classification of bacteria according to bergey s manual pdf

If the taxa have already been described, named, and classi?ed, new characteristics may be added or existing characteristics may be reinterpreted to revise existing classi?cation, update it, or formulate a new one. If the organism is new, i.e., cannot be identi?ed as an existing taxon, it is named and described according to the rules of nomenclature and placed in an appropriate position in an existing classi?cation, i.e., a new species in either an existing or a new genus. T axonomic ranks Several levels or ranks are used in bacterial classi?cation. The highest rank is called a Domain. All procar- yotic organisms (i.e., bacteria) are placed within two Domains, Archaea and Bacteria. Phylum, class, order, family, genus, species, and subspecies are successively smaller, non-overlapping subsets of the Domain. The names of these subsets from class to sub- species are given formal recognition (have “standing in nomen- clature”). An example is given in Table 1. At present, neither the kingdom nor division are used for Bacteria. In addition to these formal, hierarchical taxonomic categories, informal or ver- nacular groups that are de?ned by common descriptive names are often used; the names of such groups have no of?cial stand- ing in nomenclature. Examples of such groups are: the procar- yotes, the spirochetes, dissimilator y sulfate- and sulfur-reducing bacteria, the methane-oxidizing bacteria, methanogens, etc. Species The basic and most important taxonomic group in bacterial systematics is the species. The concept of a bacterial species is less de?nitive than for higher organisms. This differ- ence should not seem surprising, because bacteria, being pro- caryotic organisms, differ markedly from higher organisms. Sex- uality, for example, is not used in bacterial species de?nitions because relatively few bacteria undergo conjugation. Likewise, morphologic features alone are usually of little classi?catory sig- ni?

• classification of bacteria according to bergey s manual pdf, classification of bacteria according to bergey s manual pdf template, classification of bacteria according to bergey s manual pdf free, classification of bacteria according to bergey s manual pdf download, classification of bacteria according to bergey s manual pdf file.

Volume 3 deals with all of the remaining, slightly different Gram-negative bacteria, along with the Archaea.The Trust also recognizes individuals who have made outstanding contributions to bacterial taxonomy by presentation of the Bergey Award and Bergey Medal, jointly supported by funds from the Trust and from Springer, the publishers of the Manual.The Williams and Wilkins Co., Baltimore, Md. British Library no. GBA561951. British Library no. GBA561951. British Library no. GBA561951. British Library no. GBA561951. British Library no. GBA561951. British Library no. GBA561951. Alternative views: Wikispecies. By using this site, you agree to the Terms of Use and Privacy Policy. Identi?cation is the practical use of a classi?cation scheme to determine the identity of an isolate as a member of an established taxon or as a member of a previously unidenti?ed species. Some 4000 bacterial species thus far described (and the tens of thousands of postulated species that remain to be described) exhibit great diversity. In any endeavor aimed at an understand- ing of large numbers of entities it is practical, if not essential, to arrange, or classify, the objects into groups based upon their similarities. Thus classi?cation has been used to organize the bewildering and seemingly chaotic array of individual bacteria into an orderly framework. Classi?cation need not be scienti?c. Mandel said that “like cigars,.Classi?cation and adequate description of bacteria require knowledge of their morphologic, biochemical, physiological, and genetic characteristics. As a science, taxonomy is dynamic and subject to change on the basis of available data. New ?ndings often necessitate changes in taxonomy, frequently resulting in changes in the existing classi?cation, in nomenclature, in criteria for identi?cation, and in the recognition of new species. The process of classi?cation may be applied to existing, named taxa, or to newly described organisms.

