Cytobacillus
{{Short description|Genus of rod-shaped bacteria}}
{{Taxobox
|image= Cytobacillus firmus! formarly Bacillus firmus NRRL NRS-613 (Type Strain).jpg
|image_caption= Cytobacillus firmus formerly Bacillus firmus on agar plate
| domain = Bacteria
| regnum = Bacillati
| phylum = Bacillota
| classis = Bacilli
| ordo = Bacillales
| familia = Cytobacillaceae
| genus = Cytobacillus
| genus_authority = Patel and Gupta 2020
| type_species =Cytobacillus firmus
| type_species_authority =(Bredemann & Werner 1933) Patel & Gupta 2020
| subdivision_ranks = Species
| subdivision =
}}
Cytobacillus is a genus of rod-shaped bacteria that stain either Gram-positive or Gram-variable in the family Bacillaceae within the order Bacillales.{{Cite journal|last1=Patel|first1=Sudip|last2=Gupta|first2=Radhey S.|date=2020-01-01|title=A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=70|issue=1|pages=406–438|doi=10.1099/ijsem.0.003775|pmid=31617837|issn=1466-5026|doi-access=free}} The type species for this genus is Cytobacillus firmus.
Members of this genus was transferred from the Bacillus genus after comparative genomics studies have determined they were sufficiently different by phylogenetic measures than Bacillus subtilis, the type species of the genus Bacillus.{{Cite journal|last1=Gupta|first1=Radhey S.|last2=Patel|first2=Sudip|last3=Saini|first3=Navneet|last4=Chen|first4=Shu|date=2020-11-01|title=Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=70|issue=11|pages=5753–5798|doi=10.1099/ijsem.0.004475|pmid=33112222 |issn=1466-5026|doi-access=free}} The genus Bacillus has long been under close scrutiny by the scientific community due to its polyphyletic nature, displaying many distinct monophyletic groupings in various phylogenetic trees within the genus.{{Cite book|date=2005|editor-last=Brenner|editor-first=Don J.|editor2-last=Krieg|editor2-first=Noel R.|editor3-last=Staley|editor3-first=James T.|editor4-last=Garrity|editor4-first=George M.|editor5-last=Boone|editor5-first=David R.|editor6-last=De Vos|editor6-first=Paul|editor7-last=Goodfellow|editor7-first=Michael|editor8-last=Rainey|editor8-first=Fred A.|editor9-last=Schleifer|editor9-first=Karl-Heinz|title=Bergey's Manual® of Systematic Bacteriology|url=http://dx.doi.org/10.1007/0-387-28022-7|doi=10.1007/0-387-28022-7|isbn=978-0-387-24144-9}}{{Cite journal|last=Logan|first=N.A.|date=2011-12-20|title=Bacillus and relatives in foodborne illness|journal=Journal of Applied Microbiology|volume=112|issue=3|pages=417–429|doi=10.1111/j.1365-2672.2011.05204.x|pmid=22121830|issn=1364-5072|doi-access=free}}{{Cite journal|last1=La Duc|first1=Myron T|last2=Satomi|first2=Masataka|last3=Agata|first3=Norio|last4=Venkateswaran|first4=Kasthuri|date=March 2004|title=gyrB as a phylogenetic discriminator for members of the Bacillus anthracis–cereus–thuringiensis group|url=http://dx.doi.org/10.1016/j.mimet.2003.11.004|journal=Journal of Microbiological Methods|volume=56|issue=3|pages=383–394|doi=10.1016/j.mimet.2003.11.004|pmid=14967230|issn=0167-7012|url-access=subscription}} In addition, while Bacillus species have a diverse range of biochemical characteristics, there is no unique characteristic that can be used to reliably distinguish all Bacillus species from other bacteria.{{Cite journal|last1=Ash|first1=Carol|last2=Farrow|first2=J.A.E.|last3=Wallbanks|first3=Sally|last4=Collins|first4=M.D.|date=2008-06-28|title=Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences|url=http://dx.doi.org/10.1111/j.1472-765x.1991.tb00608.x|journal=Letters in Applied Microbiology|volume=13|issue=4|pages=202–206|doi=10.1111/j.1472-765x.1991.tb00608.x|s2cid=82988953 |issn=0266-8254|url-access=subscription}} Many studies have used phylogenetic and comparative genomic analyses as a means towards clarifying the complicated taxonomic relationships within Bacillus, resulting in the transfer of many species into novel genera such as Alkalihalobacillus, Virigibacillus,{{Cite journal|last1=Heyndrickx|first1=M.|last2=Lebbe|first2=L.|last3=Kersters|first3=K.|last4=Hoste|first4=B.|last5=De Wachter|first5=R.|last6=De Vos|first6=P.|last7=Forsyth|first7=G.|last8=Logan|first8=N. A.