Neobacillus: Difference between revisions

Content deleted Content added
Apple127 (talk | contribs)
Started a page with basic information on neobacillus
 
OAbot (talk | contribs)
m Open access bot: doi added to citation with #oabot.
 
(29 intermediate revisions by 11 users not shown)
Line 1:
{{Short description|Genus of rod-shaped bacteria}}
{{AfC submission|t||ts=20210520164916|u=Apple127|ns=118|demo=}}
{{Automatic taxobox
 
| taxon = Neobacillus
{{Taxobox
| authority = Patel and Gupta 2020
| phylum = [[Firmicutes]]
| classis = [[Bacilli]]
| ordo = [[Bacillales]]
| familia = [[Bacillaceae]]
| genus = '''''Neobacillus''''' <small>Patel and Gupta 2020</small>
| domain = [[Bacteria]]
| subdivision_ranks = Species
| subdivision = *''[[NeobacillusBacillus bataviensis|N. bataviensis]]''
*''[[Neobacillus cucumiscitreus|N. cucumiscitreus]]''
*''[[NeobacillusBacillus drentensiscucumis|N. drentensiscucumis]]''
*''[[NeobacillusBacillus endophyticusdrentensis|N. endophyticusdrentensis]]''
*''[[NeobacillusBacillus fumarioliendophyticus|N. fumarioliendophyticus]]''
*''[[NeobacillusBacillus ginsengisolifumarioli|N. ginsengisolifumarioli]]''
*''[[NeobacillusBacillus jeddahensisginsengisoli|N. jeddahensisginsengisoli]]''
*''[[NeobacillusBacillus mesonaejeddahensis|N. mesonaejeddahensis]]''
*''[[NeobacillusBacillus niacinimesonae|N. niacinimesonae]]''
*''[[NeobacillusBacillus notoginsengisoliniacini|N. notoginsengisoliniacini]]''
*''[[NeobacillusBacillus novalisnotoginsengisoli|N. novalisnotoginsengisoli]]''
*''[[NeobacillusBacillus piezotoleransnovalis|N. piezotoleransnovalis]]''
*''[[Neobacillus pocheonensisparidis|N. pocheonensisparidis]]''
*''[[NeobacillusBacillus solipiezotolerans|N. solipiezotolerans]]''
*''[[NeobacillusBacillus thermocopriaepocheonensis|N. thermocopriaepocheonensis]]''
*''[[Neobacillus viretirhizophilus|N. viretirhizophilus]]''
*''[[Neobacillus rhizosphaerae|N. rhizosphaerae]]''
}}<!-- Important, do not remove this line before article has been created. -->
*''[[Neobacillus sedimentimangrovi|N. sedimentimangrovi]]''
*''[[Bacillus soli|N. soli]]''
*''[[Bacillus thermocopriae|N. thermocopriae]]''
*''[[Bacillus vireti|N. vireti]]''
}}
 
'''''Neobacillus''''' is a genus of rod-shaped bacteria that show [[Gram-positive bacteria|Gram-positive]] or Gram-variable staining.<ref name=":03">{{Cite journal|lastlast1=Patel|firstfirst1=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.|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003775|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}}</ref> This genus belongs under the family ''[[Bacillaceae]]'' within the order ''[[Bacillales]]''.<ref>{{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}}</ref> The type species of ''Neobacillus'' is ''Neobacillus niacini.''<ref name=":030" />
 
