Present-day procariotic classification

8 posts / 0 new
Last post
Cherry_Juice
Cherry_Juice's picture
Present-day procariotic classification

Dear colleagues!
Inform me,please, does any generally accepted classification exist? Traditionally Bergey's manual of determinative bacteriology (9th edition in Russia and Ukraine) was commonly used for a long period. But now the classification system has changed completely according to 16s RNA sequences. Some one said to me that 10th addition of Bergey's manual of determinative bacteriology appeared already. Is it true? if it is not so, what a classification source do you use?
Thanks!

p.s. sorry for my mistake in the title

samm
samm's picture
The Bergey's Manual of

The Bergey's Manual of Systematic Bacteriology had its last edition as a three vol set, published from 2005 onwards (I think it was Springer). However, if you use Bergey's mostly for biochemial tests to identify/group a particular isolate, then rest easy - the old tests are still valid. There has been some shuffling in the grouping (and in some instances, the names), but the core remains the same! I think there are three sets based on the broad families (Archaea, Proteobacteria...)

Cherry_Juice
Cherry_Juice's picture
Samm,thank you very much! It

Samm,thank you very much! It is rumored that a new addition of The Bergey's Manual of Systematic Bacteriology would be based on 16S RNA sequences and would be suitable for non cultivated microorganisms. It is a pity, that it is not true. So, may be you know, does any genetic classification exist?

Tony Rook
Tony Rook's picture
Cherry Juice:

Cherry Juice:

Here are some references that you may find helpful on the topic of bacterial classification through genomic characterization.

Hope you find some of these useful!

Grimont PA. Use of DNA reassociation in bacterial classification. Can J Microbiol. 1988 Apr;34(4):541-6.

Abstract:
The reassociation properties of DNA provide invaluable taxonomic tools. Different methods may give different reassociation values. However, the thermal stability of reassociated DNA strands (a measurement that seems independent of method) is useful in delineating genomic species. Although many phenotypically defined species have been confirmed by DNA reassociation, some medically important genomic species previously had been split into several nomenspecies on the basis of a few characteristics whereas some environmental genomic species had been lumped into unidentifiable aggregates. It might take some time before the nomenclature can be adapted to new taxonomic findings.

_
___________________________________________________

Winker S, Woese CR. A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. Syst Appl Microbiol. 1991;14(4):305-10.

Abstract:
The number of small subunit rRNA sequences is now great enough that the three domains Archaea, Bacteria and Eucarya (Woese et al., 1990) can be reliably defined in terms of their sequence "signatures". Approximately 50 homologous positions (or nucleotide pairs) in the small subunit rRNA characterize and distinguish among the three. In addition, the three can be recognized by a variety of nonhomologous rRNA characters, either individual positions and/or higher-order structural features. The Crenarchaeota and the Euryarchaeota, the two archaeal kingdoms, can also be defined and distinguished by their characteristic compositions at approximately fifteen positions in the small subunit rRNA molecule.

____________________________________________________

Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH. http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=9588802&dopt=Citation
Electrophoresis. 1998 Apr;19(4):554-68.

Abstract:
Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.

____________________________________________________

SNEATH PH. Some thoughts on bacterial classification. J Gen Microbiol. 1957 Aug;17(1):184-200.

_____________________________________________________

Kostman JR, Alden MB, Mair M, Edlind TD, LiPuma JJ, Stull TL.
A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J Infect Dis. 1995 Jan;171(1):204-8.

Abstract:
Oligonucleotide primers complementary to conserved regions of the 16S and 23S ribosomal RNA genes were used to amplify the 16S-23S intergenic spacer region of bacterial pathogens. The amplification patterns produced were compared for their potential use in molecular epidemiologic analysis. This method, polymerase chain reaction (PCR) ribotyping, was applied to isolates of Staphylococcus aureus, Enterococcus faecium, Escherichia coli, and Enterobacter species. Length polymorphisms in the amplified DNA distinguished unrelated strains of all bacteria. The banding patterns of 3 S. aureus isolates from the blood of 1 patient on 3 consecutive days were identical. Plasmid analysis, biotyping, and antibiograms were also obtained on the Enterobacter isolates. All three of these methods showed considerable variability after in vitro passage of bacteria, but PCR ribotypes remained stable. Results demonstrate the utility of the conserved primers for PCR ribotyping, a widely applicable method for the molecular epidemiology of genetically diverse bacteria.

