Phylum Firmicutes (Low G+C Gram-positive Bacteria)

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Taxonomy

  • phylum Firmicutes
    • class Bacilli
      • order Bacillales
        • family Bacillaceae (e.g. Bacillus, Geobacillus, Halobacillus)
        • family Alicyclobacillaceae (Alicyclobacillus)
        • family Listeriaceae (e.g. Listeria, Aneurinibacillus)
        • family Paenibacillaceae (e.g. Paenibacillus, Brevibacillus)
        • family Pasteuriaceae (Pasteuria)
        • family Planococcaceae (e.g. Planococcus, Kurthia)
        • family Sporolactobacillaceae (e.g. Sporolactobacillus)
        • family Staphylococcaceae (e.g.Staphylococcus,Salinicoccus)
        • family Thermoactinomycetaceae (e.g. Thermoactinomyces)
      • order Lactobacillales
        • family Lactobacillaceae (e.g. Lactobacillus, Pediococcus)
        • family Aerococcaceae (e.g. Aerococcus, Facklamia)
        • family Carnobacteriaceae (e.g.Carnobacterium,Aptobacter)
        • family Enterococcaceae (e.g. Enterococcus, Vagococcus)
        • family Leuconostocaceae (e.g. Leuconostoc, Weissella)
        • family Streptococcaceae (e.g. Streptococcus, Lactococcus)
    • class Clostridia
      • order Clostridiales
        • family Clostridiaceae (e.g. Clostridium, Sarcina)
        • family Eubacteriaceae (e.g. Eubacterium, Acetobacterium)
        • family Gracilibacteraceae (Gracilobacter)
        • family Heliobacteriaceae (e.g.Heliobacterium,Heliophilum)
        • family Lachnospiraceae (e.g. Butyrovibrio, Coprococus)
        • family Peptococcaceae (e.g. Peptococcus,Desulfotomculum)
        • family Peptostreptococcaceae (e.g. Peptostreptococcus)
        • family Ruminococcaceae (e.g. Ruminococcus, Acetivibrio)
        • family Syntrophomonadaceae (e.g. Syntrophomonas)
        • family Veillonellaceae (e.g. Sporomusa, Megasphaera)
      • order Halanaerobiales
        • family Halanaerobiaceae (E.g. Haloanaerobium, Halocella)
        • family Halobacteroidaceae (e.g. Halanerobacter, Orenia)
      • order Thermoanaerobacterales
        • family Thermoanaerobacteraceae (e.g.Thermoanaerobacter)
        • family Thermodesulfobiaceae (e.g. Coprothermobacter)
    • class Erysipelotrichi
      • order Erysipelotrichales
        • family Erysipelotrichaceae (e.g. Erysipelothrix)
    • class Mollicutes
      • order Mycoplasmatales
        • family Mycoplasmataceae (e.g. Mycoplasma, Ureaplasma)
      • order Entomoplasmatales
        • family Entomoplasmataceae (Entomoplasma, Mesoplasma)
        • family Spiroplasmataceae (Spiroplasma)
      • order Acholeplasmatales
        • family Acholeplasmataceae (Acholeplasma, Phytoplasma)
      • order Anaeroplasmatales
        • family Anaeroplasmataceae(Anaeroplasma,Asteroleplasma)

About this phylum

Diversity

The Firmicutes are a large and diverse group of organisms, encompassing 4 Classes, 11 Orders, 35 Families, and more than 240 species. Included in the Firmicutes are the Mollicutes (a.k.a. Tenericutes), the Mycoplasma and relatives. Although not usually considered Gram-positive - they entirely lack the peptidoglycan cell wall - they are members of this phylogenetic group and like other Gram-positive Bacteria lack the outer membrane. Also amongst the Firmicutes are the members of the Family Veillonellaceae (Veillonella, Dialister, Megasphaera, and Sporomusa), that have traditional Gram-negative cell envelops (complete with outer membrane) despite being members of a Gram-positive phylogenetic group. Anaerobic, endospore-forming rods (“Clostridia”) form several deep lineages in the Firmicutes, and so this probably represents the primitive phenotype of this group.

