Clostridiaceae

{{Short description|Family of bacteria}} {{More citations needed|type=bacteria|date=December 2009}} {{Automatic taxobox | image = Clostridium botulinum 01.png | image_alt = Photomicrograph of "Clostridium botulinum" bacteria stained with crystal violet | image_caption = Photomicrograph of ''Clostridium botulinum'' bacteria stained with crystal violet | taxon = Clostridiaceae | authority = {{ill|Ernst August Pribram|lt=Pribram|de}} 1933<ref>{{ill|Ernst August Pribram|lt=Pribram, Ernst August|de}}: Klassification der Schizomyceten. F. Deuticke, Leipzig, (1933) pp. 1-143</ref> | type_genus = | type_genus_authority = | subdivision_ranks = Genera | subdivision = See text | synonyms_ref = | synonyms = * "Botulineae" Pribram 1929 * "Botulinoideae" Pribram 1929 * "Clostridioideae" corrig. Fischer 1897 * "Plectridiaceae" Prévot 1938 * "Plectridioideae" corrig. Fischer 1897 * "Putrificeae" Pribram 1929 * "Putrificoideae" Heller 1921 * "Sarcinaceae" Skuja 1956 * "Sarcineae" Trevisan 1889 * "Sarcinidae" Enderlein 1917 * "Sarcininae" corrig. Trevisan 1879 * "Welchieae" Pribram 1929 }}

The '''Clostridiaceae''' are a family of the bacterial class Clostridia, and contain the genus ''Clostridium''.

The family Clostridiaceae (scientific name) defined by the taxonomic outline of '' Bergey's Manual of Systematic Bacteriology '' contains as its core the genus ''Clostridium'' (''sensu stricto''), as well as ''Acetivibrio'', ''Acidaminobacter'', ''Alkaliphilus'', ''Anaerobacter'', ''Caloramator'', ''Caloranaerobacter'', ''Coprobacillus'', ''Dorea'', ''Natronincola'', ''Oxobacter'', ''Sarcina'', ''Sporobacter'', ''Thermobrachium'', ''Thermohalobacter'', and ''Tindallia''. The previous inclusion of these additional genera (as seen on the right) in a family Clostridiaceae is based for the most part because the type species of these genera are in many cases phylogenetically related to misclassified species of the genus ''Clostridium''. However, with the exception of ''Anaerobacter'', ''Caloramator'', ''Oxobacter'', ''Sarcina'', and ''Thermobrachium'', these genera fall outside the radiation of what can be considered the true family Clostridiaceae and are now regarded as belonging to other families within the low G + C, Gram-positive phylum.

This misclassification is the result of well-known problems of the current taxonomic structure of the traditional genus ''Clostridium''. The phylogenetic analysis of Collins (1994) was the first large-scale comparison of 16S rRNA gene sequences of species of the genus ''Clostridium'' and related taxa. The fact that the species of the genus ''Clostridium'' did not form a monophyletic group has been shown in a number of studies in which small groups of ''Clostridium'' species had been compared as far back as 1981. The comparative study of Collins (1994) and subsequent studies can be used to conclude that more than half of the species currently assigned to this genus are in fact not closely related to the type species, ''C. butyricum'', and from a phylogenetic standpoint should not be included in a newly defined genus ''Clostridium''.<ref name="pmid7981107">{{cite journal |last1=Collins |first1=MD |last2=Lawson |first2=PA |last3=Willems |first3=A |last4=Cordoba |first4=JJ |last5=Fernandez-Garayzabal |first5=J |last6=Garcia |first6=P |last7=Cai |first7=J |last8=Hippe |first8=H |last9=Farrow |first9=JA |title=The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. |journal=International Journal of Systematic Bacteriology |date=October 1994 |volume=44 |issue=4 |pages=812–26 |doi=10.1099/00207713-44-4-812 |pmid=7981107 |doi-access=free}}</ref>

This extensive genetic diversity of the genus ''Clostridium'' had been shown using 23S rRNA:DNA hybridization studies back in 1975 by Johnson and Francis, but the 16S rRNA gene sequence approach revealed the actual phylogenetic relationships between the species of this genus and other genera.

