Firmicutes

The Firmicutes (Latin: firmus, strong, and cutis, skin, referring to the cell wall) are a phylum of bacteria, most of which have gram-positive cell wall structure.[3] A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer membrane that causes them to stain gram-negative. 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 Actinobacteria. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus).

Many 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. Firmicutes play an important role in beer, wine, and cider spoilage.

Firmicutes
Bacillus subtilis Gram
Bacillus subtilis, Gram-stained
Scientific classification
Domain: Bacteria
(unranked): Terrabacteria
Phylum: Firmicutes
Gibbons and Murray 1978,[1] Murray, 1984[2]
Classes
Synonyms
  • Endospora
  • Endobacteria Cavalier-Smith 2002
  • "Endobacteria" Cavalier-Smith 1998
  • "Mollifirmicutes"
  • Mollicutes Edward & Freundt 1967
  • Mollicutaeota Oren et al. 2015
  • "Halanaerobiaeota"
  • Tenericutes Murray 1984

Classes

The group is typically divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes, and the Mollicutes, which are parasites.

On phylogenetic trees, the first two groups show up as paraphyletic or polyphyletic, as do their main genera, Clostridium and Bacillus.[4]

Phylogeny

The phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project[5], with the currently accepted taxonomy based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[6], National Center for Biotechnology Information (NCBI)[7] and some non validated clade names from Genome Taxonomic Database.[8]

Firmicutes classification
"Thermaerobacteria" ♥

Thermaerobacter {"Thermaerobacterales" ♥: "Thermaerobacteraceae" ♥}  

"Thermoanaerobacteria" ♥

Caldicellulosiruptor {"Caldicellulosiruptorales" ♥: "Caldicellulosiruptoraceae" ♥}

"Thermovenabulales" ♥

Dictyoglomus {Dictyoglomaceae}  

Tepidanaerobacter {"Tepidanaerobacteraceae" ♥}

"Thermovenabulaceae" ♥

"Ammonificaceae" ♥ {"Ammonifexales" ♥}

Thermoanaerobacteraceae {Thermoanaerobacterales}

"Moorellaceae" ♥ {"Moorellales" ♥}

"Thermacetogeniaceae" ♥ {"Thermacetogeniales" ♥}

Carboxydothermus {"Carboxydothermales" ♥: "Carboxydothermaceae" ♥}

"Symbiobacteriia" ♥

Gelria  

Symbiobacterium {"Symbiobacteriales" ♥: Symbiobacteriaceae}

Sulfobacillus {"Sulfobacillales" ♥: "Sulfobacillaceae" ♥}

Clostridia s.s.

Bacillia

Unassigned Clostridia s.s.

  • Desulfuribacillus Sorokin et al. 2014 emend. Abin & Hollibaugh 2017 {"Desulfuribacillia" ♥: "Desulfuribacillales" ♥: "Desulfuribacillaceae" ♥}
  • Limnochorda pilosa Watanabe, Kojima & Fukui 2015 {Limnochordia Watanabe, Kojima & Fukui 2015: Limnochordales Watanabe, Kojima & Fukui 2015: Limnochordaceae Watanabe, Kojima & Fukui 2015}

Notes:
♥ Clade names not lodged at National Center for Biotechnology Information (NCBI) or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)

The family Synergistaceae (Clostridiales Family XV Incertae Sedis) and Thermodesulfobiaceae have been removed from Firmicutes based on the fact, they do not form a monophyletic clade with it.