Members of this genus were previously part of the genus ''[[Bacillus]]'' genus. It has long been recognized that the genus ''Bacillus'' genus is comprised ofcomprises a wide range of phylogenetically unrelated bacteria, demonstrated through multiple phylogenetic studies and comparative genome studies.<ref name=":0">{{Cite journal|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}}</ref><ref>{{Cite journal|last=Logan|first=N.A.|date=2011-12-20|title=Bacillus and relatives in foodborne illness|url=http://dx.doi.org/10.1111/j.1365-2672.2011.05204.x|journal=Journal of Applied Microbiology|volume=112|issue=3|pages=417–429|doi=10.1111/j.1365-2672.2011.05204.x|issn=1364-5072|pmid=22121830|doi-access=free}}</ref><ref>{{Cite journal|lastlast1=La Duc|firstfirst1=Myron T|last2=Satomi|first2=Masataka|last3=Agata|first3=Norio|last4=Venkateswaran|first4=Kasthuri|date=March 2004-03|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|issn=0167-7012|pmid=14967230}}</ref> ''Bacillus'' species were assigned based on vague criteria such as the ability to form endospores in the presence of oxygen, a criterion that many diverse, unrelated bacteria share.<ref>{{Cite namejournal|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:0"//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}}</ref><ref>{{Cite journal|last1=Logan|first1=N. A.|last2=Berge|first2=O.|last3=Bishop|first3=A. H.|last4=Busse|first4=H.-J.|last5=De Vos|first5=P.|last6=Fritze|first6=D.|last7=Heyndrickx|first7=M.|last8=Kampfer|first8=P.|last9=Rabinovitch|first9=L.|last10=Salkinoja-Salonen|first10=M. S.|last11=Seldin|first11=L.|date=2009-06-30|title=Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria|journal=International Journal of Systematic and Evolutionary Microbiology|url=http://dx.doi.org/10.1099/ijs.0.013649-0|volume=59|issue=8|pages=2114–2121|doi=10.1099/ijs.0.013649-0|pmid=19567583|issn=1466-5026|doi-access=free}}</ref> The result is a big genus comprised ofcomprising over 300 species with distinct biochemical characteristics that are not uniquely shared by all members, leaving no way to reliably distinguish ''Bacillus'' species from other bacteria. Subsequently, many studies have used phylogenetic analyses as a means to clarify the complex interspecies taxonomicevolutionary relationships ofbetween ''Bacillus'' species, resulting in the establishment of many novel genera such as ''[[SolibacillusVirgibacillus]]'',<ref>{{Cite journal|last=Mual|first=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.''[[Brevibacillus]]'', and emended description of genus Solibacillus Krishnamurthi et al. 2009|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000982|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=66|issue=5|pages=2113–2120|doi=10.1099/ijsem.0.000982|issn=1466-5026}}</ref> ''[[VirgibacillusEctobacillus]],''.<ref>{{Cite journal|lastlast1=Heyndrickx|firstfirst1=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|url=http://dx.doi.org/10.1099/00207713-49-3-1083|journal=International Journal of Systematic and Evolutionary Microbiology|volume=49|issue=3|pages=1083–1090|doi=10.1099/00207713-49-3-1083|issn=1466-5026|pmid=10425765|doi-access=free}}</ref> [[Brevibacillus]],''<ref>{{Cite journal|lastlast1=Shida|firstfirst1=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.|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-46-4-939|journal=International Journal of Systematic Bacteriology|language=en|volume=46|issue=4|pages=939–946|doi=10.1099/00207713-46-4-939|issn=0020-7713|pmid=8863420|doi-access=free}}</ref> ''[[Alkalihalobacillus]],''<ref>{{Cite namejournal|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|url=https:03"//www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000982|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=66|issue=5|pages=2113–2120|doi=10.1099/ijsem.0.000982|issn=1466-5026|pmid=26907585|doi-access=free}}</ref> ''[[Ectobacillus]]''<ref name=":112">{{Cite journal|lastlast1=Gupta|firstfirst1=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|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004475|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=70|issue=11|pages=5753–5798|doi=10.1099/ijsem.0.004475|issn=1466-5026|pmid=33112222|doi-access=free}}</ref> andAdditionally, ''[[Neobacillus]].Bacillus''<ref name=":03"has />been Therestricted nameto ''Neobacillus''included isonly piecedspecies togetherclosely usingrelated the prefix "neo-" (from the Greek adjectiveto ''neos[[Bacillus subtilis]]'', translating to new) and the suffix "-bacillus" (from the Latin noun ''bacillus[[Bacillus cereus]]'', referring to a small staff or rod and Bacillus, the bacterial genus).<ref Together,name=":03" the/><ref name=":12" translates/> to "new Bacillus".
 
