Bacillota

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Bacillota
Bacillus subtilis Gram.jpg
Bacillus subtilis , Gram-stained
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Clade: Terrabacteria
Phylum: Bacillota
Gibbons and Murray 2021 [1]
Classes
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" corrig. Gibbons and Murray 1978 (Approved Lists 1980)
  • "Posibacteria" Cavalier-Smith 2002

Bacillota (synonym Firmicutes) is a phylum of bacteria, most of which have gram-positive cell wall structure. [2] 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. [3]

Contents

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. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Firmicutes, such as Megasphaera , Pectinatus , Selenomonas and Zymophilus , have a porous pseudo-outer membrane that causes them to stain gram-negative.

Many Bacillota (Firmicutes) produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through anoxygenic photosynthesis. Bacillota play an important role in beer, wine, and cider spoilage.

Classes

The group is typically divided into the Clostridia, which are anaerobic, and the Bacilli, which are obligate or facultative aerobes.[ citation needed ]

On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus . [4] However, Bacillota as a whole is generally believed to be monophyletic, or paraphyletic with the exclusion of Mollicutes. [5]

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]

The Firmicutes are thought by some [8] to be the source of the archaea, by models there 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 ]

16S rRNA based LTP_01_2022 [9] [10] [11] GTDB 08-RS214 by Genome Taxonomy Database [12] [13] [14]

Archaea

Bacteria

"Aquificida"

"Synergistetes"

Atribacterota

Firmicutes 3  

"FCB group"

♦ Paraphyletic Firmicutes

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 make up ~30% of the mouse and human gut microbiome. [15] [ failed verification ] 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. [16] [17] [18] [19] Within the gut of healthy human adults, the most abundant bacterium: Faecalibacterium prausnitzii (F. prausnitzii), which makes up 5% of the total gut microbiome, is a member of the Bacillota phylum. This species is directly associated with reduced low-grade inflammation in obesity. [20] F. prausnitzii has been found in higher levels within the guts of obese children than in non-obese children.

In multiple studies a higher abundance of Bacillota has been found in obese individuals than in lean controls. A higher level of Lactobacillus (of the Bacillota phylum) has been found in obese patients and in one study, obese patients put on weight loss diets showed a reduced amount of Bacillota within their guts. [21]

Diet changes in mice have also been shown to promote changes in Bacillota abundance. 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 linked to more adiposity and body weight within mice. [22] 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 a significant amount of fat as compared to those transplanted with the microbiota of lean mice with lower Bacillota abundance. [23]

The presence of Christensenella (Bacillota, in class Clostridia), isolated from human faeces, has been found to correlate with lower body mass index. [24]

See also

Related Research Articles

<span class="mw-page-title-main">Pseudomonadota</span> Phylum of Gram-negative bacteria

Pseudomonadota is a major phylum of Gram-negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non-parasitic) genera. The phylum comprises six classes Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.

<span class="mw-page-title-main">Bacteroidota</span> Phylum of Gram-negative bacteria

The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.

Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma. Colonies show the typical "fried-egg" appearance.

<span class="mw-page-title-main">Clostridia</span> Class of bacteria

The Clostridia are a highly polyphyletic class of Bacillota, including Clostridium and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. Species of the class Clostridia are often but not always Gram-positive and have the ability to form spores. Studies show they are not a monophyletic group, and their relationships are not entirely certain. Currently, most are placed in a single order called Clostridiales, but this is not a natural group and is likely to be redefined in the future.

<span class="mw-page-title-main">Gut microbiota</span> Community of microorganisms in the gut

Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.

Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.

<i>Bacteroides</i> Genus of bacteria

Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.

Rikenellaceae is a family of Gram-negative bacteria described by Noel R. Krieg in 2015. It contains nine genera, five of which are validly published by the International Code of Nomenclature of Prokaryotes. Bacteria with 16S ribosomal RNA highly similar to the Rikenella genus, as compared to the larger taxonomic order Bacteroidales, are classified in this family.

Jeffrey Ivan Gordon is a biologist and the Dr. Robert J. Glaser Distinguished University Professor and Director of the Center for Genome Sciences and Systems Biology at Washington University in St. Louis. He is internationally known for his research on gastrointestinal development and how gut microbial communities affect normal intestinal function, shape various aspects of human physiology including our nutritional status, and affect predisposition to diseases. He is a member of the National Academy of Sciences, the American Academy of Arts and Sciences, the Institute of Medicine of the National Academies, and the American Philosophical Society.