Genera

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

Bacilli, order Bacillales

Bacilli, order Lactobacillales

Clostridia

Erysipelotrichia

Health implications

Firmicutes make up the largest portion of the mouse and human gut microbiome.[9] The division Firmicutes as part of the gut flora has been shown to be involved in energy resorption, and potentially related to the development of diabetes and obesity.[10][11][12][13]

Firmicutes spp. are part of a normal, healthy placental microbiome.[14][15]

Presence of Christensenella (Firmicutes, in class Clostridia), isolated from human faeces, has been found to correlate with lower body mass index.[16]

Laboratory detection

The presence of Firmicutes can be reliably detected with polymerase chain reaction (PCR) techniques.[17]

References

  1. ^ Gibbons, N. E. & Murray, R. G. E. 1978. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 28:1–6, (PDF)
  2. ^ Murray, R. G. E. (1984). The higher taxa, or, a place for everything...?. In: N. R. Krieg & J. G. Holt (ed.) Bergey's Manual of Systematic Bacteriology, vol. 1, The Williams & Wilkins Co., Baltimore, p. 31–34.
  3. ^ "Firmicutes" at Dorland's Medical Dictionary
  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. doi:10.1099/ijs.0.02868-0. PMID 15143038.
  5. ^ "16S rRNA-based LTP release 132 (full tree)". All-Species Living Tree Project. Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.
  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. Retrieved 2013-03-20.
  8. ^ "GTDB taxonomy". Genome Taxonomic Database. Retrieved 2018-07-20.
  9. ^ Ley RE, Peterson DA, Gordon JI (2006). "Ecological and evolutionary forces shaping microbial diversity in the human intestine". Cell (Review). 124 (4): 837–48. doi:10.1016/j.cell.2006.02.017. PMID 16497592.
  10. ^ Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006). "Microbial ecology: human gut microbes associated with obesity". Nature (Clinical Trial). 444 (7122): 1022–3. doi:10.1038/4441022a. PMID 17183309.
  11. ^ Henig, Robin Marantz (2006-08-13). "Fat Factors". New York Times Magazine. Retrieved 2008-09-28.
  12. ^ Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (August 2005). "Obesity alters gut microbial ecology". Proc. Natl. Acad. Sci. U.S.A. (Research Support). 102 (31): 11070–5. doi:10.1073/pnas.0504978102. PMC 1176910. PMID 16033867. Retrieved 2008-09-28.
  13. ^ Komaroff AL. The Microbiome and Risk for Obesity and Diabetes. JAMA. Published online December 22, 2016. doi:10.1001/jama.2016.20099
  14. ^ Mor, Gil; Kwon, Ja-Young (2015). "Trophoblast–microbiome interaction: a new paradigm on immune regulation". American Journal of Obstetrics and Gynecology. 213 (4): S131–S137. doi:10.1016/j.ajog.2015.06.039. ISSN 0002-9378. PMID 26428492.
  15. ^ Todar, K. "Pathogenic E. coli". Online Textbook of Bacteriology. University of Wisconsin–Madison Department of Bacteriology. Retrieved 2007-11-30.
  16. ^ 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.open access publication – free to read
  17. ^ Haakensen M, Dobson CM, Deneer H, Ziola B (July 2008). "Real-time PCR detection of bacteria belonging to the Firmicutes Phylum". Int. J. Food Microbiol. (Research Support). 125 (3): 236–41. doi:10.1016/j.ijfoodmicro.2008.04.002. PMID 18501458. Retrieved 2008-09-28.

External links

'The All-Species Living Tree' Project

'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. At one stage, 23S sequences were also collected, but this has since stopped.Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.

-bacter

The suffix -bacter is in microbiology for many genera and is intended to mean "bacteria".

Bacillales

The Bacillales are an order of Gram-positive bacteria, placed within the Firmicutes. Representative genera include Bacillus, Listeria and Staphylococcus.

