The Lactobacillaceae are a family of lactic acid bacteria
'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, 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 collected, but this has since stopped. 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; the latter group consisted of 7% of species. The tree was created by maximum likelihood analysis without bootstrap: accuracy is traded off for size and many phylum level clades are not resolved.. This 16S rRNA-based phylogenetic tree is based on the ARB-SILVA release LTPs 121 and contains all type species with validly published names
Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, cutis. Individuals are small only 0.2–0.3 μm in size and have a small genome size. They vary in form. 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 plants, living on or in the host's cells. Many cause diseases in humans, attaching to cells in the respiratory or urogenital tracts species of Mycoplasma and Ureaplasma. Phytoplasma and Spiroplasma are plant pathogens associated with insect vectors. Whereas the trivial name "mycoplasma" has denoted any member of the class Mollicutes, it now refers to a member of the genus Mycoplasma. Analysis of the genomes of mycoplasmas gives solid support for the hypothesis that mycoplasmas have developed from Gram-positive bacteria by a process of reductive evolution. By adopting a parasitic mode of life with use of nutrients from their hosts, mycoplasmas were able to reduce their genetic material considerably.
On the other hand, mycoplasma lost the genes for many assimilative processes. Thus, Mycoplasma became the smallest self-replicating organism in nature. Mycoplasma genitalium, with 580,000 base pairs, has an small genome size; some phytoplasmas have a small genome size. The genera with the smallest genome are considered to be phylogenetically the most "recent" mollicutes. To maintain their parasitic mode of life the mollicutes have developed rather sophisticated mechanisms to colonize their hosts and resist the host immune system; the classification of the Mollicutes has always been difficult. The individuals are tiny, being parasites, they have to be cultivated on special media; until now, many species could not be isolated at all. In the beginning, whether they were fungi, viruses, or bacteria was not clear; the resemblance to L-forms was confusing. At first, all members of the class Mollicutes were named "mycoplasma" or pleuropneumonia-like organism. Mollicutes other than some members of genus Mycoplasma were still unidentified.
The first species of Mycoplasma/Mollicutes, that could be isolated was Mycoplasma mycoides. This bacterium was cultivated by Nocard and Roux in 1898. In 1956, D. G. Edward and E. A. Freundt made a first proposal for naming PPLOs, they left undecided, whether they belong to the bacteria or to the eukaryotes. As type species of the PPLOs/mycoplasmas and Freundt proposed Mycoplasma mycoides, being the causative organism of bovine pleuropneumonia and referring to the pleuropneumonia-like organisms; until Mycoplasma mycoides was known as Asterococcus mycoides, but that name was not recognized as valid. In their publication of 1956, they described 15 species of Mycoplasma. In 1967 the class Mollicutes, containing the order Mycoplasmatales, was proposed by the Subcommittee on Taxonomy of the Mycoplasmata. Now, the name Mycoplasma should be used for members of the genus Mycoplasma, rather than the use as a trivial name for any mollicute; as the trivial name has been used in literature for a long time, this is yet not always the case.
Traditionally, the taxonomy of bacteria was based on differences in morphology. In 1962, R. G. E. Murray proposed to divide the kingdom Bacteria into three divisions on the basis of the cell wall types: Gram-negative Gracilicutes, with a thin cell wall and little peptidoglycan. For classification and nomenclature of Mollicutes, there are special rules, which are maintained by the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes. Traditionally, Mollicutes taxonomy has been based on phenotypic characteristics. However, most modern classifications are based on DNA or RNA sequences 16S rRNA sequences; the results of Mollicutes phylogenetic analyses have been controversial. Some taxonomists place them in others in Tenericutes. Woese et al. suggested that the Mollicutes might have been derived from different branches of bacteria. They concluded, that the Mollicutes are not a phylogenetically coherent group and therefore do not form a distinct higher level taxon.