_____________________________________________________

R. Y. Stanier and C. B. Van Niel The Main Outlines of Bacterial Classification. J. Bacteriol., Vol. 42, Issue 4, 437-466, October 1, 1941

Abstract:
Although a great deal has been written on bacterial taxonomy
during the past few decades, a perusal of the literature shows that for the most part this work has been restricted to the classification of the Eubacteriales alone. Since the early days of microbiology, comparatively little attention has been paid to the broader problem of delimiting and defining the Schizomycetes as a whole and the major groups contained therein. Nevertheless, it can hardly be contended that this is an unimportant aspect of bacterial taxonomy; on the contrary, a clear recognition of the larger natural groups of bacteria, their characteristics and relationships, would seem to be an indispensable basis for more detailed work.
The increased use of Bergey's Manual of Determinative Bacteriology for purposes of identification, together with the obvious attempts made by the present Board of Editors to seek collaboration with specialists on various groups, make it likely that this Manual will ultimately become the internationally recognized and authoritative handbook on bacterial taxonomy. Nevertheless, in its main outlines the system used in Bergey's Manual is still far from satisfactory. There will in due course be a succeeding edition, and it is with the hope of contributing some constructive suggestions for its outline that the present essay is offered.

______________________________________________________

Niall A. Logan. Bacterial Systematics. Blackwell Scientific Publications (1994).

SGM Book Review:
Even allowing for the exciting developments in molecular systematics, phylogeny and biodiversity, bacterial systematics remains a challenging subject that many students find difficult. Niall Logan has produced a text on the subject that is readable and accessible, whilst remaining academically sound and scientifically critical. It comprises an introduction, four chapters covering methodologies for classification and identification along with nine chapters on the main prokaryotic groups. The text is well illustrated and there is a valuable list of further reading. As always, one could pick holes - a clear definition of systematics in an easily found glossary of terms would have been useful - but this remains a good and reasonably priced addition to the subject.

____________________________________________________

Woese, CR; Blanz, P; Hahn, CM What isn't a pseudomonad: The importance of nomenclature in bacterial classification. Systematic and Applied Microbiology. Vol. 5, no. 2, pp. 179-195. 1984.

Abstract:
A variety of pseudomonad species have been characterized by the technique of oligonucleotide cataloging of 16S robosomal RNA in order to determine their genealogical relationships to one another and to other Gram negative bacteria. By this criterion, pseudomonads are shown to comprise five distinct groupings (as originally defined by Palleroni and co-workers). However, none of the five groupings so defined is phylogenetically comprehensive - i.e., none comprises exclusively pseudomonad phenotypes. Pseudomonads are intermingled phylogenetically with a variety of other Gram negative phenotypes - purple photosynthetic bacteria, spiral bacteria, alcaligenes species, etc.

_____________________________________________________

Sneath, PHA. Analysis and interpretation of sequence data for bacterial systematics: The view of a numerical taxonomist. Systematic and Applied Microbiology. Vol. 12, no. 1, pp. 15-31. 1989.

Abstract:
The nature of sequence data is considered with particular attention to phenetic and cladistic relationships. The correct use of the terms phylogenetic, phenotypic and genomic is emphasized. Sequence data are genomic, and this is included within the concept of phenetic relationships. The primary aim of taxonomy is to construct phenetic groups, because of their high content of information. Methods of analysis of sequence data are briefly considered. Sequence relationships are subject to statistical sampling error, which is greater for smaller sequences. It is a substantial cause of uncertainty in both phenograms and cladograms. This is illustrated by examples from ribosomal RNA sequences, using a convenient graphic representation of uncertainty. Other sources of uncertainty include similarities between sequences which are not orthologous, i.e. not strictly comparable (such as paralogous similarities between genes that have undergone gene duplication and independent evolution of the duplicates), and imperfect correlation between relationships from oligonucleotide catalogues and the full sequences.