Bacillus

Bacillus (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum Firmicutes, with 266 named species. The term is also used to describe the shape (rod) of certain bacteria; and the plural Bacilli is the name of the class of bacteria to which this genus belongs. Bacillus species can be either obligate aerobes: oxygen dependent; or facultative anaerobes: having the ability to be anaerobic in the absence of oxygen. Cultured Bacillus species test positive for the enzyme catalase if oxygen has been used or is present.Bacillus can reduce themselves to oval endospores and can remain in this dormant state for years. Endospore formation is usually triggered by a lack of nutrients: the bacterium divides within its cell wall, and one side then engulfs the other. They are not true spores (i.e., not an offspring). Endospore formation originally defined the genus, but not all such species are closely related, and many species have been moved to other genera of the Firmicutes.Ubiquitous in nature, Bacillus includes both free-living (nonparasitic) species, and two parasitic pathogenic species. These two Bacillus species are medically significant: B. anthracis causes anthrax; and B. cereus causes food poisoning.

Many species of Bacillus can produce copious amounts of enzymes which are used in various industries, such as the production of alpha amylase used in starch hydrolysis, and the protease subtilisin used in detergents. B. subtilis is a valuable model for bacterial research.

Bacterial phyla

The bacterial phyla are the major lineages, known as phyla or divisions, of the domain Bacteria.

In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species (binary nomenclature), which is a lower level of a hierarchy of ranks. Currently, the most accepted mega-classification system is under the three-domain system, which is based on molecular phylogeny. In that system, bacteria are members of the domain Bacteria and "phylum" is the rank below domain, since the rank "kingdom" is disused at present in bacterial taxonomy. When bacterial nomenclature was controlled under the Botanical Code, the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria) is controlled under the Bacteriological Code, the term phylum is preferred.

In this classification scheme, Bacteria is (unofficially) subdivided into 30 phyla with representatives cultured in a lab. Many major clades of bacteria that cannot currently be cultured are known solely and somewhat indirectly through metagenomics, the analysis of bulk samples from the environment. If these possible clades, candidate phyla, are included, the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 30 in 2014, or over 50 including candidate phyla. The total number has been estimated to exceed 1,000 bacterial phyla.At the base of the clade Bacteria, close to the last universal common ancestor of all living things, some scientists believe there may be a definite branching order, whereas other scientists, such as Norman Pace, believe there was a large hard polytomy, a simultaneous multiple speciation event.

Clostridia

The Clostridia are a highly polyphyletic class of Firmicutes, 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 (see Halanaerobium hydrogenoformans) 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.

Most species of the genus Clostridium are saprophytic organisms found in many places in the environment, most notably the soil. However, the genus does contain some human pathogens (outlined below).

The toxins produced by certain members of the genus Clostridium are among the most dangerous known. Examples are tetanus toxin (known as tetanospasmin) produced by C. tetani and botulinum toxin produced by C. botulinum. Some species have been isolated from women with bacterial vaginosis.Notable species of this class include:

Clostridium perfringens (gangrene, food poisoning)

Clostridium difficile (pseudomembranous colitis)

Clostridium tetani (tetanus)

Clostridium botulinum (botulism)

Clostridium acetobutylicum

Clostridium haemolyticum

Clostridium novyi

Clostridium oedematiensHeliobacteria and Christensenella are also members of the class Clostridia.

Some of the enzymes produced by this group are used in bioremediation.

Dictyoglomus thermophilum

Dictyoglomus is a genus of bacterium, given its own subphylum, called the Dictyoglomi. This organism is extremely thermophilic, meaning it thrives at extremely high temperatures. It is chemoorganotrophic, meaning it derives energy by metabolizing organic molecules. This organism is of interest because it elaborates an enzyme, xylanase, which digests xylan, a heteropolymer of the pentose sugar xylose. By pretreating wood pulp with this enzyme, paper manufacturers can achieve comparable levels of whiteness with much less chlorine bleach.

It has been described as Gram-negative, with a triple-layered wall.

Enterococcus

Enterococcus is a large genus of lactic acid bacteria of the phylum Firmicutes. Enterococci are Gram-positive cocci that often occur in pairs (diplococci) or short chains, and are difficult to distinguish from streptococci on physical characteristics alone. Two species are common commensal organisms in the intestines of humans: E. faecalis (90–95%) and E. faecium (5–10%). Rare clusters of

infections occur with other species, including E. casseliflavus, E. gallinarum, and E. raffinosus.

