Bacillota

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Bacillota
Bacillus subtilis Gram.jpg
Bacillus subtilis , Gram-stained
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Kingdom: Bacillati
Phylum: Bacillota
Gibbons and Murray 2021 [1]
Classes and incertae sedis [2]
Synonyms
  • "Bacillaeota" Oren et al. 2015
  • "Bacillota" Whitman et al. 2018
  • "Desulfotomaculota" Watanabe et al. 2019
  • "Endobacteria" (Cavalier-Smith 1998) Cavalier-Smith 2020
  • "Endobacteria" Cavalier-Smith 1998
  • "Endospora" Margulis and Schwartz 1998
  • "Firmacutes" Gibbons and Murray 1978 (Approved Lists 1980)
  • "Firmicutes" (Gibbons & Murray 1978) Garrity & Holt 2001
  • "Posibacteria" Cavalier-Smith 2002

The Bacillota (synonym "Firmicutes") are a phylum of bacteria, most of which have Gram-positive cell wall structure. [3] They have round cells, called cocci (singular coccus), or rod-like forms (bacillus).[ citation needed ] 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 ] Many Bacillota produce endospores, which are resistant to desiccation and can survive extreme conditions.[ citation needed ] They are found in various environments, and the group includes some notable pathogens.[ citation needed ] Those in one family, the Heliobacteria, produce energy through anoxygenic photosynthesis.[ citation needed ] Bacillota play an important role in beer, wine, and cider spoilage.[ citation needed ]

Contents

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. [4] 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.[ citation needed ]

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 . [5] However, Bacillota as a whole is generally believed to be monophyletic, or paraphyletic with the exclusion of Mollicutes. [6]

Evolution

The Bacillota are thought by some [7] 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) [8] and the National Center for Biotechnology Information (NCBI). [9]

16S rRNA based LTP_01_2022 [10] [11] [12] 120 marker proteins based GTDB 10-RS226 [13] [14] [15]

♦ Paraphyletic Firmicutes

Bacillota_G
Bacillota_D
Bacillota s.s.

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

Genera

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

Bacilli, order Bacillales

Bacilli, order Lactobacillales

Clostridia

Erysipelotrichia

Clinical significance

Bacillota can make up between 11% to 95% of the human gut microbiome. [16] 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. [17] [18] [19] [20] In multiple studies a higher abundance of Bacillota has been found in obese individuals than in lean controls. [21] [22] 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. [22] The higher amount of Bacillota was also correlated with more adiposity and body weight within mice. [23] 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. [24]

The presence of Christensenella (Bacillota, in class Clostridia), isolated from human faeces, has been found to correlate with lower body mass index. [25]

Faecalibacterium prausnitzii (F. prausnitzii) is a member of the Bacillota phylum that may have anti-inflammatory effects in humans [26] . This species is associated with reduced low-grade inflammation in obesity. [27] Additionally, patients with inflammatory bowel disease tend to have lower levels of F. prausnitzii. [28] [29]

Pathogenicity

Several Bacillota species are common human pathogens. Examples include Bacillus anthracis, [30] Clostridioides difficile, [31] and Clostridium botulinum. [32] Others, such as Staphylococcus aureus and Enterococcus faecalis, are opportunistic pathogens that cause illness in a minority of their hosts. [33] [34] Antibiotic resistance is an increasingly common problem with these infections. Methicillin-resistant S. aureus (MRSA) is estimated to cause 100,000 deaths per year. [35]