Instead, they cluster within Gram-positive bacteria of the phylum Firmicutes. The results of molecular phylogenetic analyses have depend on the chosen molecular marker, like rRNA, elongation factor or another protein. Phylogenetic trees based on phosphoglycerate kinase amino acid sequences' indicated a monophyletic origin for the Mollicutes within the Firmicutes. An early edition of Bergey’s Manual of Systematic Bacteriology placed class Mollicutes within phylum Firmicutes, whereas in the announced 2nd edition, they are moved to a separate phylum Tenericutes; the change is motivated by "their unique phenotypic properties, in particular the lack of rigid cell walls, the general low support by alternative markers". In the Taxonomic Outline of Bacteria and Archaea, March 2007, the Mollicutes are a class in the phylum Firmicutes. Mollicutes at the US National Library of Medicine Medical Subject Headings
The Enterococcaceae are a family of Gram-positive bacteria placed in the order Lactobacillales. Representative genera include Enterococcus, Pilibacter and Vagococcus. In this family are some important lactic acid bacteria which produce lactic acid as the major metabolic end product. Enterococcaceae J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the gram-staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are found everywhere, in all environments on Earth that support life; the gram-negative bacteria include the model organism Escherichia coli, as well as many pathogenic bacteria, such as Pseudomonas aeruginosa, Neisseria gonorrhoeae, Chlamydia trachomatis, Yersinia pestis. They are an important medical challenge, as their outer membrane protects them from many antibiotics. Additionally, the outer leaflet of this membrane comprises a complex lipopolysaccharide whose lipid A component can cause a toxic reaction when these bacteria are lysed by immune cells; this toxic reaction can include fever, an increased respiratory rate, low blood pressure — a life-threatening condition known as septic shock.
Several classes of antibiotics have been designed to target gram-negative bacteria, including aminopenicillins, ureidopenicillins, beta-lactam-betalactamase combinations, Folate antagonists and carbapenems. Many of these antibiotics cover gram positive organisms; the drugs that target gram negative organisms include aminoglycosides and Ciprofloxacin. Gram-negative bacteria display these characteristics: An inner cell membrane is present A thin peptidoglycan layer is present Has outer membrane containing lipopolysaccharides in its outer leaflet and phospholipids in the inner leaflet Porins exist in the outer membrane, which act like pores for particular molecules Between the outer membrane and the cytoplasmic membrane there is a space filled with a concentrated gel-like substance called periplasm The S-layer is directly attached to the outer membrane rather than to the peptidoglycan If present, flagella have four supporting rings instead of two Teichoic acids or lipoteichoic acids are absent Lipoproteins are attached to the polysaccharide backbone Some contain Braun's lipoprotein, which serves as a link between the outer membrane and the peptidoglycan chain by a covalent bond Most, with few exceptions, do not form spores Along with cell shape, gram-staining is a rapid diagnostic tool and once was used to group species at the subdivision of Bacteria.
The kingdom Monera was divided into four divisions based on gram-staining: Firmacutes, Gracillicutes and Mendocutes. Since 1987, the monophyly of the gram-negative bacteria has been disproven with molecular studies; however some authors, such as Cavalier-Smith still treat them as a monophyletic taxon and refer to the group as a subkingdom "Negibacteria". Bacteria are traditionally classified based on their gram-staining response into the gram-positive and gram-negative groups, it was traditionally thought that the groups represent lineages, i.e. the extra membrane only evoved once, such that gram-negative bacteria are more related to one another than to any gram-positive bacteria. While this is true, the classification system breaks down in some cases, with lineage groupings not matching the staining result. Thus, gram-staining cannot be reliably used to assess familial relationships of bacteria. Staining gives reliable information about the composition of the cell membrane, distinguishing between the presence or absence of an outer lipid membrane.
Of these two structurally distinct groups of prokaryotic organisms, monoderm prokaryotes are thought to be ancestral. Based upon a number of different observations including that the gram-positive bacteria are the major reactors to antibiotics and that gram-negative bacteria are, in general, resistant to them, it has been proposed that the outer cell membrane in gram-negative bacteria evolved as a protective mechanism against antibiotic selection pressure; some bacteria such as Deinococcus, which stain gram-positive due to the presence of a thick peptidoglycan layer, but possess an outer cell membrane are suggested as intermediates in the transition between monoderm and diderm bacteria. The diderm bacteria can be further differentiated between simple diderms lacking lipopolysaccharide; the conventional LPS-diderm group of gram-negative bacteria are uniquely identified by a few conserved signature indel in the HSP60 protein. In addition, a number of bacterial taxa that are either part of the phylum Firmicutes or branches in its proximity are found to possess a diderm cell structure.
They lack the GroEL signature. The presence of this CSI in all se
Lactic acid bacteria
Lactic acid bacteria are an order of gram-positive, low-GC, acid-tolerant nonsporulating, either rod-shaped or spherical bacteria that share common metabolic and physiological characteristics. These bacteria found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation; this trait has, throughout history, linked LAB with food fermentations, as acidification inhibits the growth of spoilage agents. Proteinaceous bacteriocins are produced by several LAB strains and provide an additional hurdle for spoilage and pathogenic microorganisms. Furthermore, lactic acid and other metabolic products contribute to the organoleptic and textural profile of a food item; the industrial importance of the LAB is further evidenced by their recognized as safe status, due to their ubiquitous appearance in food and their contribution to the healthy microflora of human mucosal surfaces. The genera that comprise the LAB are at its core Lactobacillus, Pediococcus and Streptococcus, as well as the more peripheral Aerococcus, Enterococcus, Sporolactobacillus, Tetragenococcus and Weissella.