Metabolism

These organisms are heterotrophic, except for the photosynthetic heliobacteria, but have a wide range of heterotrophic lifestyles. The Bacilli are generally obligate aerobes, other Firmicutes are usually anaerobic, although often aerotolerant. Anaerobic metabolism is usually by substrate-level phosphorylation rather than anaerobic respiration; these organisms often lack a complete electron transport chain. Most are mesophilic, although a few psychrophilic or moderately thermophilic species exist. A wide range of carbon/energy sources are used by members of this group, and result in a similarly wide range of fermentation products.

Morphology

Familiar members of this group are either rod-shaped or cocci; these sometimes form nearly filamentous chains, as in some species of Bacillus and Streptococcus. Individual cells or pairs are also very common. Endospores are a common unique feature of this group. Morphology varies more widely in the Mollicutes, but their small size and lack of peptidoglycen means that these morphologies are less easily observed.

Habitat

Both Firmicutes and Actinobacteria are abundant in most soil and sediment communities. Firmicutes are also the predominant symbionts of the skin, mucous membranes, and gut of animals; perhaps this helps explain the large number of human and animal pathogens that also are members of this group.

Aerobic endospore-forming rods (Bacillus and relatives)

These are generally aerobic (some grow anaerobically by nitrate reduction) rod-shaped endospore-forming heterotrophs that obtain energy and carbon by respiration. These are common soil inhabitants. A few are opportunistically pathogenic to humans, and a very few are bona fide pathogens, Bacillus anthracis being the most important. Listeria and Staphylococcus, although not endospore-forming rods, are members of this phylogenetic group. Most of the endospore-forming aerobic rods were originally considered to be species of the genus Bacillus, but the size of this genus and phylogenetic considerations lead to its division into a number of new genera, most of which retain the -bacillus suffix (e.g. Paenibacillus, Brevibacillus, Geobacillus, &c)

Example : Bacillus cereus

Bacillus cereus a.k.a. Arthromitis
Bacillus cereus from insect guts, in which form it is classically known as "Arthromitis".
Margulis L, et al. 1998 Proc. Natl. Acad. Sci. USA 95:1236-1241.

B. cereus is a very close relative of the human pathogen B. anthracis, the insect pathogen B. thuringensis (the source of the widely used Bt insecticide), B. mycoides, B. pseudomycoides and B. weihenstephanensis; these may more appropriately be considered to be different strains of the same species. B. cereus is easily isolated from soil and soil has traditionally been considered to be the natural habitat of this organism. However, B. cereus is abundant in the guts of a wide range of arthropods, in which it is usually filamentous rather than the individual cells or short chains seen in cultivation. Cells shed in the arthropod feces sporulate, awaiting ingestion by a new arthropod host. This life cycle is very similar to that of B. anthracis and B. thuringensis, except that the host is not (apparently) harmed. B. cereus is often considered to be a food-born opportunistic pathogen, although it is unclear whether these are typically infections or reactions to Bt-like toxin.

Anaerobic endospore-forming rods (Clostridium and relatives)

These organisms, and their non-spore-forming relatives (Eubacterium) are abundant in anaerobic soils and sediments. They constitute the bulk of the Bacteria in the gut contents (and feces) of humans, and are particularly important in animal decay. Many species are opportunistically pathogenic, and some are well known pathogens, for example C. tetani (the causative agent of tetanus) and C. perfringens (the causative agent of gas-gangrene). Clostridia lack the electron transport chain, and obtain energy (ATP) from a wide variety of substrate-level phosphorylation reactions. The proton gradient, which is required to drive many active transport pumps, seems to be maintained by a traditional ATPase run in reverse; protons are pumped from inside to outside at the expense of the hydrolysis of ATP.

