Biology:Bacillota

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The Bacillota (synonym "Firmicutes") are a phylum of bacteria, most of which have Gram-positive cell wall structure.[1] They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as Megasphaera, Pectinatus, Selenomonas, and Zymophilus from the class Negativicutes, have a porous pseudo-outer membrane that causes them to stain Gram-negative.[citation needed] Bacillota play an important role in beer, wine, and cider spoilage.{{Citation needed|date=April 2025

Taxonomy

The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature.[2] The name "Firmicutes" was derived from the Latin words for 'tough skin', referring to the thick cell wall typical of bacteria in this phylum. Scientists once classified the Firmicutes to include all Gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinomycetota. The group is typically divided into the Clostridia, which are anaerobic, and the Bacilli, which are obligate or optional aerobes.[citation needed] On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus.[3] However, Bacillota as a whole is generally believed to be monophyletic, or paraphyletic with the exclusion of Mollicutes.[4]

Evolution

The Bacillota are thought by some [5] to be the source of the archaea, by models where the archaea branched relatively late from bacteria, rather than forming an independently originating early lineage (domain of life) from the last universal common ancestor of cellular life (LUCA).[citation needed]

Phylogeny

The currently accepted taxonomy based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[6] and the National Center for Biotechnology Information (NCBI).[7]

16S rRNA based LTP_01_2022[8][9][10] 120 marker proteins based GTDB 10-RS226[11][12][13]
 
"Thermodesulfobiota"
"Thermodesulfobiia"

"Thermodesulfobiales" ♦

 
 
 
"Clostridiia"
 
 
 
 

Peptococcales

 
 

Proteinivoracales

 
 
 

Eubacteriales

 
 
 
 
 
 
 

Limnochordales

 
 

"Capillibacteriales"

 
 
 
 

Sulfobacillales

 
 
 

Symbiobacteriales

 
 

Thermaerobacterales

 
 
 
 
 
 
 

Dethiobacterales

 
 

Natranaerobiales

 
 
 
 

Gelria

 
 
 
 

Koleobacterales

 
 
 

Caldicellulosiruptorales

 
 

"Caldanaerobiales"

 
 
 
 
 
 

Thermacetogeniales

 
 

Carboxydothermales

 
 
 
 
 
 

Desulfovirgulaceae

 
 

Ammonificales

 
 
 
 

"Brockiales"

 
 
 

Dictyoglomerales

 
 

Thermosediminibacterales

 
 
 
 
 

Thermoanaerobacterales

 
 
 
 
 
 
 
 
 

Tissierellales 1

 
 
 

Tissierellales

 
 

Peptostreptococcales

 
 
 
 
 
 
 
 

Thermolithobacterales

 
 

Carboxydocellales

 
 
 
 
 
 
 

Desulfitibacterales

 
 

Desulfitisporales

 
 
 
 
 

Calderihabitantales

 
 

Neomoorellales

 
 
 
 

Zhaonellaceae

 
 

Syntrophomonadales

 
 
 
 
 
 
 
 
 

"Thermanaerosceptrales"

 
 

Thermincolales

 
 
 
 

"Heliobacteriales"

 
 

Desulfitobacteriales

 
 
 
 

Desulfotomaculales

 
 
 
 

Halanaerobiales

 
 
 

"Hydrogenisporales"

 
 

Selenomonadales

 
 
 
 
 
 
 
 
 

Gracilibacteraceae

 
 

Lutisporales

 
 
 

Clostridiales

 
 
 
 
 

Christensenellales

 
 
 

Aristaeellaceae

 
 
 

Mahellales

 
 

Caldicoprobacterales

 
 
 
 
 
 
 

Monoglobales

 
 
 

Acetivibrionales

 
 

"Oscillospirales"

 
 
 
 

Lachnospirales

 
 
 
 
 
 
{Clostridiota"} ♦
"Bacillia"
 
 
 

Hydrogenibacillus

 
 

Thermicanales

 
 
 
 

Alicyclobacillales

 
 

Paenibacillales

 
 
 
 
 

Thermoactinomycetales

 
 
 
 

Novibacillaceae

 
 
 

Caldalkalibacillales

 
 
 

Caldibacillaceae

 
 

Calditerricolales

 
 
 
 
 
 
 
 

Microaerobacter

 
 
 

Desulfuribacillales

 
 

Tepidibacillales

 
 
 
 
