwara N, et al. Porphyromonas pogonae sp. nov., an anaerobic but low concentration oxygen adapted coccobacillus isolated from lizards (Pogona vitticeps) or human clinical specimens, and emended description of the genus Porphyromonas Shah and Collins 1988. Syst Appl Microbiol. 2015;38:104-109. https://doi.org/10.1016/j.syapm.2014.11.004   DOI
18 Kook JK, Park SN, Lim YK, Cho E, Jo E, Roh H, et al. Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level. Curr Microbiol. 2017;74:1137-1147. https://doi.org/10.1007/s00284-017-1296-9   DOI
19 Conrads G, Claros MC, Citron DM, Tyrrell KL, Merriam V, Goldstein EJC. 16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium. Int J Syst Evol Microbiol. 2002;52:493-499. https://doi.org/10.1099/00207713-52-2-493   DOI
20 Kook JK, Park SN, Lim YK, Choi MH, Cho E, Kong SW, et al. Fusobacterium nucleatum subsp. fusiforme Gharbia and Shah 1992 is a later synonym of Fusobacterium nucleatum subsp. vincentii Dzink et al. 1990. Curr Microbiol. 2013;66:414-417. https://doi.org/10.1007/s00284-012-0289-y   DOI
21 Dorsch M, Lovet DN, Bailey GD. Fusobacterium equinum sp. nov., from the oral cavity of horses. Int J Syst Evol Microbiol. 2001;51:1959-1963. https://doi.org/10.1099/00207713-51-6-1959   DOI
22 Jalava J, Eerola E. Phylogenetic analysis of Fusobacterium alocis and Fusobacterium sulci based on 16S rRNA gene sequences: proposal of Filifactor alocis (Cato, Moore and Moore) comb. nov. and Eubacterium sulci (Cato, Moore and Moore) comb. nov. Int J Syst Bacteriol. 1999;49:1375-1379. https://doi.org/10.1099/00207713-49-4-1375   DOI
23 Park SN, Lim YK, Shin JH, Kim HS, Jo E, Lee WP, et al. Fusobacterium pseudoperiodonticum sp. nov., Isolated from the Human Oral Cavity. Curr Microbiol. 2019;76:659-665. https://doi.org/10.1007/s00284-019-01675-y   DOI
24 Downes J, Munson M, Wade WG. Dialister invisus sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol. 2003;53:1937-1940. https://doi.org/10.1099/ijs.0.02640-0   DOI
25 Rocas IN, Siqueira JF Jr, Debelian GJ. Analysis of symptomatic and asymptomatic primary root canal infections in adult Norwegian patients. J Endod. 2011;37:1206-1212. https://doi.org/10.1016/j.joen.2011.05.026   DOI
26 Huys G, Vancanneyt M, D'Haene K, Falsen E, Wauters G, Vandamme P. Alloscardovia omnicolens gen. nov., sp. nov., from human clinical samples. Int J Syst Evol Microbiol. 2007;57:1442-1446. https://doi.org/10.1099/ijs.0.64812-0   DOI
27 Wexler HM, Reeves D, Summanen PH, Molitoris E, McTeague M, Duncan J, et al. Sutterella wadsworthensis gen. nov., sp. nov., bile-resistant microaerophilic Campylobacter gracilis-like clinical isolates. Int J Syst Bacteriol. 1996;46:252-258. https://doi.org/10.1099/00207713-46-1-252   DOI
28 Baron EJ. Bilophila wadsworthia: a unique Gram-negative anaerobic rod. Anaerobe. 1997;3:83-86. https://doi.org/10.1006/anae.1997.0075   DOI
29 Scholz CFP, Kilian M. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol. 2016;66:4422-4432. https://doi.org/10.1099/ijsem.0.001367   DOI
30 Jian W, Dong X. Transfer of Bifidobacterium inopinatum and Bifidobacterium denticolens to Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol. 2002;52:809-812. https://doi.org/10.1099/00207713-52-3-809   DOI
31 Kaur S, Yawar M, Kumar PA, Suresh K. Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov. Int J Syst Evol Microbiol. 2014;64:710-718. https://doi.org/10.1099/ijs.0.056986-0   DOI
32 Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev. 2007;20:593-621. https://doi.org/10.1128/CMR.00008-07   DOI
33 Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M, Komiya H, et al. ParaBacteroides gordonii sp. nov., isolated from human blood cultures. Int J Syst Evol Microbiol. 2009;59:2843-2847. https://doi.org/10.1099/ijs.0.010611-0   DOI
34 Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol. 1990;40:205-208. https://doi.org/10.1099/00207713-40-2-205   DOI
35 Shah HN, Collins MD. Proposal for reclassification of Bacteroides asaccharolyticus, Bacteroides gingivalis, and Bacteroides endodontalis in a new genus, Porphyromonas. Int J Syst Bacteriol. 1988;38:128-131. https://doi.org/10.1099/00207713-38-1-128   DOI
36 Sakamoto M, Benno Y. Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as ParaBacteroides distasonis gen. nov., comb. nov., ParaBacteroides goldsteinii comb. nov. and ParaBacteroides merdae comb. nov. Int J Syst Evol Microbiol. 2006;56:1599-1605. https://doi.org/10.1099/ijs.0.64192-0   DOI
37 Sakamoto M, Kitahara M, Benno Y. ParaBacteroides johnsonii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2007;57:293-296. https://doi.org/10.1099/ijs.0.010611-0   DOI
38 Kim H, Im WT, Kim M, Kim D, Seo YH, Yong D, et al. ParaBacteroides chongii sp. nov., isolated from blood of a patient with peritonitis. J Microbiol. 2018;56:722-726. http://www. springerlink.com/content/120956.   DOI
39 Downes J, Liu M, Kononen E, Wade WG. Prevotella micans sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol. 2009;59:771-774. https://doi.org/10.1099/ijs.0.002337-0   DOI
40 Janda JM. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2015. Diagn Microbiol Infect Dis. 2016;86:123-127. https://doi.org/10.1016/j.diagmicrobio.2016.06.021   DOI
41 Kuijper EJ, Barbut F, Brazier JS, Kleinkauf N, Eckmanns T, Lambert ML, et al. Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008. Euro Surveill. 2008;13:18942.