The lactic acid bacteria are either rod-shaped, or spherical, are characterized by an increased tolerance to acidity. This aspect helps LAB to outcompete other bacteria in a natural fermentation, as they can withstand the increased acidity from organic acid production. Laboratory media used for LAB include a carbohydrate source, as most species are incapable of respiration. LAB are catalase negative, they consist of the organelles of a simple bacterial structure. LAB are amongst the most important groups of microorganisms used in the food industry. Two main hexose fermentation pathways are used to classify LAB genera. Under conditions of excess glucose and limited oxygen, homolactic LAB catabolize one mole of glucose in the Embden-Meyerhof-Parnas pathway to yield two moles of pyruvate. Intracellular redox balance is maintained through the oxidation of NADH, concomitant with pyruvate reduction to lactic acid; this process yields two moles of ATP per mole of glucose consumed. Representative homolactic LAB genera include Lactococcus, Streptococcus and group I lactobacilli.
Heterofermentative LAB use the pentose phosphate pathway, alternatively referred to as the pentose phosphoketolase pathway. One mole of glucose-6-phosphate is dehydrogenated to 6-phosphogluconate and subsequently decarboxylated to yield one mole of CO2; the resulting pentose-5-phosphate is cleaved into one mole glyceraldehyde phosphate and one mole acetyl phosphate. GAP is further metabolized to lactate as in homofermentation, with the acetyl phosphate reduced to ethanol via acetyl-CoA and acetaldehyde intermediates. In theory, end products are produced in equimolar quantities from the catabolism of one mole of glucose. Obligate heterofermentative LAB include Leuconostoc, Oenococcus and group III lactobacilli. In 1985, members of the diverse genus Streptococcus were reclassified into Lactococcus, Enterococcus and Streptococcus based on biochemical characteristics, as well as molecular features. Streptococci were segregated based on serology, which has proven to correlate well with the current taxonomic definitions.
Lactococci are used extensively as fermentation starters in dairy production, with humans estimated to consume 1018 lactococci annually. Due to their industrial relevance, both L. lactis subspecies are used as generic LAB models for research. L. lactis ssp. cremoris, used in the production of hard cheeses, is represented by the laboratory strains LM0230 and MG1363. In similar manner, L. lactis ssp. lactis is employed in soft cheese fermentations, with the workhorse strain IL1403 ubiquitous in LAB research laboratories. In 2001, Bolotin et al. sequenced the genome of IL1403, which coincided with a significant shift of resources to understanding LAB genomics and related applications. The accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and the phylogeny is based on 16S rRNA-based LTP release 106 by'The All-Species Living Tree' Project. Notes: ♠ Strains found at the National Center for Biotechnology Information, but not listed in the List of Prokaryotic names with Standing in Nomenclature A broad number of food products, commodity chemicals, biotechnology products are manufactured industrially by large-scale bacterial fermentation of various organic substrates.
Because enormous amounts of bacteria are being cultivated each day in large fermentation vats, the risk that bacteriophage contamination brings fermentations to a halt and cause economical setbacks is a serious threat in these industries. The relationship between bacteriophages and their bacterial hosts is important in the context of the food fermentation industry. Sources of phage contamination, measures to control their propagation and dissemination, biotechnological defence strategies developed to restrain phages are of interest; the dairy fermentation industry has acknowledged the problem of phage contamination, has been working with academia and starter culture companies to develop defence strategies and systems to curtail the propagation and evolution of phages for decades. The first contact between an infecting phage and its bacterial host is the attachment of the phage to the host cell; this attachment is mediated by the phage's receptor binding protein, which recognizes and binds to a r
Staphylococcus is a genus of Gram-positive bacteria in the family Staphylococcaceae in the order Bacillales. Under the microscope, they appear spherical, form in grape-like clusters. Staphylococcus species are facultative anaerobic organisms; the name was coined in 1882 by Scottish surgeon and bacteriologist Alexander Ogston, following the pattern established five years earlier with the naming of Streptococcus. It combines the prefix "staphylo-", suffixed by the Modern Latin: coccus, lit.'spherical bacterium'. Staphylococcus includes at least 40 species. Of these, nine have two subspecies, one has three subspecies, one has four subspecies. Most are harmless and reside on the skin and mucous membranes of humans and other organisms. Staphylococcus has been found to be a nectar-inhabiting microbe. Found worldwide, they are a small component of soil microbial flora; the taxonomy is based on 16s rRNA sequences, most of the staphylococcal species fall into 11 clusters: S. aureus group – S. argenteus, S. aureus, S. schweitzeri, S. simiae S. auricularis group – S. auricularis S. carnosus group – S. carnosus, S. condimenti, S. massiliensis, S. piscifermentans, S. simulans S. epidermidis group – S. capitis, S. caprae, S. epidermidis, S. saccharolyticus S. haemolyticus group – S. devriesei, S. haemolyticus, S. hominis S. hyicus-intermedius group – S. agnetis, S. chromogenes, S. cornubiensis, S. felis, S. delphini, S. hyicus, S. intermedius, S. lutrae, S. microti, S. muscae, S. pseudintermedius, S. rostri, S. schleiferi S. lugdunensis group – S. lugdunensis S. saprophyticus group – S. arlettae, S. caeli, S. cohnii, S. equorum, S. gallinarum, S. kloosii, S. leei, S. nepalensis, S. saprophyticus, S. succinus, S. xylosus S. sciuri group – S. fleurettii, S. lentus, S. sciuri, S. stepanovicii, S. vitulinus S. simulans group – S. simulans S. warneri group – S. pasteuri, S. warneriA 12th group – that of S. caseolyticus – has now been removed to a new genus, the species of which are the closest known relatives of Staphylococcus.
