Editing Bacillus (section)

==Phylogeny==
It's been long known that the (pre-2020) definition of ''Bacillus'' is overly vague.<ref name=Ash/>
* Xu and Côté (2003) uses 16S and ITS rRNA regions to divide the genus ''Bacillus'' into 10 groups, including the nested genera ''[[Paenibacillus]]'', ''[[Brevibacillus]]'', ''[[Geobacillus]]'', ''Marinibacillus'' and ''[[Virgibacillus]]''.<ref>{{cite journal | vauthors = Xu D, Côté JC | title = Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 53 | issue = Pt 3 | pages = 695–704 | date = May 2003 | pmid = 12807189 | doi = 10.1099/Ijs.0.02346-0 | doi-access = free }}</ref>
* Ash and Carol (2008) also uses 16S rRNA and found extensive "phylogenetic heterogenity".<ref name=Ash>{{Cite journal|last1=Ash|first1=Carol|last2=Farrow|first2=J.A.E.|last3=Wallbanks|first3=Sally|last4=Collins|first4=M.D.|date=28 June 2008|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}}</ref> 
* [['The All-Species Living Tree' Project]], which has been in operation since 2008, also maintains a 16S (and 23S if available) tree of all validated species.<ref>{{cite journal | vauthors = Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R | title = The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains | journal = Systematic and Applied Microbiology | volume = 31 | issue = 4 | pages = 241–250 | date = September 2008 | pmid = 18692976 | doi = 10.1016/j.syapm.2008.07.001 | hdl-access = free | hdl = 10261/103580 | url = https://tede.ufrrj.br/jspui/handle/jspui/5297 }}</ref><ref>{{cite journal | vauthors = Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R | title = Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses | journal = Systematic and Applied Microbiology | volume = 33 | issue = 6 | pages = 291–299 | date = October 2010 | pmid = 20817437 | doi = 10.1016/j.syapm.2010.08.001 | hdl = 10261/54801 }}</ref><ref>{{cite journal | vauthors = Munoz R, Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R | title = Release LTPs104 of the all-species living tree | journal = Systematic and Applied Microbiology | date = May 2011 | volume = 34 | issue = 3 | pages = 169–70 | doi = 10.1016/j.syapm.2011.03.001 | pmid = 21497273 | url = http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_104/LTPs104_SSU_tree.pdf | archive-url = https://web.archive.org/web/20150923172916/http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_104/LTPs104_SSU_tree.pdf | archive-date = 23 September 2015 }}</ref> In this tree, the genus ''Bacillus'' contains a very large number of nested taxa and majorly in both 16S and 23S. It is [[paraphyletic]] to the [[Lactobacillales]] (''Lactobacillus, Streptococcus, Staphylococcus, Listeria'', etc.), due to ''[[Bacillus coahuilensis]]'' and others.<ref>{{cite journal | vauthors = Salvetti E, Harris HM, Felis GE, O'Toole PW | title = Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification | journal = Applied and Environmental Microbiology | volume = 84 | issue = 17 | date = September 2018 | pmid = 29915113 | pmc = 6102987 | doi = 10.1128/AEM.00993-18 | bibcode = 2018ApEnM..84E.993S | veditors = Björkroth J }}</ref>
* Alcaraz ''et al.'' 2010 presents a gene [[concatenation]] study, which found results similar to the All-Species Living Tree, but with a much more limited number of species in terms of groups.<ref name="Alcaraz2010">{{cite journal | vauthors = Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, Herrera-Estrella L, Olmedo G | title = Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics | journal = BMC Genomics | volume = 11 | pages = 332 | date = May 2010 | pmid = 20504335 | pmc = 2890564 | doi = 10.1186/1471-2164-11-332 | id = 1471216411332 | doi-access = free }}</ref> (This scheme used ''Listeria'' as an outgroup, so in light of the ARB tree, it may be "inside-out").