|date=1999-07-01|title=Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998|journal=International Journal of Systematic and Evolutionary Microbiology|volume=49|issue=3|pages=1083–1090|doi=10.1099/00207713-49-3-1083|pmid=10425765|issn=1466-5026|doi-access=free}} Brevibacillus,{{Cite journal|last1=Shida|first1=O.|last2=Takagi|first2=H.|last3=Kadowaki|first3=K.|last4=Komagata|first4=K.|date=1996-10-01|title=Proposal for Two New Genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov.|journal=International Journal of Systematic Bacteriology|language=en|volume=46|issue=4|pages=939–946|doi=10.1099/00207713-46-4-939|pmid=8863420|issn=0020-7713|doi-access=free}} Solibacillus{{Cite journal|last1=Mual|first1=Poonam|last2=Singh|first2=Nitin Kumar|last3=Verma|first3=Ashish|last4=Schumann|first4=Peter|last5=Krishnamurthi|first5=Srinivasan|last6=Dastager|first6=Syed|last7=Mayilraj|first7=Shanmugam|date=2016-05-01|title=Reclassification of Bacillus isronensis Shivaji et al. 2009 as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al. 2009|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=66|issue=5|pages=2113–2120|doi=10.1099/ijsem.0.000982|pmid=26907585|issn=1466-5026|doi-access=free}} and Evansella. In addition, the genus Bacillus has been restricted to include only species closely related to Bacillus subtilis and Bacillus cereus.
The name Cytobacillus can be broken down into the prefix "cyto-" (from the Greek noun kytos, referring to hollow, vessel, jar or a cell in biology) and the suffix "-bacillus" (from the Latin noun bacillus, referring to a small staff or rod and Bacillus, the bacterial genus). Together, Cytobacillus refers to a rod-shaped cell.
Biochemical characteristics and molecular signatures
Members of Cytobacillus can be either aerobic or facultatively anaerobic. All studied species of this genus has been observed to produce endospores under adverse environmental or nutritional conditions. Cytobacillus can be isolated and found a diverse range of locations, ranging from natural locations (soil, marine sediments), living organisms (human gut, earthworm) to pharmaceutical production sites. Most species are motile, and some are able to tolerate moderate saline conditions and high alkalinity environments. While Cytobacillus species can grow in temperatures ranging from 10–45°C, optimum growth occurs in the range 25–37°C.
Three conserved signature indels (CSIs) have been identified as exclusively shared by most/all members of Cytobacillus in the following proteins: PDZ domain-containing protein, histidinol dehydrogenase and transcription-repair coupling factor. These CSIs were identified through the analysis of genome sequences from Cytobacillus species and provide novel molecular means to differentiate this genus from other Bacillaceae genera.
Taxonomy
As of May 2021, there are a total of 13 species with validly published names in the genus Cytobacillus.{{cite web |author=A.C. Parte |url=https://lpsn.dsmz.de/genus/cytobacillus |title=Cytobacillus |access-date=2025-02-28 |publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN) |display-authors=et al.}}{{cite web |author=C.L. Schoch |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=2675230&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Cytobacillus |access-date=2025-02-28 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database |display-authors=et al.}} Members of Cytobacillus are observed to group together in a monophyletic clade in phylogenetic trees created based on different datasets of conserved proteins as well as 16S rRNA genome sequences. This branching pattern is also observed in the Genome Taxonomy Database (GTDB).{{Cite web|title=GTDB – Tree|url=https://gtdb.ecogenomic.org/tree?r=d__Bacteria|access-date=2021-05-25|website=gtdb.ecogenomic.org}}
In addition to these species with published names, several non-validly published species (‘Bacillus dabaoshanensis', ‘Bacillus dafuensis’, ‘Bacillus massiliogabonensis’, and ‘Bacillus mesophilum') been observed to branch with other Cytobacillus species and share molecular markers (in the form of conserved signature indels) exclusively unique for this genus. However the lack of culture strain information prevented the transfer of these species into the genus. It is important to note as genome and strain information becomes available, it is necessary to conduct additional analyses of these classifications to account for any required amendments.
