Bacillota

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. 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. On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus. However, Bacillota as a whole is generally believed to be monophyletic, or paraphyletic with the exclusion of Mollicutes.

Evolution

The Bacillota are thought by some 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).

Phylogeny

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

Genera

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

Bacilli, order Bacillales

• Bacillus
• Listeria
• Staphylococcus Bacilli, order Lactobacillales
• Enterococcus
• Lactobacillus
• Leuconostoc
• Streptococcus Clostridia
• Clostridioides
• Clostridium
• Selenomonas Erysipelotrichia
• Erysipelothrix

Health implications

Clinical significance

Bacillota can make up between 11% to 95% of the human gut microbiome. 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. In multiple studies a higher abundance of Bacillota has been found in obese individuals than in lean controls. 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. The higher amount of Bacillota was also correlated with more adiposity and body weight within mice. 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.

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

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

Pathogenicity

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

References

References

1. (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol.
2. {{lpsn. phylum/bacillota. Bacillota
3. {{DorlandsDict. three/000040400. Firmicutes
4. (4 January 2022). "Newly Renamed Prokaryote Phyla Cause Uproar". The Scientist Magazine.
5. (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..
6. Ciccarelli, FD. (2006). "Toward automatic reconstruction of a highly resolved tree of life.". Science.
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 2011; 6:16.
8. J. P. Euzéby. "Firmicutes". [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN).
9. Sayers. "Firmicutes". [[National Center for Biotechnology Information]] (NCBI) taxonomy database.
10. "The LTP".
11. "LTP_all tree in newick format".
12. "LTP_01_2022 Release Notes".
13. "GTDB release 10-RS226".
14. "bac120_r226.sp_label".
15. "Taxon History".
16. (2020-05-19). "The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?". Nutrients.
17. (2006). "Microbial ecology: human gut microbes associated with obesity". Nature.
18. Henig, Robin Marantz. (2006-08-13). "Fat Factors". [[The New York Times]] Magazine.
19. (August 2005). "Obesity alters gut microbial ecology". Proc. Natl. Acad. Sci. USA.
20. Komaroff AL. The Microbiome and Risk for Obesity and Diabetes. JAMA. Published online December 22, 2016. doi:10.1001/jama.2016.20099
21. (September 2025). "The Gut Microbiome in Human Obesity: A Comprehensive Review". Biomedicines.
22. (April 2013). "Gut bacterial microbiota and obesity". Clinical Microbiology and Infection.
23. (17 April 2008). "Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome". Cell Host & Microbe.
24. (April 2013). "Gut bacterial microbiota and obesity". Cell Microbiology and Infection.
25. (2014). "Human Genetics Shape the Gut Microbiome". Cell.
26. (2015-04-21). "Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii". mBio.
27. (15 November 2015). "New-found link between microbiota and obesity". World Journal of Gastrointestinal Pathophysiology.
28. (2021). "Systematic review and meta-analysis of the role of Faecalibacterium prausnitzii alteration in inflammatory bowel disease". Journal of Gastroenterology and Hepatology.
29. (2016-03-01). "Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease". Gut.
30. CDC. (2025-12-18). "About Anthrax".
31. (2024-06-13). "Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options". Clinical Microbiology Reviews.
32. Sobel, J.. (2005-10-15). "Botulism". Clinical Infectious Diseases.
33. (July 2015). "Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management". Clinical Microbiology Reviews.
34. "Enterococcal Infections - Infectious Diseases".
35. Antimicrobial Resistance Collaborators. (2022-02-12). "Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis". Lancet (London, England).