* Gupta ''et al.'' 2020<ref name="Gupta20">{{Cite journal|last1=Gupta|first1=Radhey S.|last2=Patel|first2=Sudip|last3=Saini|first3=Navneet|last4=Chen|first4=Shu|date=1 November 2020|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}}</ref> and Patel ''et al.'' 2020<ref name="Patel20">{{Cite journal|last1=Patel|first1=Sudip|last2=Gupta|first2=Radhey S.|date=1 January 2020|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}}</ref> use [[phylogenomics]] and [[comparative genomics]] to resolve the structure in ''Bacillus'' sensu lato. They propose (and '''[[Validly published name|validly publish]]''') a number of new genus names, thereby restricting ''Bacillus'' has been restricted to only include species closely related to ''[[Bacillus subtilis]]'' and ''[[Bacillus cereus]].''<ref name="Patel20"/> (This does not make the genus monophyletic, however: a number of nested genera persists between the two groups.)<ref name="Gupta20"/> The newly created genera are: ''[[Peribacillus]]'', ''[[Cytobacillus]]'', ''[[Mesobacillus]]'', ''[[Neobacillus]]'', ''[[Metabacillus]]'', ''[[Alkalihalobacillus]]'', ''[[Alteribacter]]'', ''[[Ectobacillus]]'', ''[[Evansella]]'', ''[[Ferdinandcohnia]]'', ''[[Gottfriedia]]'', ''[[Heyndrickxia]]'', ''[[Lederbergia]]'', ''[[Litchfieldia]]'', ''[[Margalitia]]'', ''[[Niallia]]'', ''[[Priestia]]'', ''[[Robertmurraya]]'', ''[[Rossellomorea]]'', ''[[Schinkia]]'', ''[[Siminovitchia]]'', ''[[Sutcliffiella]]'' and ''[[Weizmannia]]''.
* Nikolaidis ''et al.'' 2022 studied 1104 ''Bacillus'' proteomes using a gene concatenation based on 114 core proteins and delineated the relationships among the various species, defined as ''Bacillus'' from the NCBI taxonomy.<ref name=":0">{{cite journal | vauthors = Nikolaidis M, Hesketh A, Mossialos D, Iliopoulos I, Oliver SG, Amoutzias GD | title = A Comparative Analysis of the Core Proteomes within and among the ''Bacillus subtilis'' and ''Bacillus cereus'' Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations | journal = Microorganisms | volume = 10 | issue = 9 | pages = 1720 | date = August 2022 | pmid = 36144322 | pmc = 9505155 | doi = 10.3390/microorganisms10091720 | doi-access = free }}</ref> The various strains were clustered into species, based on Average Nucleotide identity (ANI) values, with a species cutoff of 95%.<ref name=":0" />

One clade, formed by ''Bacillus anthracis'', ''Bacillus cereus'', ''Bacillus mycoides'', ''Bacillus pseudomycoides'', ''Bacillus thuringiensis'', and ''Bacillus weihenstephanensis'' under the 2011 classification standards, should be a single species (within 97% 16S identity), but for medical reasons, they are considered separate species<ref>{{cite book | vauthors = Økstad OA, Kolstø AB | chapter = Chapter 2: Genomics of Bacillus species | veditors = Wiedmann M, Zhang W | title = Genomics of Foodborne Bacterial Pathogens | date = December 2010 | pages = 29–53 (34–35) | location = New York, NY | publisher = Springer | doi = 10.1007/978-1-4419-7686-4_2 | isbn = 978-1-4419-7686-4 | volume = 29 | series = Food Microbiology and Food Safety }}</ref> (an issue also present for four species of ''[[Shigella]]'' and ''[[Escherichia coli]]'').<ref>{{cite book | vauthors = Brenner DJ | chapter = Family I. Enterobacteriaceae Rahn 1937, Nom. fam. cons. Opin. 15, Jud. Com. 1958, 73; Ewing, Farmer, and Brenner 1980, 674; Judicial Commission 1981, 104. | veditors = Krieg NR, Holt JG | title = Bergey's Manual of Systematic Bacteriology | edition = first | volume = 1 | publisher = The Williams & Wilkins Co | location = Baltimore| date = 1984 | pages = 408–420 }}</ref>

{| class="wikitable"
|-
! colspan=1 | Alcaraz et al. 2010<ref name="Alcaraz2010"/>
! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_10_2024<ref>{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}</ref><ref>{{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}}</ref><ref>{{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}}</ref>