=Phylogeny=
| class="wikitable" |
| colspan=1 | 16S rRNA based LTP_10_2024{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}{{cite web |title=LTP_all tree in newick format |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_10_2024.ntree |access-date=10 December 2024}}{{cite web |title=LTP_10_2024 Release Notes |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_10_2024_release_notes.pdf |access-date=10 December 2024}}
! colspan=1 | 120 marker proteins based GTDB 09-RS220{{cite web |title=GTDB release 09-RS220 |url=https://gtdb.ecogenomic.org/about#4%7C |website=Genome Taxonomy Database |access-date=10 May 2024}}{{cite web |title=bac120_r220.sp_labels |url=https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/bac120_r220.sp_labels.tree |website=Genome Taxonomy Database |access-date=10 May 2024}}{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=Genome Taxonomy Database |access-date=10 May 2024}} |
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{{Clade | style=font-size:90%;line-height:80% |1={{clade |1={{clade |label1=Cytobacillus~2, 3, 4 |1={{clade |1={{clade |1=C. eiseniae |2={{clade |1="C. massiliigabonensis" |2={{clade |1=C. praedii |2=C. solani }} }} }} |2={{clade |1={{clade |1=C. depressus |2=C. formosensis (Lin et al. 2015) Patel & Gupta 2020 }} |2={{clade |1={{clade |1=C. kochii |2={{clade |1=C. horneckiae |2=C. purgationiresistens }} }} |2={{clade |1=C. spongiae Gao et al. 2023 |2={{clade |1=C. citreus |2="C. dafuensis" }} }} }} }} }} }} |2={{clade |1=Cytobacillus gottheilii |2={{clade |1=Bacillus infantis Ko et al. 2006 |2={{clade |label1=Cytobacillus |1={{clade |1=C. oceanisediminis |2={{clade |1=C. firmus |2=C. pseudoceanisediminis }} }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |label1=Cytobacillus |1={{clade |1={{clade |1={{clade |1=C. gottheilii (Seiler et al. 2013) Patel & Gupta 2020 |2="Bacillus mesophilum" Manickam et al. 2014 non Zhou et al. 2017 }} |2={{clade |1={{clade |1=C. horneckiae (Vaishampayan et al. 2010) Patel & Gupta 2020 |2=C. purgationiresistens (Vaz-Moreira et al. 2012) Patel & Gupta 2020 }} |2={{clade |1=C. kochii (Seiler et al. 2012) Patel & Gupta 2020 |2=C. stercorigallinarum Pallen 2024 }} }} }} |2={{clade |1={{clade |1=C. oceanisediminis (Zhang et al. 2010) Patel & Gupta 2020 |2={{clade |1=Bacillus globisporus Larkin & Stokes 1967 |2={{clade |1=C. firmus (Bredemann & Werner 1933) Patel & Gupta 2020 |2=C. pseudoceanisediminis Tarasov et al. 2023 }} }} }} |2={{clade |1={{clade |1=C. depressus (Wei et al. 2016) Patel & Gupta 2020 |2={{clade |1=C. citreus Liu et al. 2023 |2="C. dafuensis" (Zheng et al. 2023) Liu et al. 2023 }} }} |2={{clade |1=C. eiseniae (Hong et al. 2012) Patel & Gupta 2020 |2={{clade |1="C. massiliigabonensis" (Sarr et al. 2021) Liu et al. 2023 |2={{clade |1=C. praedii (Liu et al. 2017) Patel & Gupta 2020 |2=C. solani (Liu et al. 2015) Patel & Gupta 2020 }} }} }} }} }} }} }} |
See also
References
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