The genus ''Clostridium'' currently comprises 152 validly described species in nomenclature.<ref>[http://www.bacterio.net www.bacterio.net]</ref> However, on the basis of 16S rRNA gene sequence analyses, only 73 of these fall within the radiation of the type species of the genus ''Clostridium''.

==Subdivisions== The polyphyletic family '''Clostridiaceae''' comprises the following: {|class="wikitable" |- ! colspan=1 |LPSN<ref name=LPSN>{{cite web | author=J.P. Euzéby | url=https://lpsn.dsmz.de/family/clostridiaceae | title=Clostridiaceae | access-date=2 March 2022 | publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN)}}</ref> & NCBI<ref name=NCBI>{{cite web |author = Sayers| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=31979&lvl=3&keep=1&srchmode=1&unlock |title=Clostridiaceae |access-date=2 March 2022 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database|display-authors=etal}}</ref> ! colspan=1 |16S rRNA based LTP_10_2024<ref name=LTP></ref><ref name=newick></ref><ref name=Notes></ref> & 120 marker proteins based GTDB 09-RS220<ref name="about"></ref><ref name="tree"></ref><ref name="taxon_history"></ref> |- style="vertical-align:top;" |style="width:1000px"| {{div col|colwidth=250px}} * ''Acidaminobacter'' Stams & Hansen 1985 * ''Agathobaculum'' Ahn et al. 2016 * ''Alkaliphilus'' Takai et al. 2001 * ''Anaeromicrobium'' Zhang et al. 2017 * ''Anaeromonas'' Zhang et al. 2022 * "''Anaerophilus''" Zhang et al. 2020 * ''Anaerosolibacter'' Hong et al. 2015 * ''Anaerovirgula'' Pikuta et al. 2006 * ''Anoxynatronum'' Garnova & Zhilina 2003 * "''Ca.'' Arthromitus" * ''Brassicibacter'' Fang et al. 2012 * ''Butyricicoccus'' Eeckhaut et al. 2008 * ''Caldanaerocella'' Diaz et al. 2004 * ''Caldisalinibacter'' Ben Hania et al. 2015 * ''Caloramator'' Collins et al. 1994 * ''Caloranaerobacter'' Wery et al. 2001 * ''Caminicella'' Alain et al. 2002 * ''Clostridiisalibacter'' Liebgott et al. 2008 * ''Clostridium'' Trécul 1865 ex Prazmowski 1880 * ''Crassaminicella'' Lakhal et al. 2015<ref>{{cite journal|last1=Lakhal|first1=R|last2=Pradel|first2=N|last3=Postec|first3=A|last4=Ollivier|first4=B|last5=Cayol|first5=JL|last6=Godfroy|first6=A|last7=Fardeau|first7=ML|last8=Galés|first8=G|title=Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.|journal=International Journal of Systematic and Evolutionary Microbiology|date=September 2015|volume=65|issue=9|pages=3097–102|doi=10.1099/ijsem.0.000386 |pmid=26296351 |url=https://archimer.ifremer.fr/doc/00296/40742/39992.pdf |doi-access=free}}</ref> * ''"Desnuesiella"'' Hadjadj et al. 2016 * ''Fervidicella'' Ogg & Patel 2010 * ''Fonticella'' Fraj et al. 2013 * ''Fusibacter'' Ravot et al. 1999 * ''Geosporobacter'' Klouche et al. 2007 * ''Haloimpatiens'' Wu et al. 2016 * ''Hathewaya'' Lawson & Rainey 2016 * "''Inediibacterium''" Alou et al. 2017 * "''Intestinibacillus''" Ricaboni et al. 2017 * ''Linmingia'' Ming, Nanqi & Yang 2002 * ''Lutispora'' Shiratori et al. 2008 * ''Maledivibacter'' Li et al. 2016 * ''Marinisporobacter'' Vandieken et al. 2017 * ''Natronincola'' Zhilina et al. 1999 * ''Oceanirhabdus'' Pi et al. 2013 * ''Oxobacter'' Collins et al. 1994 * ''Paramaledivibacter'' Li et al. 2016 * "''Ca.'' Petromonas" Christman et al. 2020 * ''Proteiniclasticum'' Zhang, Song & Dong 2010 * "''Ca.'' Pseudobutyricicoccus" Glendinning et al. 2020 * ''Salimesophilobacter'' Zhang et al. 2013 * "''Ca.'' Savagella" Thompson et al. 2012 * ''Serpentinicella'' Mei et al. 2016 * ''Sporosalibacterium'' Rezgui et al. 2011 * ''Thermobrachium'' ngle et al. 1996 * ''Thermohalobacter'' Cayol et al. 2000 * ''Thermotalea'' Ogg & Patel 2009 * ''Tindallia'' Kevbrin et al. 1999 * "''Ca.'' Ventrousia" Gilroy et al. 2021 * ''Wukongibacter'' Li et al. 2016 * ''Youngiibacter'' Lawson et al. 2014 {{div col end}} |style="width:750px"| {{div col|colwidth=200px}} * "Lutisporales" ** "Lutisporaceae" *** ''Lutispora'' * Clostridiales ** "Oxobacteraceae" *** ''Oxobacter'' ** Clostridiaceae *** ''Anaeromonas'' *** ''Clostridium'' *** "''Desnuesiella''" *** ''Haloimpatiens'' *** ''Hathewaya'' *** ''Oceanirhabdus'' *** ''Proteiniclasticum'' *** "''Ca.'' Savagella" *** ''Youngiibacter'' ** "Caloramatoraceae" *** ''Caloramator'' *** ''Fervidicella'' *** ''Fonticella'' *** ''Thermobrachium'' * Tissierellales ** "Clostridiisalibacteraceae" *** ''Clostridiisalibacter'' ** VENL01 *** ''Sporosalibacterium'' ** "Caldisalinibacteraceae" *** ''Caldisalinibacter'' ** Thermohalobacteraceae *** ''Brassicibacter'' *** ''Caloranaerobacter'' *** ''Thermohalobacter'' * "Peptostreptococcales" ** "Caminicellaceae" *** ''Caminicella'' *** ''Maledivibacter'' *** "''Ca.'' Petromonas" *** ''Paramaledivibacter'' *** ''Wukongibacter'' ** "Acidaminobacteraceae" *** ''Acidaminobacter'' *** ''Fusibacter'' ** "Thermotaleaceae" *** ''Anaeromicrobium'' *** "''Anaerophilus''" *** ''Anaerosolibacter'' *** ''Crassaminicella'' *** ''Geosporobacter'' *** "''Inediibacterium''" *** ''Marinisporobacter'' *** ''Salimesophilobacter'' *** ''Thermotalea'' ** "Tindalliaceae" *** ''Anoxynatronum'' *** ''Tindallia'' ** "Natronincolaceae" *** ''Alkaliphilus'' *** ''Anaerovirgula'' *** ''Natronincola'' *** ''Serpentinicella'' * "Oscillospirales" ** "Butyricicoccaceae" *** ''Agathobaculum'' *** ''Butyricicoccus'' *** "''Intestinibacillus''" *** "''Ca.'' Pseudobutyricicoccus" *** "''Ca.'' Ventrousia" {{div col end}} |}