_____________________________________________________

Michael Goodfellow. Chemical Methods in Bacterial Systematics. Academic Press, 1985.

_____________________________________________________

Michael Goodfellow. Chemical Methods in Prokaryotic Systematics. John Wiley & Sons Inc, 1994.

Overview:
Modern Microbiological Methods Chemical Methods in Prokaryotic Systematics Edited by M. Goodfellow Department of Microbiology, University of Newcastle upon Tyne, UK and A. G. ODonnell Department of Agriculture and Environmental Science, University of Newcastle upon Tyne, UK The use of chemical techniques is having a profound effect on approaches to the characterization, classification and identification of prokaryotes, i.e. archaea and bacteria. This book provides a comprehensive, up-to-date treatment of such methods used in prokaryotic systematics and is written by leading specialists in this field. Designed as a laboratory manual, this volume describes the latest applications to prokaryote systematics of powerful techniques such as protein electrophoresis, pyrolysis mass spectrometry and rapid enzyme testing. The extraction, purification and characterization of specific components such as fatty acids, lipid A, peptidoglycan, pigments (carotenoids and bacteriochlorophylls) and isoprenoid quinones are explained. The value of these methods in the circumscription and identification of archaea and bacteria is demonstrated. The book is aimed at microbiologists and microbial technologists interested in characterizing and identifying bacteria.

Cherry_Juice
Cherry_Juice's picture
Dear Tony Rook!

Dear Tony Rook!
Thank you very much for your answer! This literature will help me greatly!

Tony Rook
Tony Rook's picture
I'm glad I can help. It

I'm glad I can help. It would help the rest of the board and future users to know which references were most helpful to solve your question.

After reviewing this literature, could I ask you to post a short response about which references were most useful?

Good luck!

By the way, I personally prefer the old school methods of metabolic utilization for bacterial classifications schemes. Even, though genetic analysis offers many useful characteristics and has given new insights to bacterial classification. The broad classification of metabolic utilization offer a more fundamental tool for understanding bacterial classification. Just my two cents!

Cherry_Juice
Cherry_Juice's picture
Dear Tony!

Dear Tony!
Of course, I will post my IMHO following the articles. I am out of my work place current cause of my holliday, that is why I have no access to scientific libraries.When I will be back I will leave Ukraine for two weeks (a scientific experiment will start). So, I will not post my rewiev in nearest feature, but I promis to do it by all means.
Tell me,please, why do you prefer classic approaches in Procaryotic classification? not more than 0,1-0,01% of microorganisms may be cultivated in artificial (laboratory) conditions,you know.So, an extremely limited number of microorganisms may be explored via biochemical and metabolic tests. In addition, you know, that some microorganisms growth on mediums only being in association with other bacteria, so they can not exist in pure culture.
As for me, I work at ecological topiks. One of aspects of my work is phyllosphere microflora. I work with unculturable microorganisms. And they really can not growth on agar plates.

Tony Rook
Tony Rook's picture
Cherry:

Cherry:

I believe my bias for phenotypic bacterial identification methodologies stems from my past experiences with mis-identification of environmental strains within a manufacturing setting. In my experience, carbon utilization methods such as the technology offered by Biolog had a lower rate of mis-identification of environmental strains. Much of this is due to the fact that early identification efforts were geared towards clinical strains and did not account for environmental strain uncertainity.

However, I do understand the benefits genotypic identification methodologies have - especially in regards to VBNC (viable but not culturable) organisms. As some studies demonstrate improved accuracy against clinical isolates - Comparison of Phenotypic and Genotypic Techniques forIdentification of Unusual Aerobic Pathogenic Gram-Negative Bacilli - I still believe phenotypic methods a very useful when applied to areas such as environmental monitoring.

But I also realize that there is never one method which gives you all the information you need. Each methodology (genotypic or phenotypic) has its pros and cons.