 

Oxalophagaceae

 
 
 

Aneurinibacillales

 
 

Brevibacillales

 
 
 
 
 
 

"Bacillus thermozeamaize"

 
 
 

Bacillales

 
 
 

Listeriaceae

 
 
 

Exiguobacteriales

 
 
 

Staphylococcales

 
 
 
 

Gemellaceae

 
 
 

Culicoidibacterales

 
 
 

Turicibacteraceae

 
 
 

Haloplasmatales

 
 
 

Acholeplasmatales

 
 
 

Erysipelotrichales

 
 

Mycoplasmatales

 
 
 
 
 
 
 
 

Lactobacillales

 
 
 
 
 
 
 
 
 
 
{Bacillota} ♦

♦ Paraphyletic Firmicutes

 
 
Bacillota_G
 

Limnochordia

 
 

"Hydrogenisporia" (UBA4882)

 
 
 
 
 
Bacillota_E
 

"Ca. Acetocimmeria" {UBA3575}

 
 
 

Thermaerobacteria

 
 
 

Symbiobacteriia

 
 
 

"Fermentithermobacillia"

 
 

Sulfobacillia

 
 
 
 
 
 
 
 
Bacillota_D
 

"Proteinivoracia"

 
 
 

Dethiobacteria

 
 

Natranaerobiia

 
 
 
Bacillota s.s.

"Bacillia" [incl. Alicyclobacillia; Desulfuribacillia; Culicoidibacteria; Erysipelotrichia; "Izemoplasmatia"; Mollicutes]

 
 
 
 
"Selenobacteria"

"Selenomonadia" [Negativicutes]

 
"Desulfotomaculota"
 

Peptococcia

 
 
 
 
 

"Thermacetogeniia" [DSM-12270]

 
 

Syntrophomonadia

 
 
 
 

"Dehalobacteriia"

 
 
 
 

Desulfitibacterales {DSM-16504}

 
 
 

Calderihabitantales {KKC1}

 
 

"Metallumcola" {JADQBR01}

 
 
 
 
 

Zhaonellaceae {DULZ01}

 
 

Neomoorellales {"Moorellia"}

 
 
 
 
 
 
 

Desulfitobacteriia

 
 
 
 

"Carboxydocellia"

 
 

Thermincolia

 
 
 
 

"Carboxydothermia"

 
 

Desulfotomaculia

 
 
 
 
 
 
 
 
"Halanaerobiota"

"Halanaerobiia"

 
"Clostridiota"
 

Thermosediminibacteria

 
 
 

"Thermoanaerobacteria"

 
 

"Clostridiia" s.s. [incl. Tissierellia]

 
 
 
 
 
 
 
 

Genera

More than 274 genera were considered as of 2016 to be within the Bacillota phylum, notable genera of Bacillota include:

Bacilli, order Bacillales

Bacilli, order Lactobacillales

Clostridia

Erysipelotrichia

Clinical significance

See also: Biology:Infectobesity

Bacillota can make up between 11% to 95% of the human gut microbiome.[14] The phylum Bacillota as part of the gut microbiota has been shown to be involved in energy resorption, and potentially related to the development of diabetes and obesity.[15][16][17][18] In multiple studies a higher abundance of Bacillota has been found in obese individuals than in lean controls.[19][20] A higher relative abundance of Bacillota was seen in mice fed a western diet (high fat/high sugar) than in mice fed a standard low fat/ high polysaccharide diet.[20] The higher amount of Bacillota was also correlated with more adiposity and body weight within mice.[21] Specifically, within obese mice, the class Mollicutes (within the Bacillota phylum) was the most common. When the microbiota of obese mice with this higher Bacillota abundance was transplanted into the guts of germ-free mice, the germ-free mice gained more fat than those transplanted with the microbiota of lean mice with lower Bacillota abundance.[22]

The presence of Christensenella (Bacillota, in class Clostridia), isolated from human faeces, has been found to correlate with lower body mass index.[23]

Faecalibacterium prausnitzii (F. prausnitzii) is a member of the Bacillota phylum that may have anti-inflammatory effects in humans[24]. This species is associated with reduced low-grade inflammation in obesity.[25] Additionally, patients with inflammatory bowel disease tend to have lower levels of F. prausnitzii.[26][27]