==Phylogeny== The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)<ref name=LPSN></ref> and National Center for Biotechnology Information (NCBI)<ref name=NCBI></ref>

{| class="wikitable" |- ! colspan=1 | 16S rRNA based LTP_10_2024<ref name=LTP>{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}</ref><ref name=newick>{{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 name=Notes>{{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 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=Clostridiaceae |1={{clade |1=''Oxobacter'' |2={{clade |1={{clade |1=''Fervidicella'' |2={{clade |1=''Fonticella'' |2={{clade |1=''Clostridium cylindrosporum'' |2={{clade |1=''Caloramator'' species-group 2 |2={{clade |1=''Caloramator'' |2=''Thermobrachium'' }} }} }} }} }} |2={{clade |1=''Clostridium'' ~2 |2={{clade |1=''Clostridium'' ~3 |2={{clade |1=''Clostridium'' ~4 |2={{clade |1={{clade |1=''Clostridium cadaveris'' (Klein 1899) McClung & McCoy 1957 |2={{clade |1=''Youngiibacter'' |2=''Proteiniclasticum'' }} }} |2={{clade |1=''Clostridium'' ~5 |2={{clade |1=''Clostridium'' ~6 |2={{clade |1={{clade |1=''Inconstantimicrobium'' |2=''Clostridium'' ~7 }} |2={{clade |1={{clade |1=''Clostridium perfringens'' (Veillon & Zuber 1898) Holland 1920 ex Hauduroy et al. 1937 |2={{clade |1=''Clostridium tarantellae'' (Udey, Young & Sallman 1977) Lawson & Rainey 2016 |2=''Sarcina'' Goodsir 1842 }} }} |2=''Clostridium'' Trécul 1865 ex Prazmowski 1880 }} }} }} }} }} }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |1={{clade |1={{clade |label1=Oxobacteraceae |1=''Oxobacter'' Collins et al. 1994 }} |2={{clade |label1=Caloramatoraceae |1={{clade |1=''Clostridium cylindrosporum'' Barker & Beck 1942 ex Andreesen, Zindel & Durre 1985 |2={{clade |1={{clade |1=''Fervidicella'' Ogg & Patel 2010 |2=''Fonticella'' Fraj et al. 2013 }} |2={{clade |1=''Caloramator'' species-group 2 |2={{clade |1=''Thermobrachium'' Engle et al. 1996 |2=''Caloramator'' Collins et al. 1994 }} }} }} }} |label2=Clostridiaceae |2={{clade |1="''Ca.'' Dwaynesavagella" corrig. Gilroy et al. 2021 |2={{clade |1={{clade |1=''Youngiibacter'' Lawson et al. 2014 |2=''Proteiniclasticum'' Zhang, Song & Dong 2010 }} |2={{clade |1={{clade |1=''Clostridium'' AE & AU |2={{clade |1=''Clostridium'' K & AN |2={{clade |1=''Clostridium'' AT |2={{clade |1={{clade |1=''Clostridium'' I & S |2=''Clostridium'' B, C, F, G, AK, AM, AO, AS, AV & AW }} |2={{clade |1={{clade |1=''Haloimpatiens'' Wu et al. 2016 |2=''Clostridium'' H & AF }} |2={{clade |1={{clade |1={{clade |1=''Clostridium tepidiprofundi'' Slobodkina et al. 2008 |2=''Oceanirhabdus'' Pi et al. 2013 }} |2={{clade |1=''Clostridium collagenovorans'' Jain & Zeikus 1988 |2=''Hathewaya'' Lawson & Rainey 2016 }} }} |2=''Clostridium'' J & AD }} }} }} }} }} }} |2={{clade |1={{clade |1=''Clostridium'' X & Z |2={{clade |1="''Desnuesiella''" Hadjadj et al. 2016 |2=''Clostridium'' L }} }} |2={{clade |1=''Clostridium'' AA |2={{clade |1={{clade |1=''Inconstantimicrobium'' Wylensek et al. 2021 |2={{clade |1={{clade |1="''Vallorillus''" Heller 1922 |2=''Anaerobacter'' Duda et al. 1996 }} |2={{clade |1=''Clostridium cavendishii'' Bowman et al. 2010 |2=''Sarcina'' Goodsir 1842 }} }} }} |2=''Clostridium'' Trécul 1865 ex Prazmowski 1880 }} }} }} }} }} }} }} }} }} |}

== References == {{Reflist}}

Category:Clostridiaceae Category:Bacteria families