42 Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol. 2014;64:384-391. https://doi.org/10.1099/ijs.0.057091-0   DOI
43 Munson E. Moving targets of bacterial taxonomy revision: what are they and why should we care?. Clin Microbiol Newsl. 2020;42:111-120. https://doi.org/10.1016/j.clinmicnews.2020.06.002   DOI
44 Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing; 28th ed, M100. Wayne: Clinical and Laboratory Standards Institute; 2018.
45 Jousimies-Somer H, Summanen P, Citron DM, Baron EJ, Wexler HM, Finegold SM. Wadsworch-KTL Anaerobic Bacteriology Manual. 6th ed. Belmont: Star Publishing Co; 2002.
46 Nagy E. Anaerobic infections: update on treatment considerations. Drugs. 2010 May 7;70(7):841-58. https://doi.org/10.2165/11534490-000000000-00000   DOI
47 Park Y, Lee Y, Kim M, Choi JY, Yong D, Jeong SH, et al. Recent trends of anaerobic bacteria isolated from clinical specimens and clinical characteristics of anaerobic bacteremia. Infect Chemother. 2009;41:216-223.   DOI
48 Ezaki T, Yamamoto N, Ninomiya K, Suzuki S, Yauuchi E. Transfer of Peptococcus indolicus, Peptococcus asaccharolyticus, Peptococcus prevotii and Peptococcus magnus to the genus Peptostreptococcus and proposal of Peptostreptococcus tetradius sp. nov. Int J Syst Bacteriol. 1983;33:683-698. https://doi.org/10.1099/00207713-33-4-683   DOI
49 Lotte R, Lotte L, Ruimy R. Actinotignum schaalii (formerly Actinobaculum schaalii): a newly recognized pathogen-review of the literature. Clin Microbiol Infect. 2016;22:28-36. https://doi.org/10.1016/j.cmi.2015.10.038   DOI
50 Murdoch DA. Gram-positive anaerobic cocci. Clin Microbiol Rev. 1998;11:81-120. https://doi.org/10.1128/CMR.11.1.81   DOI
51 Murdoch DA, Shah HN. Reclassification of Peptostreptococcus magnus (Prevot 1933) Holdeman and Moore 1972 as Finegoldia magna comb. nov. and Peptostreptococcus micros (Prevot 1933) Smith 1957 as Micromonas micros comb. nov. Anaerobe. 1999;5:555-559. https://doi.org/10.1006/anae.1999.0197   DOI
52 Tindall BJ, Euzeby JP. Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names Micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002, respectively. Int J Syst Evol Microbiol. 2006;56:2711-2713. https://doi.org/10.1099/ijs.0.64338-0   DOI
53 Ezaki T, Kawamura Y, Li N, Li ZY, Zhao L, Shu S. Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus. Int J Syst Evol Microbiol. 2001;51:1521-1528. https://doi.org/10.1099/00207713-51-4-1521   DOI
54 Ueki A, Abe K, Suzuki D, Kaku N, Watanabe K, Ueki K. Anaerosphaera aminiphila gen. nov., sp. nov., a glutamate-degrading, Gram-positive anaerobic coccus isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol. 2009;59:3161-3167. https://doi.org/10.1099/ijs.0.011858-0   DOI
55 Collins MD, Wallbanks S. Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium. FEMS Microbiol Lett. 1992;74:235-240. https://doi.org/10.1111/j.1574-6968.1992.tb05372.x   DOI
56 Henssge U, Do T, Radford DR, Gilbert SC, Clark D, Beighton D. Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963. Int J Syst Evol Microbiol. 2009;59:509-516. https://doi.org/10.1099/ijs.0.000950-0   DOI
57 Liu C, Finegold SM, Song Y, Lawson PA. Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2008;58:1896-1902. https://doi.org/10.1099/ijs.0.65208-0   DOI
58 Marchandin H, Teyssier C, Campos J, Jean-Pierre H, Roger F, Gay B, et al. Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes. Int J Syst Evol Microbiol. 2010;60:1271-1279. https://doi.org/10.1099/ijs.0.013102-0   DOI
59 Marchandin H, Teyssier C, Simeon de Buochberg M, Jean-Pierre H, Carriere C, Jumas-Bilak E. Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiology (Reading). 2003;149:1493-1501. https://doi.org/10.1099/mic.0.26132-0   DOI
60 Greub G, Raoult D. "Actinobaculum massiliae," a new species causing chronic urinary tract infection. J Clin Microbiol. 2002;40: 3938-3941. https://doi.org/10.1128/JCM.40.11.3938-3941.2002   DOI