See also

References

  1. ↑ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987. S2CID   239887308.
  2. ↑ Bacillota in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi: 10.1099/ijsem.0.004332 .
  3. ↑ "Firmicutes" at Dorland's Medical Dictionary
  4. ↑ Robitzki, Dan (4 January 2022). "Newly Renamed Prokaryote Phyla Cause Uproar". The Scientist Magazine. Archived from the original on 20 May 2022. Retrieved 23 May 2022.
  5. ↑ Wolf M, Müller T, Dandekar T, Pollack JD (May 2004). "Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data". Int. J. Syst. Evol. Microbiol. (Comparative Study). 54 (Pt 3): 871–5. Bibcode:2004IJSEM..54..871W. CiteSeerX   10.1.1.126.3863 . doi:10.1099/ijs.0.02868-0. PMID   15143038. Archived from the original on 2012-12-09.
  6. ↑ Ciccarelli, FD (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C. CiteSeerX   10.1.1.381.9514 . doi:10.1126/science.1123061. PMID   16513982. S2CID   1615592. Archived from the original on 2010-07-24. Retrieved 2020-12-02.
  7. ↑ 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. 6. Biology Direct 2011; 6:16: 16. doi: 10.1186/1745-6150-6-16 . PMC   3056875 . PMID   21356104.
  8. ↑ J. P. Euzéby. "Firmicutes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on January 27, 2013. Retrieved 2013-03-20.
  9. ↑ Sayers; et al. "Firmicutes". National Center for Biotechnology Information (NCBI) taxonomy database. Archived from the original on 28 July 2018. Retrieved 24 April 2019.
  10. ↑ "The LTP". Archived from the original on 14 June 2021. Retrieved 20 June 2022.
  11. ↑ "LTP_all tree in newick format". Archived from the original on 4 September 2022. Retrieved 20 June 2022.
  12. ↑ "LTP_01_2022 Release Notes" (PDF). Archived (PDF) from the original on 26 August 2023. Retrieved 20 June 2022.
  13. ↑ "GTDB release 10-RS226". Genome Taxonomy Database . Retrieved 1 May 2025.
  14. ↑ "bac120_r226.sp_label". Genome Taxonomy Database . Retrieved 1 May 2025.
  15. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 1 May 2025.
  16. ↑ 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. PMC   7285218 . PMID   32438689.
  17. ↑ Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006). "Microbial ecology: human gut microbes associated with obesity". Nature (Clinical Trial). 444 (7122): 1022–1023. Bibcode:2006Natur.444.1022L. doi:10.1038/4441022a. PMID   17183309. S2CID   205034045.
  18. ↑ Henig, Robin Marantz (2006-08-13). "Fat Factors". The New York Times Magazine. Archived from the original on 2015-05-08. Retrieved 2008-09-28.
  19. ↑ Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (August 2005). "Obesity alters gut microbial ecology". Proc. Natl. Acad. Sci. USA (Research Support). 102 (31): 11070–11075. Bibcode:2005PNAS..10211070L. doi: 10.1073/pnas.0504978102 . PMC   1176910 . PMID   16033867.
  20. ↑ Komaroff AL. The Microbiome and Risk for Obesity and Diabetes. JAMA. Published online December 22, 2016. doi:10.1001/jama.2016.20099
  21. ↑ Alejandro, Borrego-Ruiz; J., Borrego, Juan (September 2025). "The Gut Microbiome in Human Obesity: A Comprehensive Review". Biomedicines. 13 (9). doi: 10.3390/biomedicine (inactive 26 January 2026). ISSN   2227-9059. Archived from the original on 2026-01-07.{{cite journal}}: CS1 maint: DOI inactive as of January 2026 (link) CS1 maint: multiple names: authors list (link)
  22. 1 2 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.
  23. ↑ 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. PMC   3687783 . PMID   18407065.
  24. ↑ 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.
  25. ↑ Goodrich, Julia K.; Waters, Jillian L.; Poole, Angela C.; Sutter, Jessica L.; Koren, Omry; Blekhman, Ran; Beaumont, Michelle; Van Treuren, William; Knight, Rob; Bell, Jordana T.; Spector, Timothy D.; Clark, Andrew G.; Ley, Ruth E. (2014). "Human Genetics Shape the Gut Microbiome". Cell. 159 (4): 789–799. doi:10.1016/j.cell.2014.09.053. ISSN   0092-8674. PMC   4255478 . PMID   25417156. Open Access logo PLoS transparent.svg
  26. ↑ Miquel, Sylvie; Leclerc, Marion; Martin, Rebeca; Chain, Florian; Lenoir, Marion; Raguideau, Sébastien; Hudault, Sylvie; Bridonneau, Chantal; Northen, Trent; Bowen, Benjamin; Bermúdez-Humarán, Luis G.; Sokol, Harry; Thomas, Muriel; Langella, Philippe (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 . PMC   4453580 . PMID   25900655.
  27. ↑ 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 . PMC   4644874 . PMID   26600968.
  28. ↑ 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". Journal of Gastroenterology and Hepatology. 36 (2): 320–328. doi:10.1111/jgh.15222. ISSN   1440-1746. PMID   32815163.
  29. ↑ Quévrain, E.; Maubert, M. A.; Michon, C.; Chain, F.; Marquant, R.; Tailhades, J.; Miquel, S.; Carlier, L.; Bermúdez-Humarán, L. G.; Pigneur, B.; Lequin, O.; Kharrat, P.; Thomas, G.; Rainteau, D.; Aubry, C. (2016-03-01). "Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease". Gut. 65 (3): 415–425. doi:10.1136/gutjnl-2014-307649. ISSN   0017-5749. PMC   5136800 . PMID   26045134.
  30. ↑ CDC (2025-12-18). "About Anthrax". Anthrax. Retrieved 2026-01-25.
  31. ↑ 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. PMC   11324037 . PMID   38421181.
  32. ↑ Sobel, J. (2005-10-15). "Botulism". Clinical Infectious Diseases. 41 (8): 1167–1173. Bibcode:2005CliID..41.1167S. doi:10.1086/444507. ISSN   1058-4838.
  33. ↑ 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. Bibcode:2015CliMR..28..603T. doi:10.1128/CMR.00134-14. ISSN   1098-6618. PMC   4451395 . PMID   26016486.
  34. ↑ "Enterococcal Infections - Infectious Diseases". Merck Manual Professional Edition. Retrieved 2026-01-25.
  35. ↑ 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. PMC   8841637 . PMID   35065702.{{cite journal}}: |last= has generic name (help)
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