Two species were described in 2015 - Staphylococcus argenteus and Staphylococcus schweitzeri - both of which were considered variants of S. aureus. A new coagulase negative species - Staphylococcus edaphicus - has been isolated from Antarctica; this species is a member of the S. saprophyticus group. S. aureus subsp. AureusS. Aureus subsp. Anaerobius S. capitis subsp. CapitisS. Capitis subsp. Urealyticus S. carnosus subsp. CarnosusS. Carnosus subsp. Utilis S. cohnii subsp. CohniiS. Cohnii subsp. Urealyticus S. equorum subsp. EquorumS. Equorum subsp. Linens S. hominis subsp. HominisS. Hominis subsp. Novobiosepticus S petrasii subsp. CroceilyticusS petrasii subsp. JettensisS petrasii subsp. PetrasiiS petrasii subsp. Pragensis S. saprophyticus subsp. BovisS. Saprophyticus subsp. Saprophyticus S. schleiferi subsp. CoagulansS. Schleiferi subsp. Schleiferi S. sciuri subsp. CarnaticusS. Sciuri subsp. RodentiumS. Sciuri subsp. Sciuri S. succinus subsp. CaseiS. Succinus subsp. Succinus Based on an analysis of orthologous gene content three groups have been proposed.
Group A includes S. aureus, S. capitis, S. epidermidis, S. haemolyticus, S. hominis, S. lugdunensis, S. pettenkoferi, S. simiae and S. warneri. Group B includes S. cohnii, S. equorum, S. saprophyticus and S. xylosus. Group C includes S. intermedius and S. pseudintermedius. The S. saprophyticus and S. sciuri groups are novobiocin-resistant, as is S. hominis subsp. Novobiosepticus. Members of the S. sciuri group are oxidase-positive due to their possession of the enzyme cytochrome c oxidase. This group is the only clade within the staphylococci to possess this gene; the S. sciuri group appears to be the closest relations to the genus Macrococcus. S. pulvereri has been shown to be a junior synonym of S. vitulinus. Within these clades, the S. haemolyticus and S. simulans groups appear to be related, as do the S. aureus and S. epidermidis groups. S. Lugdunensis appears to be related to the S. haemolyticus group. S. petrasii may be related to S. haemolyticus. The taxonomic position of S. lyticans, S. pettenkoferi, S. petrasii, S. pseudolugdunensis has yet to be clarified.
The published descriptions of these species do not appear to have been validly published. Assignment of a strain to the genus Staphylococcus requires it to be a Gram-positive coccus that forms clusters, has an appropriate cell wall structure and G + C content of DNA in a range of 30–40 mol%. Staphylococcus species can be differentiated from other aerobic and facultative anaerobic, Gram-positive cocci by several simple tests. Staphylococcus species are facultative anaerobes. All species grow in the presence of bile salts. All species of Staphylococcus aureus were once thought to be coagulase-positive, but this has since been disproven. Growth can occur in a 6.5% NaCl solution. On Baird Parker medium, Staphylococcus species grow fermentatively, except for S. saprophyticus, which grows oxidatively. Staphylococcus species are susceptible to furazolidone. Further biochemical testing is needed to identify to the species level; when these bacteria divide, they do so along two axes. This is as opposed to streptococci.
One of the most important phenot