Helicobacter

Helicobacter is a genus of gram-negative bacteria possessing a characteristic helical shape. They were initially considered to be members of the genus Campylobacter, but in 1989, Goodwin et al. published sufficient reasons to justify the new genus name Helicobacter.^[2] The genus Helicobacter contains about 35 species.^[3][4][5]

Helicobacter
Scanning electron micrograph of Helicobacter bilis bacteria
Scientific classification
Domain:	Bacteria
Phylum:	Campylobacterota
Class:	"Campylobacteria"
Order:	Campylobacterales
Family:	Helicobacteraceae
Genus:	Helicobacter Goodwin et al. 1989[1]
Type species
Helicobacter pylori (Marshall et al. 1985) Goodwin et al. 1989
Species
See text
Synonyms
"Gastrospirillum" McNulty et al. 1989

Some species have been found living in the lining of the upper gastrointestinal tract, as well as the liver of mammals and some birds.^[6] The most widely known species of the genus is H. pylori, which infects up to 50% of the human population.^[5] It also serves as the type species of the genus. Some strains of this bacterium are pathogenic to humans, as they are strongly associated with peptic ulcers, chronic gastritis, duodenitis, and stomach cancer.

Helicobacter species are able to thrive in the very acidic mammalian stomach by producing large quantities of the enzyme urease, which locally raises the pH from about 2 to a more biocompatible range of 6 to 7.^[7] Bacteria belonging to this genus are usually susceptible to antibiotics such as penicillin, are microaerophilic (optimal oxygen concentration between 5 and 14%) capnophiles, and are fast-moving with their flagella.^[8][9]

Molecular signatures

Comparative genomic analysis has led to the identification of 11 proteins that are uniquely found in the Helicobacteraceae. Of these proteins, seven are found in all species of the family, while the remaining four are not found in any Helicobacter strains and are unique to Wollinella. Additionally, a rare genetic event has led to the fusion of the rpoB and rpoC genes in this family, which is characteristic of them.^[10]

Non-H. pylori species

Recently, new gastric (H. suis and H. baculiformis) and enterohepatic (H. equorum) species have been reported. H. pylori is of primary importance for medicine, but non-H. pylori species, which naturally inhabit mammals (except humans) and birds, have been detected in human clinical specimens. These encompass two (gastric and enterohepatic) groups, showing different organ specificity. Importantly, some species, such as H. hepaticus, H. mustelae, and probably H. bilis, exhibit carcinogenic potential in animals. They harbour many virulence genes and may cause diseases not only in animals, but also in humans. Gastric species such as H. suis (most often), H. felis, H. bizzozeronii, and H. salomonis have been associated with chronic gastritis and peptic ulcers in humans, and importantly, with higher risk for MALT lymphoma compared to H. pylori.

Enterohepatic species e.g., H. hepaticus, H. bilis, and H. ganmani, have been detected by PCR, but still are not isolated from specimens of patients with hepatobiliary diseases. Moreover, they may be associated with Crohn's disease and ulcerative colitis. The significance of avian helicobacters (H. pullorum, H. anseris, and H. brantae) also has been evaluated extensively. H. cinaedi and H. canis can cause severe infections, mostly in immunocompromised patients with animal exposure. Briefly, the role of these species in veterinary and human medicine is increasingly recognised. Several other topics such as isolation of still uncultured species, antibiotic resistance, and treatment regimens for infections and pathogenesis and possible carcinogenesis in humans should be evaluated.^[3]

H. heilmannii sensu lato

Helicobacter heilmannii sensu lato (i.e. H. heilmanni s.l.) is a grouping of non-H. pylori Helicobacter species that take as part of their definition a similarity to H. pylori in being associated with the development of stomach inflammation, stomach ulcers,^[11] duodenum ulcers,^[12] stomach cancers that are not lymphomas, and extranodal marginal B cell lymphoma of the stomach in humans and animals.^[11] Most clinical studies have not identified the exact species of H. heilmanii associated with these diseases, so designated these species as H. heilmanni s.l. However, investigative studies have identified these species in some patients with the cited H. heilmanni s.l.-associated upper gastrointestinal tract diseases. The H. heilmani species identified to date in the stomachs of humans with the cited upper gastrointestinal tract diseases are: Helicobacter bizzozeronii, Helicobacter felis, Helicobacter salomonis, Helicobacter suis, and Helicobacter heilmannii s.s.^[11] It is important to recognize the association of H. heilmannii sensu lato with these upper gastrointestinal tract diseases, particularly extranodal marginal zone lymphoma of the stomach, because some of them have been successfully treated using antibiotic-based drug regimens directed against the instigating H. heilmannii sensu lato species.^[13] The H. heilmanni s.l.-associated human diseases appear to be acquired from pets and farm animals, so are considered to be zoonotic diseases.^[11]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)^[1] and National Center for Biotechnology Information (NCBI)^[14]