Pathogenicity

Several Bacillota species are common human pathogens. Examples include Bacillus anthracis,[28] Clostridioides difficile,[29] and Clostridium botulinum.[30] Others, such as Staphylococcus aureus and Enterococcus faecalis, are opportunistic pathogens that cause illness in a minority of their hosts.[31][32] Antibiotic resistance is an increasingly common problem with these infections. Methicillin-resistant S. aureus (MRSA) is estimated to cause 100,000 deaths per year.[33]

See also

References

  1. ↑ "Firmicutes" at Dorland's Medical Dictionary
  2. ↑ Robitzki, Dan (4 January 2022). "Newly Renamed Prokaryote Phyla Cause Uproar" (in en). The Scientist Magazine. https://www.the-scientist.com/news-opinion/newly-renamed-prokaryote-phyla-cause-uproar-69578. 
  3. ↑ "Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data". Int. J. Syst. Evol. Microbiol. 54 (Pt 3): 871–5. May 2004. doi:10.1099/ijs.0.02868-0. PMID 15143038. Bibcode: 2004IJSEM..54..871W. http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=15143038. 
  4. ↑ Ciccarelli, FD (2006). "Toward automatic reconstruction of a highly resolved tree of life.". Science 311 (5765): 1283–1287. doi:10.1126/science.1123061. PMID 16513982. Bibcode: 2006Sci...311.1283C. http://www.sciencemag.org/cgi/content/full/311/5765/1283. Retrieved 2020-12-02. 
  5. ↑ Ruben E Valas, Philip E Bourne (2011). "The origin of a derived superkingdom: how a Gram-positive bacterium crossed the desert to become an archaeon". Biology Direct (Biology Direct 2011; 6:16) 6: 16. doi:10.1186/1745-6150-6-16. PMID 21356104. 
  6. ↑ J. P. Euzéby. "Firmicutes". List of Prokaryotic names with Standing in Nomenclature (LPSN). http://www.bacterio.cict.fr/classifphyla.html#Firmicutes. 
  7. ↑ Sayers. "Firmicutes". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1239&lvl=3&lin. 
  8. ↑ "The LTP". https://imedea.uib-csic.es/mmg/ltp/#LTP. 
  9. ↑ "LTP_all tree in newick format". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/Tree_LTP_all_01_2022.ntree. 
  10. ↑ "LTP_01_2022 Release Notes". https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_01_2022_release_notes.pdf. 
  11. ↑ "GTDB release 10-RS226". https://gtdb.ecogenomic.org/about#4%7C. 
  12. ↑ "bac120_r226.sp_label". https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/bac120_r226.sp_labels.tree. 
  13. ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/. 
  14. ↑ Magne, Fabien; Gotteland, Martin; Gauthier, Lea; Zazueta, Alejandra; Pesoa, Susana; Navarrete, Paola; Balamurugan, Ramadass (2020-05-19). "The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?". Nutrients 12 (5): 1474. doi:10.3390/nu12051474. ISSN 2072-6643. PMID 32438689. 
  15. ↑ "Microbial ecology: human gut microbes associated with obesity". Nature 444 (7122): 1022–1023. 2006. doi:10.1038/4441022a. PMID 17183309. Bibcode: 2006Natur.444.1022L. 
  16. ↑ Henig, Robin Marantz (2006-08-13). "Fat Factors". The New York Times Magazine. https://www.nytimes.com/2006/08/13/magazine/13obesity.html?pagewanted=3&ei=5070&en=0c39c5880e4d7067&ex=1166850000. 
  17. ↑ "Obesity alters gut microbial ecology". Proc. Natl. Acad. Sci. USA 102 (31): 11070–11075. August 2005. doi:10.1073/pnas.0504978102. PMID 16033867. Bibcode: 2005PNAS..10211070L. 
  18. ↑ Komaroff AL. The Microbiome and Risk for Obesity and Diabetes. JAMA. Published online December 22, 2016. doi:10.1001/jama.2016.20099
  19. ↑ Alejandro, Borrego-Ruiz; J., Borrego, Juan (September 2025). "The Gut Microbiome in Human Obesity: A Comprehensive Review" (in en). Biomedicines 13 (9). doi:10.3390/biomedicine. ISSN 2227-9059. https://www.mdpi.com/2227-9059/13/9/2173. 