! colspan=1 | 120 marker proteins based [[Genome Taxonomy Database|GTDB]] 09-RS220<ref name="about">{{cite web |title=GTDB release 09-RS220 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]] |access-date=10 May 2024}}</ref><ref name="tree">{{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}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]] |access-date=10 May 2024}}</ref>
|- 
| style="vertical-align:top|
{{Clade | style=font-size:90%;line-height:80%
|label1=Root
|1={{clade
  |1={{clade
  |label1="pathogenic"
  |1={{clade
    |1=''[[Bacillus weihenstephanensis]]''
    |2=''[[Bacillus cereus]]''/''[[Bacillus thuringiensis|thuringiensis]]''/''[[Bacillus anthracis|anthracis]]''
     }}
     }}
  |2={{clade
    |1={{clade
    |label1="soil"
    |1={{clade
      |1=''[[Bacillus pumilus]]''
      |2={{clade
        |1=''[[Bacillus subtilis]]''
        |2=''[[Bacillus licheniformis]]''
         }}
       }}
       }}
    |2={{clade
      |1={{clade
      |label1="benthic"
      |1=''[[Geobacillus kaustophilus]]''
         }}
      |2={{clade
        |1={{clade
        |label1="aquatic"
        |1={{clade
          |1={{clade
            |1=''[[Bacillus coahuilensis]]''
            |2=''Bacillus'' sp. m3-13
             }}
          |2=''Bacillus'' sp. NRRLB-14911
           }}
           }}
        |2={{clade
          |label1="benthic"
          |1=''[[Oceanobacillus iheyensis]]''
          |label2="halophiles"
          |2={{clade
            |1=''[[Bacillus halodurans]]''
            |2=''[[Bacillus clausii]]''
             }}
           }}
         }}
       }}
     }}
   }}
}}
|
{{Clade | style=font-size:90%;line-height:80%
|label1=''Bacillus'' s.s.
|1={{clade
  |1={{clade
    |1=''B. capparidis'' <small>Wang et al. 2017</small>
    |2=''B. gobiensis'' <small>Liu et al. 2016</small>
     }}
  |2={{clade
    |1={{clade
      |1={{clade
        |1=''B. changyiensis'' <small>Xiao et al. 2023</small>
        |2=''B. haynesii'' <small>Dunlap et al. 2017</small>
         }}
      |2={{clade
        |1=''B. glycinifermentans'' <small>Kim et al. 2015</small>
        |2={{clade
          |1=''B. paralicheniformis'' <small>Dunlap et al. 2015</small>
          |2={{clade
            |1={{clade
              |1=''[[Bacillus aerius|B. aerius]]'' <small>Shivaji et al. 2006</small>
              |2=''[[Bacillus licheniformis|B. licheniformis]]'' <small>(Weigmann 1898) Chester 1901</small>
               }}
            |2={{clade
              |1=''[[Bacillus sonorensis|B. sonorensis]]'' <small>Palmisano et al. 2001</small>
              |2=''B. swezeyi'' <small>Dunlap et al. 2017</small>
               }}
             }}
           }}
         }}
       }}
    |2={{clade
      |1=''[[Bacillus atrophaeus|B. atrophaeus]]'' <small>Nakamura 1989</small>
      |2={{clade
        |1={{clade
          |1=''[[Bacillus altitudinis|B. altitudinis]]'' <small>Shivaji et al. 2006</small>
          |2={{clade
            |1={{clade
              |1=''[[Bacillus aerophilus|B. aerophilus]]'' <small>Shivaji et al. 2006</small>
              |2=''B. xiamenensis'' <small>Lai, Liu & Shao 2014</small>
               }}
            |2={{clade
              |1=''[[Bacillus safensis|B. safensis]]'' <small>Satomi, La Duc & Venkateswaran 2006</small>
              |2={{clade
                |1=''B. australimaris'' <small>Liu et al. 2016</small>
                |2={{clade
                  |1=''[[Bacillus pumilus|B. pumilus]]'' <small>Meyer & Gottheil 1901</small>
                  |2=''B. zhangzhouensis'' <small>Liu et al. 2016</small>
                   }}
                 }}
               }}
             }}
           }}
        |2={{clade
          |1=''B. velezensis'' <small>Ruiz-Garcia et al. 2005</small>
          |2={{clade
            |1={{clade
              |1=''B. siamensis'' <small>Sumpavapol et al. 2010</small>
              |2=''[[Bacillus amyloliquefaciens|B. amyloliquefaciens]]'' <small>Fukumoto 1943 ex Priest et al. 1987</small>
               }}
            |2={{clade
              |1={{clade
                |1=''[[Bacillus vallismortis|B. vallismortis]]'' <small>Roberts, Nakamura & Cohan 1996</small>
                |2={{clade
                  |1=''B. mexicanus'' <small>de los Santos Villalobos et al. 2023</small>