Example : Clostridium botulinum

Clostridium
Clostridium botulinum : CDC

C. botulinum produces a potent neurotoxin (sometimes said to be the most deadly toxin known); it is this neurotoxin, rather than the organism itself, that produces the disease Botulism. The most common form of botulism is infantile botulism, in which C. botulinum colonizes the gut amongst the wide range of other normal Clostridium species; the toxin is then absorbed through the gut mucosa. Sudden Infant Death Syndrome (SIDS) is sometimes (and probably incorrectly) attributed to C. botulinum acquired from honey. In wound botulism, C. botulinum grows in a gangrenous wound; the toxin is absorbed directly into the surrounding tissue and circulation. This is in many ways analogous to tetanus, caused by a related specie Clostridium tetani. The most well-known form of botulism, however, is the food-borne type. The organism grows in anaerobic canned food or sausage; the toxin is absorbed through the gut mucosa upon ingestion. The botulism toxin inhibits neurotransmission, resulting in flaccid paralysis. The botulism toxin (Botox) has important medical uses in a wide variety of conditions in which muscles contract inappropriately.

Lactic Acid Bacteria

The lactic acid Bacteria (commonly know by the acronym LAB) are acid-tolerant, non-sporulating relatives of the Bacilli and Clostridia. Like the Clostridia, the LAB lack the electron transport chain, and so generate ATP by substrate-level phosphorylation. Unlike Clostridia, most are aerotolerant. In nature, these organisms are usually associated with the decomposition of plant material, but are also important human and animal symbionts. Most grow on simple carbohydrates (sugars), either producing lactic acid alone via glycolysis (homofermentation) or lactic acid, ethanol, and CO2 via the pentose-phosphate pathway (heterofermentation). The LAB are widely used in the food industry for the production of fermented vegetable (pickles, sauerkraut), dairy (yogurt, cheese), and meat (fermented sausages). Although generally nonpathogenic, and very often beneficial to humans, some members of the genus Streptococcus are harmful (S. mutans causes tooth decay) or pathogenic (S. pyogenes causes Strep throat and scarlet fever).

Example : Leuconostoc mesenteroides

Leuconostoc
Leuconostoc mesenteroides : The Prokaryotes pp1523

Species of the genus Leuconostoc are strictly heterofermentative LAB with distinctly oval cells that grow in chains. L. mesenteroides produces dextran slime when grown on sucrose; colonies will become so slimy that they will drip onto the lid of culture plates. L. mesenteroides predominates most lactic fermentations in the initial stages; they are succeeded in later stages of these fermentations by the more acidophilic Lactobacillus species.

Mollicutes (Tenericutes; Mycoplasma and relatives)

The Mollicutes are not often considered to be Gram-positive Bacteria; lacking peptidoglycan, they stain Gram-negative. Historically, they were often considered with the viruses, because of their small size and obligately parasitic lifestyle. But they are phylogenetic members of the Firmicutes, being an offshoot of the Clostridium innocuum branch, and like other Gram-positive Bacteria lack an outer membrane. The mollicutes are obligate extracellular symbionts or parasites of plants and animals. Most are unusual in that they have sterols in their membrane in addition to the usual fatty-acid esters; they don't make sterols themselves, it is acquired from its eukaryotic host. They are very small, typically about 0.25um in diameter, amongst the smallest known cellular organisms with the smallest genomes. Genomes lack the genes for the Krebs cycle, animo acid biosynthesis, purine and pyrimidine biosynthesis, and many other metabolic pathways. Most do contain the genes for the glycolytic pathway, which they use for energy production by substrate-level phosphorylation. They are often motile by gliding. Members of this group have a wide range of complex morphologies, but are usually described as amorphous or pleomorphous because of their size (at or below the resolving power of light microscopy) and the fact that their relatively non-rigid envelop cannot withstand traditional fixing treatments.

Example : Mycoplasma hominis

Mycoplasma
Mycoplasma hominis (green) endosymbionts of Trichomonas vaginalis (red)
Infect Immun. 2005 73: 1180–1186. PMC546971