  20. ↑ 20.0 20.1 Million, M.; Lagier, J.-C; Yahav, D.; Paul, M. (April 2013). "Gut bacterial microbiota and obesity". Clinical Microbiology and Infection 19 (4): 305–313. doi:10.1111/1469-0691.12172. PMID 23452229. 
  21. ↑ Turnbaugh, Peter J. (17 April 2008). "Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome". Cell Host & Microbe 3 (4): 213–223. doi:10.1016/j.chom.2008.02.015. PMID 18407065. 
  22. ↑ Million, M. (April 2013). "Gut bacterial microbiota and obesity". Cell Microbiology and Infection 19 (4): 305–313. doi:10.1111/1469-0691.12172. PMID 23452229. 
  23. ↑ Goodrich, Julia K.; Waters, Jillian L.; Poole, Angela C.; Sutter, Jessica L.; Koren, Omry; Blekhman, Ran; Beaumont, Michelle; Van Treuren, William et al. (2014). "Human Genetics Shape the Gut Microbiome". Cell 159 (4): 789–799. doi:10.1016/j.cell.2014.09.053. ISSN 0092-8674. PMID 25417156. open access
  24. ↑ Miquel, Sylvie; Leclerc, Marion; Martin, Rebeca; Chain, Florian; Lenoir, Marion; Raguideau, Sébastien; Hudault, Sylvie; Bridonneau, Chantal et al. (2015-04-21). "Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii". mBio 6 (2): 10.1128/mbio.00300–15. doi:10.1128/mbio.00300-15. PMID 25900655. 
  25. ↑ Chakraborti, Chandra Kanti (15 November 2015). "New-found link between microbiota and obesity". World Journal of Gastrointestinal Pathophysiology 6 (4): 110–119. doi:10.4291/wjgp.v6.i4.110. PMID 26600968. 
  26. ↑ Zhao, Hailan; Xu, Haoming; Chen, Shuzhen; He, Jie; Zhou, Youlian; Nie, Yuqiang (2021). "Systematic review and meta-analysis of the role of Faecalibacterium prausnitzii alteration in inflammatory bowel disease" (in en). Journal of Gastroenterology and Hepatology 36 (2): 320–328. doi:10.1111/jgh.15222. ISSN 1440-1746. PMID 32815163. https://onlinelibrary.wiley.com/doi/abs/10.1111/jgh.15222. 
  27. ↑ Quévrain, E.; Maubert, M. A.; Michon, C.; Chain, F.; Marquant, R.; Tailhades, J.; Miquel, S.; Carlier, L. et al. (2016-03-01). "Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease" (in en). Gut 65 (3): 415–425. doi:10.1136/gutjnl-2014-307649. ISSN 0017-5749. PMID 26045134. PMC 5136800. https://gut.bmj.com/content/65/3/415. 
  28. ↑ CDC (2025-12-18). "About Anthrax" (in en-us). https://www.cdc.gov/anthrax/about/index.html. 
  29. ↑ Di Bella, Stefano; Sanson, Gianfranco; Monticelli, Jacopo; Zerbato, Verena; Principe, Luigi; Giuffrè, Mauro; Pipitone, Giuseppe; Luzzati, Roberto (2024-06-13). "Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options". Clinical Microbiology Reviews 37 (2): e0013523. doi:10.1128/cmr.00135-23. ISSN 1098-6618. PMID 38421181. 
  30. ↑ Sobel, J. (2005-10-15). "Botulism" (in en). Clinical Infectious Diseases 41 (8): 1167–1173. doi:10.1086/444507. ISSN 1058-4838. Bibcode: 2005CliID..41.1167S. https://academic.oup.com/cid/article-lookup/doi/10.1086/444507. 
  31. ↑ Tong, Steven Y. C.; Davis, Joshua S.; Eichenberger, Emily; Holland, Thomas L.; Fowler, Vance G. (July 2015). "Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management". Clinical Microbiology Reviews 28 (3): 603–661. doi:10.1128/CMR.00134-14. ISSN 1098-6618. PMID 26016486. Bibcode: 2015CliMR..28..603T. 
  32. ↑ "Enterococcal Infections - Infectious Diseases" (in en-US). https://www.merckmanuals.com/professional/infectious-diseases/gram-positive-cocci/enterococcal-infections. 
  33. ↑ Antimicrobial Resistance Collaborators (2022-02-12). "Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis". Lancet (London, England) 399 (10325): 629–655. doi:10.1016/S0140-6736(21)02724-0. ISSN 1474-547X. PMID 35065702. 

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