User:Wickey-nl/bacteria

http://ijs.sgmjournals.org/cgi/reprint/43/2/378.pdf

Revised Taxonomy of the Class Mollicutes - 1993

Some genera do have the candidatus status, because they could not be cultured yet.

Orders in Mollicutes

 * Note: An official classification of bacteria does not exist.

Currently the class Mollicutes comprises five orders.

Acholeplasmatales
This order has one family "Acholeplasmataceae", consisting of the genera Acholeplasma and Candidatus Phytoplasma.

http://ijs.sgmjournals.org/cgi/reprint/34/3/346 E. A. FREUNDT, R. F. WHITCOMB, M. F. BARILE, S. RAZIN, and J. G. TULLY Proposal for Elevation of the Family Acholeplasmataceae to Ordinal Rank: Acholeplasmatales Int J Syst Bacteriol 1984 34: 346-349.

phytoplasmas:

http://www.ncbi.nlm.nih.gov/pubmed/8071198

Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. 1994

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=196707&blobtype=pdf.pdf

http://ijs.sgmjournals.org/cgi/content/full/54/4/1243

‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects.

http://ijs.s gmjournals.org/cgi/content/full/55/5/2131

Phylogenetic positions of ‘Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. (2005)

In the consensus phylogeny, all mollicutes, including plant-pathogenic spiroplasmas and phytoplasmas, appear to be monophyletic and to share a common Clostridium-like ancestor.

http://ijs.sgmjournals.org/cgi/content/abstract/44/1/119

http://ijs.sgmjournals.org/cgi/reprint/44/1/119.pdf 1994 It was also evident that the nonhelical plant-pathogenic members of the class Mollicutes, referred to as mycoplasmalike organisms or phytoplasmas, are more closely related to the true acholeplasmas (Acholeplasma laidlawii and strain J233) than to other members of the Mollicutes.

Anaeroplasmatales

http://ijs.sgmjournals.org/cgi/reprint/37/1/78.pdf

ROBINSON (I.M.) and FREUNDT (E.A.): Proposal for an amended classification of anaerobic mollicutes. Int. J. Syst. Bacteriol., 1987, 37, 78-81.

Entomoplasmatales : http://www.bacterio.cict.fr/e/entomoplasmatales.html

Spiroplasma The genus Spiroplasma and its non-helical descendants: phylogenetic classification, correlation with phenotype and roots of the Mycoplasma mycoides clade.
 * 1973, Spiroplasma citri gen. and sp. n.: A Mycoplasma-Like Organism Associated with "Stubborn" Disease of Citrus
 * http://ijs.sgmjournals.org/cgi/reprint/43/2/378 1993 Tully, et al.
 * http://ijs.sgmjournals.org/cgi/content/full/54/3/893 PDF (2004)

M. mycoides cluster arose from Spiroplasma through an intermediate group of non-helical spiroplasmal descendants – the Entomoplasmataceae.

Haloplasmatales

Mycoplasmatales

http://www.ncbi.nlm.nih.gov/pubmed/19043295

Intracellular survival and replication of legionella pneumophila within host cells

http://www.ncbi.nlm.nih.gov/pubmed/14763969

Cellular engineering in a minimal microbe: structure and assembly of the terminal organelle of Mycoplasma pneumoniae.

http://jem.rupress.org/cgi/reprint/79/6/649.pdf

Eaton MD, Meiklejohn G, van Herick W.

STUDIES ON THE ETIOLOGY OF PRIMARY ATYPICAL PNEUMONIA: a filterable agent transmissible to cotton rats, hamsters, and chick embryos. (june 1944)

http://www.ajph.org/cgi/reprint/34/4/347.pdf

Primary Atypical Pneumonia

AMERICAN-JOURNAL OF PUBLIC HEALTH, April, 1944; Vol. 34

http://www.ncbi.nlm.nih.gov/pubmed/2109871

Eaton agent--science and scientific acceptance: a historical commentary.

http://resources.metapress.com/pdf-preview.axd?code=v7402082q7411578&size=largest

Cultivation of Eaton's agent ...