Species of the genus Mycoplasma are obligate parasites of animals, usually infecting the lung (e.g. M. pneumoniae) or urogenital tract (e.g. M. genitalium). M. hominis is an opportunistic pathogen; it seems to reside asymptomatically in the vagina of healthy women, but is also one of many causes of bacterial vaginitis and pelvic inflammatory disease. Disease is usually associated either with invasive surgical procedures or coinfection with the obligately parasitic protist Trichomonas vaginalis. In the former case, the parasite proliferates in deep surgical wounds and can be difficult to identify or treat; lacking peptoglycan cell walls, they are resistant to many commonly-used post-surgical broad-spectrum antibiotics. In the latter case, there is a symbiosis between T. vaginalis and M. hominis, and most infected women are co-infected. Although typically an extracellular parasite, M. hominis can reside and replicate in the cytoplasm of T. vaginalis; this may facilitate both the transfer of M. hominis to new human hosts and the resistance of M. hominis to antibiotics. In both females and males, M. hominis is associated with reduced fertility. M. hominis cells can attach to and invade sperm cells, suggesting that the ability to persist intracellularly may be a general mechanism for infecting new hosts. M. hominis is generally spherical, lacking the elongated “flask” shape of most other species. Also unlike other Mycoplasma species, M. hominis is not saccharolytic, but instead uses only arginine for both carbon and energy.

Heliobacteria (Green photosynthetic Gram-positives)

The heliobacteria are the only phototrophic Gram-positive Bacteria. They carry out cyclic photophosphorylation, growing photoheterotrophically using pyruvate or similar organic acids as their sole carbon sources. Heliobacteria use a chlorophyl g, that absorbs wavelengths in the range of 790nm not utilized by other photopigments and so can avoid competition for light with other phototrophs. Unlike other phototrophs, heliobacteria house their photosynthetic complexes in the cytoplasmic membrane; no internal membranous structures or membranous invaginations are present. However, the photo reaction cycle of the heliobacteria is very similar to that of the Chlorobi. The heliobacteria are rod-shaped (sometimes slightly helical) anaerobic endospore-formers, motile by gliding or flagella. They lack the typical thick Gram-positive cell wall; the thin peptidoglycan layer is covered in a regular array of 11nm protein beads. The heliobacteria are commonly found in soil, and are very efficient nitrogen fixers.

Example : Heliobacterium chlorum

Heliobacterium
Heliobacterium chlorum, showing it's "beaded" cell wall
Howard Gest, Indiana University, from The Prokaryotes

Heliobacterium chlorum is a long rod-shaped organism (1 x 6-10μm), forming green-brown to emerald green colonies due to the presence of both chlorophyl g and the green accessory carotinoid neurosporene. H. chlorum is motile by gliding rather than the flagella present in other heliobacteria. The only carbon sources known to support its photoheterotrophic lifestyle are pyruvate and lactate. Sporulation is rarely observed; older cultures usually degenerate into spheroplasts and lyse.

Veillonelli (Firmicutes with Gram-negative envelops)

This little-known group of organisms is unique amongst the Gram-positive phylogenetic group of Bacteria; they have Gram-negative envelops, including an outer membrane and (generally) lipopolysaccharide layer. It is unclear whether this represents a re-acquisition of the Gram-negative envelop by an Gram-positive ancestor of this group, or if this branch separated from the Gram-positive phylogenetic group prior to the loss in the remainder of the group of the outer membrane. Members of this group are anaerobic heterotrophs, and are common symbionts of the GI tract, except for Pectinatus and Megasphaera, which are found in spoiled unpasteurized beer. Pectinatus and Selenomonas are rod-shaped organisms motile by flagella that occur only on one side of the cell; they swim sideways in a distinct tumbling “X” shape. Sporomusa and Sporohalobacter produce endospores similar to those of other Firmicutes. Syntrophomonas is an gut-dwelling obligate syntroph, growing only in association methanogenic Archaea.

Example : Veillonella atypica

Veillonella
Veillonella atypica (cocci) associated with Fusobacterium (long rods)
from The Prokaryotes pp2040

Veillonella are the most numerous cultivable anaerobes in human saliva. These small (ca. 0.5m) cocci grow by decarboxylation of lactate and other organic acids produced by primary oral colonizers such as Streptococcus salivarius, fusobacteria, and actinomycetes, to which they adhere. Species of Veillonella are specialized to adhere to the primary colonizers of specific portions of the oral cavity; V. atypica adheres specifically to Streptococcus salivarius and Fusobacterium nucleatum, inhabitants of the saliva and upper surface of the tongue.