The name ''Neobacillus'' is pieced together using the prefix "neo-" (from the Greek adjective {{Lang|el|neos}}, translating to new) and the suffix "-bacillus" (from the Latin noun {{Lang|la|bacillus}}, referring to a small staff or rod and ''Bacillus'', the bacterial genus). Together, the name translates to "new ''Bacillus''".<ref name=":03" />
== Biochemical Characteristics<ref name=":03" /> ==
 
Members of ''Neobacillus'' can be either [[aerobic]] or [[Facultative anaerobic organism|facultatively anaerobic.]] [[Motility]] is variable, some species are motile while others are non-motile. All studied species are observed to form [[Endospore|endospores]] under adverse environmental or nutritional conditions. ''Neobacillus'' can be found in a variety of environments, including soil, human origin (gut and skin) and plant roots. ''Neobacillus'' can grow in temperatures up to 50-55°C, but optimal growth occurs in the range of 25-37°C.
== Biochemical Characteristics<ref name=":03"and />Molecular Signatures ==
Members of ''Neobacillus'' can be either [[Aerobic organism|aerobic]] or [[Facultative anaerobic organism|facultatively anaerobic.]] [[Motility]] is variable, some species are motile while others are non-motile. All studied species are observed to form [[Endospore|endospores]] under adverse environmental or nutritional conditions. ''Neobacillus'' can be found in a variety of environments, including soil, human origin (gut and skin) and plant roots. ''Neobacillus'' can grow in temperatures up to 50-55°C, but optimal growth occurs in the range of 25-37°C.
 
11 [[conserved signature indels]] (CSIs) have been identified through genomic analysis as exclusive for ''Neobacillus'' in proteins such as 50S ribosomal protein L24, flagellar M-ring protein FliF, 50S ribosomal protein L11 methyltransferase, imidazole glycerol phosphate synthase subunit HisH, ATP phosphoribosyltransferase regulatory subunit, LTA synthase family protein, [[type I DNA topoisomerase]], [[nicotinate phosphoribosyltransferase]], bifunctional hydroxymethylpyrimidine kinase/phospho- methylpyrimidine kinase, single-stranded-DNA-specific exonuclease RecJ and [[1-deoxy-D-xylulose-5-phosphate synthase|1-deoxy-d-xylulose-5-phosphate synthase]].<ref name=":03" /> These CSIs provide reliable methods to differentiate ''Neobacillus'' from other ''Bacillaceae'' genera and bacteria in molecular terms.
 
== Taxonomy ==
As of May 2021, there are a total of 17 species with validly published names in the genus ''Neobacillus''.<ref name=":0">{{Cite web|title=Genus: Neobacillus|url=https://lpsn.dsmz.de/genus/neobacillus|access-date=2021-05-20|website=lpsn.dsmz.de|language=en}}</ref> Members of this genus group together and forms a [[Monophyly|monophyletic]] branch in phylogenetic trees created from concatenated sequences from various datasets of conserved proteins as well as [[16S rRNA]] gene sequences.<ref name=":03" /> Additional phylogenetic studies have identified a number of non-validly published species ("Bacillus dielmoensis", "Bacillus ferrooxidans", "Bacillus rubiinfantis", and "Bacillus marasmi") that are considered to be members of this genus based on taxonomic placement in phylogenetic trees as well as shared molecular markers (specificallyThe [[conservedGenome signatureTaxonomy indelsDatabase]] (GTDB) withalso othershows members of ''Neobacillus'' grouping together.<ref>{{Cite nameweb|title="GTDB - Tree|url=https:1" /> However, transfer was not proposed due to the lack of strain culture information/gtdb. As additional culture information and genome sequences become available in the future, it would be necessary to revisit the taxonomic classifications proposed for this genus to update and validate the resultsecogenomic. org/tree?r=d__Bacteria|access-date=2021-05-25|website=gtdb.ecogenomic.org}}</ref>
 