G. Ya. Kazan1, R. S. Dreizin1, S. V. Prozorovskii1 and E. M. Bikhnovich

http://www.pnas.org/content/77/1/494.full.pdf C. R. WOESE*, J. MANILOFFt, AND L. B. ZABLEN* Phylogenetic analysis of the mycoplasmas; Proc. Natl. Acad. Sci. USA Vol. 77, No. 1, pp. 494-498, January 1980

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=210534&blobtype=pdf

A phylogenetic analysis of the mycoplasmas: basis for their classification. W G Weisburg, J G Tully, D L Rose, J P Petzel, H Oyaizu, D Yang, L Mandelco, J Sechrest, T G Lawrence, J Van Etten; J Bacteriol. 1989 December; 171(12): 6455–6467 --->

http://books.google.com/books?hl=nl&lr=&id=G3rURFq6u84C&oi=fnd&pg=PR5

Razin, S. 1992. Mycoplasma taxonomy and ecology, p. 3-22. In J. Maniloff, R. N. McElhaney, L. R. Finch, and J. B. Baseman (ed.), Mycoplasmas: molecular biology and pathogenesis. American Society for Microbiology, Washington, D.C.

http://mmbr.asm.org/cgi/content/full/62/4/1094?view=long&pmid=9841667

PDF http://mmbr.asm.org/cgi/reprint/62/4/1094

Molecular Biology and Pathogenicity of Mycoplasmas (1998)

Shmuel Razin, David Yogev and Yehudith Naot

http://books.google.com/books?id=WuMVqDapIbEC&pg=PA31

Molecular biology and pathogenicity of mycoplasmas (2002)

Johansson, K.-E. & Pettersson, B.

http://www.bacterio.cict.fr/classifphyla.html#Tenericutes

http://mmbr.asm.org/cgi/reprint/29/2/185.pdf Mycoplasma Species of Man LEONARD HAYFLICK AND ROBERT M. CHANOCK (1965)

http://www.ajph.org/cgi/reprint/42/8/913.pdf PPLO

http://mmbr.asm.org/cgi/reprint/5/1/1.pdf

ALBERT B. SABIN, THE FILTRABLE MICROORGANISMS OF THE PLEUROPNEUMONIA GROUP (1941)

foto's

http://ijs.sgmjournals.org/cgi/content/full/54/3/871

Matthias Wolf, Tobias Müller, Thomas Dandekar and J. Dennis Pollack, Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data

Int J Syst Evol Microbiol 54 (2004), 871-875; DOI 10.1099/ijs.0.02868-0

http://rdp.cme.msu.edu/hierarchy/hierarchy_browser.jsp?qvector=2570&depth=4&openNode=0&seqid=&currentRoot=0&searchStr=&endDataValue=&showOpt=

Ribosomal Database Project (RDP)

Mycoplasmas are members of the class Mollicutes, a large group of bacteria that lack a cell wall and have a characteristically low G+C content (Razin et al. 1998). These diverse organisms are parasites in a wide range of hosts, including humans, animals, insects, plants, and cells grown in tissue culture (Razin et al. 1998).

http://www.ncbi.nlm.nih.gov/pubmed/11031124

Intracellular DNA replication and long-term survival of pathogenic mycoplasmas. Microb Pathog. 2000 Nov;29(5):301-9.Click here to read

http://www.ncbi.nlm.nih.gov/pubmed/12466555

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12466555

The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. 2002.

History of the classification
The classification of the Mollicutes has always been difficult. The individuals are tiny and being parasites they have to be cultivated on special media. Until now many species could not be isolated at all. In the beginning it was not clear whether they were fungi, viruses or bacteria. Also the resemblance to L-forms was confusing.

At first all members of the class Mollicutes were generally named "mycoplasma" or "PleuroPneumonia-Like Organism" (PPLO). Mollicutes other than the species 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 classifying and naming PPLO's. They left undecided, however, wether they belong to the bacteria (prokaryotes, in 1956 called "Schizomycetes") or to the eukaryotes. As type species (name giving species) of the PPLO's/Mycoplasma's Edward and Freundt proposed Mycoplasma mycoides, being the causative organism of "bovine pleuropneumonia" and refering to the "pleuropneumonia-like organisms". Until then Mycoplasma mycoides was known as Asterococcus mycoides, but later that name was recognized as not 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 exclusively 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.

Three divisions of the kingdom "Procaryotae"
Traditionally the taxonomy of bacteria was based on similarities and differences in morphology (Linnaean taxonomy).

In 1962 R.G.E. Murray proposed to divide the Kingdom Bacteria into three divisions (= phyla) on the basis of the cell wall types:

1. gram-negative "Gracilicutes", with a thin cell wall and little peptidoglycan; 2. gram-positive "Firmacutes", with a thicker cell wall and more peptidoglycan (the name was later changed in "Firmicutes") and 3. the "Mollicutes", without a cell wall.