16S rRNA based LTP_08_2023[15][16][17]

120 single copy marker proteins based GTDB 08-RS214[18][19][20]

Wolinella Helicobacter H. valdiviensis H. ganmani H. mesocricetorum H. rodentium H. enhydrae H. cholecystus H. brantae H. pametensis H. kayseriensis H. anseris H. anatolicus H. mustelae H. canis H. bilis H. canicola Kawamura et al. 2016 H. cinaedi H. hepaticus H. trogontum H. japonicus H. muridarum H. typhlonius H. mastomyrinus Shen et al. 2006 H. apri Zanoni et al. 2016 H. equorum Moyaert et al. 2007 H. kumamotonensis Kawamura et al. 2023 H. pullorum H. canadensis H. colisuis Gruntar et al. 2022 H. turcicus H. marmotae H. macacae H. himalayensis H. fennelliae H. jaachi H. saguini H. aurati H. monodelphidis Shen et al. 2020 H. didelphidarum H. acinonychis H. pylori H. cetorum H. delphinicola Segawa et al. 2021 H. suis H. labacensis H. bizzozeronii H. felis H. salomonis H. cynogastricus H. baculiformis H. ailurogastricus H. heilmannii H. mehlei H. vulpis

Wolinella Pseudohelicobacter "Helicobacter burdigaliensis" Berthenet et al. 2019 Helicobacter valdiviensis Collado, Jara & Gonzalez 2014 Helicobacter turcicus Aydin et al. 2022 "Helicobacter winghamensis" Melito et al. Helicobacter ganmani Robertson et al. 2001 "P. rodentium" (Shen et al. 1997) Waite, Chuvochina & Hugenholtz 2019 Helicobacter apodemus Jeon et al. 2015 Helicobacter mesocricetorum Simmons et al. 2000 "P. canadensis" (Fox et al. 2002) Waite, Chuvochina & Hugenholtz 2019 "P. pullorum" (Stanley et al. 1995) Waite, Chuvochina & Hugenholtz 2019 Helicobacter H. saguini Shen et al. 2017 H. aurati Patterson et al. 2002 H. muridarum Lee et al. 1992 H. didelphidarum Shen et al. 2020 H. trogontum Mendes et al. 1996 H. bilis Fox et al. 1997 "H. rappini" Dewhirst et al. 2000 H. enhydrae Shen et al. 2020 H. kayseriensis Aydin et al. 2022 H. pametensis Dewhirst et al. 1994 H. brantae Fox et al. 2006 "Ca. H. avistercoris" Gilroy et al. 2021 H. cholecystus Franklin et al. 1997 "Ca. H. avicola" Gilroy et al. 2021 H. himalayensis Hu et al. 2015 "H. labetoulli" Berthenet et al. 2019 H. cinaedi (Totten et al. 1988) Vandamme et al. 1991 "H. magdeburgensis" Traverso et al. 2010 H. jaachi Shen et al. 2017 H. hepaticus Fox et al. 1994 H. marmotae Fox et al. 2006 H. japonicus corrig. Shen et al. 2017 H. typhlonius Franklin et al. 2002 H. fennelliae (Totten et al. 1988) Vandamme et al. 1991 H. macacae Fox et al. 2013 H. canis Stanley et al. 1994 H. anseris Fox et al. 2006 H. anatolicus Aydin et al. 2023 H. mustelae (Fox et al. 1988) Goodwin et al. 1989 H. cetorum Harper et al. 2006 H. acinonychis corrig. Eaton et al. 1993 H. pylori (Marshall et al. 1985) Goodwin et al. 1989 H. bizzozeronii Hanninen et al. 1996 H. mehlei Gruntar et al. 2020 H. suis Baele et al. 2008 H. ailurogastricus Joosten et al. 2017 H. heilmannii Smet et al. 2012 H. cynogastricus Van den Bulck et al. 2006 H. felis Paster et al. 1991 H. salomonis Jalava et al. 1997 H. baculiformis Baele et al. 2008 H. labacensis Gruntar et al. 2020 H. vulpis Gruntar et al. 2020