ne a species and the weight assigned to these characteristics frequently re?ected the interests and prejudices of the investigators who described the species. These practices probably led Cowan to state that “taxonomy.Edwards and Ewing (1962, 1986) were pioneers in establishing phenotypic principles for characterization, classi?cation and identi?cation of bacteria. They based classi?cation and identi- ?cation on the overall morphologic and biochemical pattern of a species, realizing that a single characteristic (e.g., pathogenicity, host range, or biochemical reaction) regardless of its importance was not a suf?cient basis for speciation or identi?cation. They employed a large number of biochemical tests, used a large and diverse strain sample, and expressed results as percentages. They also realized that atypical strains, when adequately studied, are often perfectly typical members of a given biogroup (biovar) within an existing species, or typical members of a new species. Although there is no similarity value that de?nes a tax- ospecies (species determined by numerical taxonomy), 80% sim- ilarity is commonly seen among strains in a given taxospecies. It has long been recognized that the most accurate basis for classi?cation is phylogenetic. Kluyver and van Niel (1936) stated that “many systems of classi?cation are almost entirely the out- come of purely practical considerations... (and) are often ul- timately impractical... ” They recognized that “taxonomic boundaries imposed by the intuition of investigators will always be somewhat arbitrar y—especially at the ultimate systematic unit, the species. One must create as many species as there are or- ganisms that differ in suf?ciently fundamental characters” and they realized that “the only truly scienti?c foundation of classi- ?cation is in appreciating the available facts from a phylogenetic view”. The data necessary to develop a natural (phylogenetic) species de?

cance because the relative morphologic simplicity of most procaryotic organisms does not provide much useful taxonomic information. Consequently, morphologic features are relegated to a less important role in bacterial taxonomy in comparison with the taxonomy of higher organisms. The term “species” as applied to bacteria has been de?ned as a distinct group of strains that have certain distinguishing features and that generally bear a close resemblance to one an- other in the more essential features of organization. (A strain is made up of the descendants of a single isolation in pure culture, and usually is made up of a succession of cultures ultimately Each species differs con- siderably and can be distinguished from all other species. One strain of a species is designated as the type strain; this strain serves as the name-bearer strain of the species and is the permanent example of the species, i.e., the reference specimen for the name. (See the chapter on Nomenclature for more de- tailed information about nomenclatural types). The type strain has great importance for classi?cation at the species level, be- cause a species consists of the type strain and all other strains that are considered to be suf?ciently similar to it as to warrant inclusion with it in the species. Any strain can be designated as the type strain, although, for new species, the ?rst strain isolated is usually designated. The type strain need not be a typical strain. The species de?nition given above is one that was loosely followed until the mid-1960s. Unfortunately, it is extremely sub- jective because one cannot accurately determine “a close resem- blance”, “essential features”, or how many “distinguishing fea- tures” are suf?cient to create a species. Species were often de- ?ned solely on the basis of relatively few phenotypic or mor- phologic characteristics, pathogenicity, and source of isolation. The choice of the characteristics used to de?

These methods have been shown to be com- parable (Grimont et al., 1980). An in-depth discussion of DNA hybridization methods has been presented by Grimont et al. (1980) and by Johnson (1985). C or less D T m. Both values must be considered” (Wayne et al., 1987). They further recommended that a genomospecies not be named if it cannot be differentiated from other ge- nomospecies on the basis of some phenotypic property. DNA relatedness provides a single species de?nition that can be ap- plied equally to all organisms and is not subject to phenotypic variation, mutations, or variations in metabolic or other plasmids. The major advantage of DNA relatedness is that it measures overall relatedness, and therefore the effects of atypical bio- chemical re- Escherichia hermannii Urea positive, KCN positive, citrate positive, cellobiose positive. Citrobacter amalonaticus actions, mutations, and plasmids are minimal since they affect only a very small percentage of the total DNA. Once genomospecies have been established, it is simple to determine which variable biochemical reactions are species spe- ci?c, and therefore to have an identi?cation scheme that is com- patible with the genetic concept of species. The technique is also extremely useful in determining the biochemical boundaries of a species, as exempli?ed for Escherichia coli in Table 2. The use of DNA relatedness and a variety of phenotypic characteristics in classifying bacteria has been called polyphasic taxonomy (Col- well, 1970), and seems to be the best approach to a valid de- scription of species. DNA relatedness studies have now been car- ried out on more than 10,000 strains representing some 2000 species and hundreds of genera, with, to our knowledge, no instance where other data invalidated the genomospecies de?- nition. Stackebrandt and Goebel (1994) reviewed new species de- scriptions published in the International Journal of Systematic Bac- teriology.