Additional phylogenetic studies have identified a number of non-validly published species ("''Bacillus ferrooxidans", "Bacillus rubiinfantis",'' ''"Bacillus marasmi"'' and "''Bacillus salipaludis''") that are considered to be members of this genus based on taxonomic placement in phylogenetic trees as well as shared molecular markers (specifically [[conserved signature indels]]) with other members of ''Neobacillus''.<ref name=":12" /><ref name=":13">{{cite journal |last1=Kämpfer |first1=Peter |last2=Glaeser |first2=Stefanie P. |last3=McInroy |first3=John A. |last4=Clermont |first4=Dominique |last5=Lipski |first5=André |last6=Criscuolo |first6=Alexis |title=''Neobacillus rhizosphaerae'' sp. nov., isolated from the rhizosphere, and reclassification of ''Bacillus dielmonensis'' as ''Neobacillus dielmonensis'' comb. nov. |journal=International Journal of Systematic and Evolutionary Microbiology |date=2022 |volume=72 |page=005636 |doi=10.1099/ijsem.0.005636 |pmid=36327328}}</ref> However, transfer was not proposed due to the lack of strain culture information. As additional culture information and genome sequences become available in the future, it would be necessary to revisit the taxonomic classifications proposed for this genus to update and validate the results, as done in 2022 for ''Bacillus dielmonensis''.<ref name=":13" />
== Molecular signatures ==
In addition to phylogenetic analyses, members of Neobacillus can be distinguished from all other bacteria through molecular markers known as [[conserved signature indels]] (CSIs).<ref name=":2">{{Cite journal|last=Naushad|first=Hafiz Sohail|last2=Lee|first2=Brian|last3=Gupta|first3=Radhey S.|date=2014-02-01|title=Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria|url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.054213-0|journal=International Journal of Systematic and Evolutionary Microbiology|language=en|volume=64|issue=Pt_2|pages=366–383|doi=10.1099/ijs.0.054213-0|issn=1466-5026}}</ref> CSIs arise when a bacteria undergoes a rare genetic change in a highly conserved protein sequence and then subsequently passes on this genetic change laterally to its descendants.<ref name=":2" /> The specific genetic mutation (an insertion or deletion of a number of amino acids) is flanked on both sides by conserved sequences and are often found in essential proteins, indicating their reliability as a molecular marker.<ref name=":2" /> 11 CSIs were identified for ''Neobacillus'' in proteins such as 50S ribosomal protein L24, flagellar M-ring protein FliF, 50S ribosomal protein L11 methyltransferase, imidazole glycerol phosphate synthase subunit HisH, ATP phosphoribosyltrans- ferase regulatory subunit, LTA synthase family protein, type I DNA topoisomerase, nicotinate phosphoribosyltransferase, bifunctional hydroxymethylpyrimidine kinase/phospho- methylpyrimidine kinase, single-stranded-DNA-specific exonuclease RecJ and 1-deoxy-d-xylulose-5-phosphate synthase.<ref name=":03" /> Majority of the CSIs are exclusively shared by all/most members of the Neobacillus genus and are not found in any other bacteria.
 
== References ==
{{Reflist}}
<!-- Inline citations added to your article will automatically display here. See en.wikipedia.org/wiki/WP:REFB for instructions on how to add citations. -->
 
{{reflist}}
{{Taxonbar|from=Q107182597}}
 
| familia = [[Category:Bacillaceae]]
[[Category:Taxa described in 2020]]
[[Category:Bacteria genera]]