Species incertae sedis:

• "Ca. H. bovis" De Groote et al. 1999
• "H. callitrichis" Won et al. 2007
• "Ca. H. cebus" Gueneau de Novoa et al. 2001a
• H. ibis Lopez-Cantillo et al. 2023
• "H. muricola" Won et al. 2002
• "H. peregrinus" Coldham et al. 2004
• "H. suncus" Goto et al. 1998
• "H. tursiopsae" Gueneau de Novoa et al. 2001b
• "H. vulpecula" Coldham et al. 2004

See also

• List of bacterial orders
• List of bacteria genera

References

1. A.C. Parte; et al. "Helicobacter". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 9 September 2023.
2. Goodwin CS, Armstrong JA, Chilvers T, et al. (1989). "Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov. as Helicobacter pylori comb. nov. and Helicobacter mustelae comb. nov., respectively". Int. J. Syst. Bacteriol. 39 (4): 397–405. doi:10.1099/00207713-39-4-397.
3. Boyanova, L, ed. (2011). Helicobacter pylori. Caister Academic Press. ISBN 978-1-904455-84-4.
4. Vandamme P, Falsen E, Rossaq R, et al. (1991). "Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov". Int. J. Syst. Bacteriol. 41 (1): 88–103. doi:10.1099/00207713-41-1-88. PMID 1704793.
5. Yamaoka, Y., ed. (2008). Helicobacter pylori: Molecular Genetics and Cellular Biology. Caister Academic Press. ISBN 978-1-904455-31-8. .
6. Ryan, KJ; Ray, CG, eds. (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 0-8385-8529-9.
7. Dunn BE, Cohen H, Blaser MJ (1 October 1997). "Helicobacter pylori". Clin Microbiol Rev. 10 (4): 720–741. doi:10.1128/cmr.10.4.720. PMC 172942. PMID 9336670.
8. Hua JS, Zheng PY, Ho B (1999). "Species differentiation and identification in the genus of Helicobacter". World Journal of Gastroenterology. 5 (1): 7–9. doi:10.3748/wjg.v5.i1.7. PMC 4688506. PMID 11819372.
9. Rust; et al. (2008). "Helicobacter Flagella, Motility and Chemotaxis". Helicobacter pylori: Molecular Genetics and Cellular Biology (Yamaoka Y, ed.). Caister Academic Press. ISBN 978-1-904455-31-8. .
10. Zakharova N.; Paster B. J.; Wesley I.; Dewhirst F. E.; Berg D. E.; Severinov K. V. (1999). "Fused and overlapping rpoB and rpoC genes in Helicobacters, Campylobacters, and related bacteria". J Bacteriol. 181 (12): 3857–3859. doi:10.1128/JB.181.12.3857-3859.1999. PMC 93870. PMID 10368167.
11. Bento-Miranda M, Figueiredo C (December 2014). "Helicobacter heilmannii sensu lato: an overview of the infection in humans". World Journal of Gastroenterology. 20 (47): 17779–87. doi:10.3748/wjg.v20.i47.17779. PMC 4273128. PMID 25548476.
12. Iwanczak B, Biernat M, Iwanczak F, Grabinska J, Matusiewicz K, Gosciniak G (April 2012). "The clinical aspects of Helicobacter heilmannii infection in children with dyspeptic symptoms". Journal of Physiology and Pharmacology. 63 (2): 133–6. PMID 22653899.
13. Ménard A, Smet A (September 2019). "Review: Other Helicobacter species". Helicobacter. 24 (Suppl 1): e12645. doi:10.1111/hel.12645. PMID 31486233.
14. Sayers; et al. "Helicobacter". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 9 September 2023.
15. "The LTP". Retrieved 20 November 2023.
16. "LTP_all tree in newick format". Retrieved 20 November 2023.
17. "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
18. "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
19. "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
20. "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.

External links

• Helicobacter genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID
• List of species in Helicobacter, with links to sequence information
• Helicobacter at BacDive - the Bacterial Diversity Metadatabase