Erysipelotrichia

The Erysipelotrichia are a subclass of bacteria of the phylum Firmicutes. Species of this subclass 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.

Gram-positive bacteria

Gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall.

Gram-positive bacteria take up the crystal violet stain used in the test, and then appear to be purple-coloured when seen through a microscope. This is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test.

Gram-negative bacteria cannot retain the violet stain after the decolorization step; alcohol used in this stage degrades the outer membrane of gram-negative cells, making the cell wall more porous and incapable of retaining the crystal violet stain. Their peptidoglycan layer is much thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain (safranin or fuchsine) and appear red or pink.

Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to certain cell wall targeting antibiotics than gram-negative bacteria, due to the absence of the outer membrane.

Halanaerobiales

The Halanaerobiales are an order of bacteria placed within the class Clostridia, and encompassing two families, the Halanaerobiaceae and the Halobacteroidaceae. Originally placed within the highly polyphyletic class Clostridia, according to the NCBI and LPSN, it is now thought to lie outside the Firmicutes. Halanaerobiales are halophilic obligate anaerobes with a fermentative or homoacetogenic metabolism.

List of bacterial orders

This article lists the orders of the Bacteria.

Megasphaera

Megasphaera is a genus of Firmicutes bacteria classified within the class Negativicutes.This classification has been reexamined. It appears that this genus is a member of the Clostridia.

Mollicutes

Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis (meaning "soft" or "pliable"), and cutis (meaning "skin"). Individuals are very small, typically only 0.2–0.3 μm (200-300 nm) 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.

Mollicutes are parasites of various animals and plants, living on or in the host's cells. Many cause diseases in humans, attaching to cells in the respiratory or urogenital tracts, particularly species of Mycoplasma and Ureaplasma. Phytoplasma and Spiroplasma are plant pathogens associated with insect vectors.

Whereas formerly the trivial name "mycoplasma" has commonly denoted any member of the class Mollicutes, it now refers exclusively to a member of the genus Mycoplasma.

Negativicutes

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

Most members of this class are obligate anaerobes, and occur in habitats such as rivers, lakes, and the intestines of vertebrates. They range from spherical forms, such as Megasphaera and Veillonella, to curved rods, as typified by the selenomonads. Selenomonas has a characteristic crescent shape, with flagella inserted on the concave side, while Sporomusa is similar, but nonmotile. Their names refer to this distinctive morphology: selene means moon, and musa means banana.

Selenomonadales

The Selenomonadales are an order of bacteria within the class Negativicutes; unlike most other members of Firmicutes, they are Gram-negative. The phylogeny of this order was initially determined by 16S rRNA comparisons. More recently, molecular markers in the form of conserved signature indels (CSIs) have been found specific for all Selenomonadales species. On the basis of these markers, the Selenomonadales are inclusive of two distinct families, and are no longer the sole order within the Negativicutes. Several CSIs have also been found specific for both families, Sporomusaceae and Selenomonadceae. Samples of bacterial strains within this order have been isolated from the root canals of healthy human teeth.

Thermolithobacteria

Thermolithobacteria is a class of rod-shaped Gram-positive bacteria within phylum Firmicutes. Species within this class are thermophilic lithotrophs isolated from sediment in Calcite Springs in Yellowstone National Park. Thermolithobacter ferrireducens strain JW/KA-2(T) metabolism consists of the oxidation of hydrogen gas and reduction of ferric oxide to magnetite. Thermolithobacter carboxydivorans strain R1(T) is hydrogenic and oxidizes carbon monoxide.

Veillonella

Veillonella are Gram-negative bacteria (Gram stain pink) anaerobic cocci. This bacterium is well known for its lactate fermenting abilities. They are a normal bacterium in the intestines and oral mucosa of mammals. In humans they have been rarely implicated in cases of osteomyelitis and endocarditis, for example with the species Veillonella parvula.

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