Modern taxonomy
The present taxonomy of mollicutes is based on: 1. molecular analysis, especially of 16S rRNA; 2. serology (reactions on antiserum) and 3. phenotype (morphology, requirements for grow).

For classification and nomenclature of species there are special rules, which are maintained by the International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the Taxonomy of Mollicutes (formerly the International Committee on Systematic Bacteriology (ICSB) Subcommittee on taxonomy of Mycoplasmatales).

Traditional versus phylogenetic classification
The classification of organisms can be made on the basis of morphology (Linnaean taxonomy) or according to ancestry/genetic origin (cladistics). In taxonomy, bacteria are preferably classified according to their decent.

Although the group Mollicutes phenotypically (without a cellwall and therefore resistant to antibiotics like penicillin and not Gram-positive) clearly is distinguished from Gram-positive bacteria with a cell wall, the morphology does not say anything about their position in the phylogenetic tree. Some evolutionary solutions, like wall-lessness, can rise (and distinct) several times, even within a lineage. For example, the unrelated Thermoplasmas also lack a cell wall. For that reason cell wall-lessness cannot be a valid criterium to define Mollicutes as a phylogenetically coherent group , or to determine whether a species developed earlier or later in the evolution.

The phylum for Mollicutes
The phylum in which the class Mollicutes should be placed is controversial. Some taxonomists place them in Firmicutes, others in Tenericutes. The results of molecular phylogenetics are not straightforward. Beside the limitation of the amount of available data there are also intrinsic limitations of the used methods, that give uncertainties about the evolutionary development. The results partly depend on the choosen molecular marker, like rRNA, elongation factor or another protein. Moreover cladistic analyses are often based on assumptions that are hidden in the used computational algorithms, with techniques like maximum parsimony and likelihood. Such elements do have a somewhat arbitrary character.

This is illustrated by the fact that in an early edition of Bergey’s Manual of Systematic Bacteriology the Mollicutes are a class within the phylum Firmicutes , whereas in the announced 2nd edition, vol. 3 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, and the general low support by alternative markers.

The phylum Tenericutes was already validly published in 1984 by R.G.E. Murray.

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.

Phylogenetic trees based on phosphoglycerate kinase (Pgk) amino acid sequences indicated a monophyletic origin for the Mollicutes within the Firmicutes.

In the Taxonomic Outline of Bacteria and Archaea (TOBA Release 7.7), march 2007, the Mollicutes are a class in the phylum Firmicutes.

Evolution of Mollicutes
Morphologically and microbiologically, Mollicutes are classified as Bacteria that were probably derived from lactobacilli, bacilli or streptococci by regressive evolution and genome reduction, to produce the smallest and simplest free-living and self-replicating cells (Razin et al., 1998; http://ijs.sgmjournals.org/cgi/ijlink?linkType=ABST&journalCode=mmbr&resid=62/4/1094; Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62, 1094–1156).

Phylogenetic trees based on Pgk data indicated a monophyletic origin for the Mollicutes within the Firmicutes. http://ijs.sgmjournals.org/cgi/content/full/54/3/871

- http://ijsb.sgmjournals.org/cgi/content/abstract/57/9/2037

Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas.

The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group.

- The Mollicutes were probably derived from lactobacilli, bacilli or streptococci by regressive evolution and genome reduction.

http://ijs.sgmjournals.org/cgi/content/full/54/3/893

Molecular phylogenetics shows that

the Mollicutes and gram-positive cellwalled members of the phylum Firmicutes have evolved from a common ancestor.

Analysis of the ribosomal RNA sequences (rRNA) suggests that the Bacilli, Clostridia and Mollicutes share a common root, but the monophyletic status of the phylum Firmicutes is not shown straightforward by alternative markers.

Amino acid sequences of phosphoglycerate kinase (Pgk) as alternative marker in molecular research confirm this relationship, with Mollicutes placed within the phylum Firmicutes. Mollicutes appears to be monophyletic.

- The genus Mycoplasma is not monophyletic. It is distributed in different orders (p.12 + 17)

Phylogenetic studies show that the genus Mycoplasma is polyphyletic and M. mycoides and four allied Mycoplasma species developed from the Entomoplasmataceae, which in turn arose from Spiroplasma. The Mycoides clade is a sister clade of the Entomoplasmataceae clade. However, a revision of the Mycoplasma taxonomy has not taken place, because of the implications it would have on medicine and mycoplasmology. Also the genera Entomoplasma and Mesoplasma are polyphyletic.