                  |2=''B. stercoris'' <small>(Adelskov & Patel 2017) Dunlap, Bowman & Zeigler 2020</small>
                   }}
                 }}
              |2={{clade
                |1=''B. spizizenii'' <small>(Nakamura et al. 1999) Dunlap, Bowman & Zeigler 2020</small>
                |2={{clade
                  |1={{clade
                    |1=''B. tequilensis'' <small>Gatson et al. 2006</small>
                    |2={{clade
                      |1=''B. halotolerans'' <small>(Delaporte & Sasson 1967) Tindall 2017</small>
                      |2=''[[Bacillus mojavensis|B. mojavensis]]'' <small>Roberts, Nakamura & Cohan 1994</small>
                       }}
                     }}
                  |2={{clade
                    |1=''B. nakamurai'' <small>Dunlap et al. 2016</small>
                    |2={{clade
                      |1=''B. cabrialesii tritici'' <small>de los Santos-Villalobos et al. 2023</small>
                      |2={{clade
                        |1=''B. cabrialesii'' <small>de los Santos Villalobos et al. 2019</small>
                        |2={{clade
                          |1=''B. inaquosorum'' <small>(Rooney et al. 2009) Dunlap, Bowman & Zeigler 2020</small>
                          |2=''[[Bacillus subtilis|B. subtilis]]'' <small>(Ehrenberg 1835) Cohn 1872</small>
                           }}
                         }}
                       }}
                     }}
                   }}
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
   }}
}}
|
{{Clade | style=font-size:90%;line-height:80%
|label1=''Bacillus'' s.s.
|1={{clade
  |1=''B. gobiensis'' [''B. capparidis'']
  |2={{clade
    |1={{clade
      |1={{clade
        |1=''B. glycinifermentans''
        |2=''[[Bacillus sonorensis|B. sonorensis]]''
         }}
      |2={{clade
        |1=''B. swezeyi''
        |2={{clade
          |1=''[[Bacillus licheniformis|B. licheniformis]]''
          |2={{clade
            |1=''B. haynesii''
            |2=''B. paralicheniformis'' [''B. crescens'' <small>Shivani et al. 2015</small>]
             }}
           }}
         }}
       }}
    |2={{clade
      |1={{clade
        |1={{clade
          |1=''[[Bacillus altitudinis|B. altitudinis]]'' [''[[Bacillus aerius|B. aerius]]''; ''[[Bacillus aerophilus|B. aerophilus]]'']
          |2=''B. xiamenensis''
           }}
        |2={{clade
          |1=''B. zhangzhouensis''
          |2={{clade
            |1=''[[Bacillus pumilus|B. pumilus]]''
            |2={{clade
              |1=''B. australimaris''
              |2=''[[Bacillus safensis|B. safensis]]''
               }}
             }}
           }}
         }}
      |2={{clade
        |1=''[[Bacillus atrophaeus|B. atrophaeus]]''
        |2={{clade
          |1={{clade
            |1=''B. nakamurai''
            |2={{clade
              |1=''[[Bacillus amyloliquefaciens|B. amyloliquefaciens]]''
              |2={{clade
                |1=''B. siamensis''
                |2=''B. velezensis'' [''[[Bacillus lentimorbus|B. lentimorbus]]'' <small>Dutky 1940</small>]
                 }}
               }}
             }}
          |2={{clade
            |1={{clade
              |1=''B. halotolerans''
              |2=''[[Bacillus mojavensis|B. mojavensis]]''
               }}
            |2={{clade
              |1=''B. tequilensis''
              |2={{clade
                |1={{clade
                  |1=''[[Bacillus vallismortis|B. vallismortis]]''
                  |2={{clade
                    |1="''B. rugosus''" <small>Bhattacharya et al. 2020</small>
                    |2=''B. spizizenii''
                     }}
                   }}
                |2={{clade
                  |1=''B. cabrialesii''
                  |2={{clade
                    |1=''B. inaquosorum''
                    |2={{clade
                      |1=''B. stercoris''
                      |2=''[[Bacillus subtilis|B. subtilis]]'' [''Paenibacillus solisilvae'' <small>Kong et al. 2020</small>]
                       }}
                     }}
                   }}
                 }}
               }}
             }}
           }}
         }}
       }}
     }}
   }}
}}
|}