<span class="mw-page-title-main">Microbiota</span> Community of microorganisms

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

The Veillonellaceae are a family of the Clostridia, formerly known as Acidaminococcaceae. Bacteria in this family are grouped together mainly based on genetic studies, which place them among the Bacillota. Supporting this placement, several species are capable of forming endospores. However, they differ from most other Bacillota in having Gram-negative stains. The cell wall composition is peculiar.

Prevotella is a genus of Gram-negative bacteria.

The Negativicutes are a class of bacteria in the phylum Bacillota, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Bacillota. Although several neighbouring Clostridia species also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Pseudomonadota. Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

<span class="mw-page-title-main">Erysipelotrichia</span> Class of bacteria

The Erysipelotrichia are a class of bacteria of the phylum Bacillota. Species of this class are known to be common in the gut microbiome, as they have been isolated from swine manure and increase in composition of the mouse gut microbiome for mice switched to diets high in fat.

Parasutterella is a genus of Gram-negative, circular/rod-shaped, obligate anaerobic, non-spore forming bacteria from the Pseudomonadota phylum, Betaproteobacteria class and the family Sutterellaceae. Previously, this genus was considered "unculturable," meaning that it could not be characterized through conventional laboratory techniques, such as grow in culture due its unique requirements of anaerobic environment. The genus was initially discovered through 16S rRNA sequencing and bioinformatics analysis. By analyzing the sequence similarity, Parasutterella was determined to be related most closely to the genus Sutterella and previously classified in the family Alcaligenaceae.

Roseburia is a genus of butyrate-producing, Gram-positive anaerobic bacteria that inhabit the human colon. Named in honor of Theodor Rosebury, they are members of the phylum Bacillota.

Christensenella is a genus of non-spore-forming, anaerobic, and nonmotile bacteria from the family Christensenellaceae. They are also part of the order Clostridiales, the class Clostridia and the phylum Firmicutes. Phylogenetic analyzes of 16S rRNA gene sequences are used to describe this family. Due to the recent discovery of the Christensenellaceae family, it was not given importance until a few years ago. This is why very little is known about its ecology and how it may be associated with host factors and other microbiota. However, recent studies establish that members of this family, with exceptions, may be associated with a healthy phenotype for humans. The species C. minuta has been published and validated, and C. timonensis and C. massiliensis have been proposed as novel species of the genus Christensenella, all isolated from human feces.

<i>Bacteroides thetaiotaomicron</i> Species of bacterium

Bacteroides thetaiotaomicron is a gram-negative, rod shaped obligate anaerobic bacterium that is a prominent member of the normal gut microbiome in the distal intestines. Its proteome, consisting of 4,779 members, includes a system for obtaining and breaking down dietary polysaccharides that would otherwise be difficult to digest. B. thetaiotaomicron is also an opportunistic pathogen, meaning it may become virulent in immunocompromised individuals. It is often used in research as a model organism for functional studies of the human microbiota.

<span class="mw-page-title-main">Cetacean microbiome</span> Group of communities of microorganisms that reside within whales

The cetacean microbiome is the group of communities of microorganisms that reside within whales.

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. "Firmicutes" at Dorland's Medical Dictionary
  3. 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.
  4. 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. CiteSeerX   10.1.1.126.3863 . doi:10.1099/ijs.0.02868-0. PMID   15143038. Archived from the original on 2012-12-09.
  5. 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.
  6. 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.
  7. Sayers; et al. "Firmicutes". National Center for Biotechnology Information (NCBI) taxonomy database. Archived from the original on 28 July 2018. Retrieved 24 April 2019.
  8. 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.
  9. "The LTP". Archived from the original on 14 June 2021. Retrieved 20 June 2022.
  10. "LTP_all tree in newick format". Archived from the original on 4 September 2022. Retrieved 20 June 2022.
  11. "LTP_01_2022 Release Notes" (PDF). Archived (PDF) from the original on 26 August 2023. Retrieved 20 June 2022.
  12. "GTDB release 08-RS214". Genome Taxonomy Database . Archived from the original on 26 October 2022. Retrieved 10 May 2023.
  13. "bac120_r214.sp_label". Genome Taxonomy Database . Archived from the original on 16 May 2023. Retrieved 10 May 2023.
  14. "Taxon History". Genome Taxonomy Database . Archived from the original on 1 November 2021. Retrieved 10 May 2023.
  15. Ley RE, Peterson DA, Gordon JI (2006). "Ecological and evolutionary forces shaping microbial diversity in the human intestine". Cell (Review). 124 (4): 837–848. doi: 10.1016/j.cell.2006.02.017 . PMID   16497592. S2CID   17203181.
  16. 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.
  17. 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.
  18. 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.
  19. Komaroff AL. The Microbiome and Risk for Obesity and Diabetes. JAMA. Published online December 22, 2016. doi:10.1001/jama.2016.20099
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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