nition became available when DNA hybridization was utilized to determine relatedness among bacteria. DNA hybridization is based upon the ability of native (double- stranded) DNA to reversibly dissociate or be denatured into its two complementary single strands. Dissociation is accomplished at high temperature. Denatured DNA will remain as single strands when it is quickly cooled to room temperature after de- naturation. If it is then placed at a temperature between 25 and 30. C below its denaturation point, the complementary strains will reassociate to again form a double-stranded molecule that is extremely similar, if not identical, to native DNA (Marmur and Doty, 1961). This is the method used to determine DNA relatedness among bacteria. Perfectly complementar y sequences are not necessar y for hy- bridization; the degree of complementary required for hetero- duplex formation can be governed experimentally by changing the incubation temperature or the salt concentration. The percentage of unpaired bases within a heteroduplex is an indication of the degree of divergence present. One can approximate the amount of unpaired bases by comparing the thermal stability of the heteroduplex to the thermal stability of a homologous duplex. This is done by stepwise increases in tem- perature and measuring strand separation. The thermal stability is calculated as the temperature at which 50% of strand sepa- ration has occurred and is represented by the term “ T m(e) ”. The D T m values of heteroduplexes range from 0 (perfect pair- ing) to ? 20 ? C, with each degree of instability indicative of ap- proximately 1% divergence (unpaired bases). As DNA related- ness between two strains decreases, divergence usually increases. Two of these, free solution reassoci- ation with separation of single- and double-stranded DNA on hydroxyapatite (Brenner et al., 1982) and the S-1 endonuclease method (Crosa et al., 1973) are currently the most widely used for this purpose.

pestis, the plague bacillus. If one agrees that a true species de?nition is not possible, the genomospecies de?nition is still useful in providing a single, uni- versally applicable basis for designating species. To criticize DNA relatedness because results obtained using different methods may not be totally comparable seems some- what unjusti?ed. When compared, the most frequently used methods have given similar results. Obviously, one should be careful in comparing data from various laboratories, especially when different methods are used. However, this is at least equally true for sequence data and phenotypic tests. It is true that large amounts of DNA are required for the DNA relatedness protocols now used for taxonomic purposes, and that it is necessary to use radioactive isotopes. Efforts can and should be made to automate the system, to min- iaturize it, and to substitute nonradioactive compounds for the radioactive isotopes. With these improvements, the method will be available for use in virtually any laboratory. Even withoutthem, one can argue that DNA hybridization is more affordable and practical than a consensus classi?cation system in which several hundred tests must be done on each strain. It is noteworthy that bacterial species can be compared to higher organisms on a molecular basis using mol% G. When this is done, it is apparent that the bacterial species is much broader than that of its hosts. For ex- ample, humans and our closest relative, the chimpanzee ( Pan troglodytes ), show 98.4% relatedness by this technique (Sibley and Ahlquist, 1987; Sibley et al., 1990). Indeed, even lemurs, which exhibit 78% DNA relatedness with humans, would be included in the same species as humans if the de?nition of a bacterial species was used. Furthermore, none of the primates would be considered to be threatened species using the bacterial de?ni- tion. Likewise, the range of mol% G. C and the range of small subunit ribosomal RNA within E.

coli strains shows a similar result, namely, that the bacterial species is much broader than that of animals (Staley, 1999). One consequence of the broad bacterial species de?nition is that very few species have been described, fewer than 5000, com- pared with over a million animals. This has led some biologists to erroneously conclude that bacteria comprise only a minor part of the biological diversity on Earth (Mayr, 1998). In addition, with such a broad de?nition, not a single free-living bacterial species can be considered to be threatened with extinction (Staley, 1997). Therefore, biologists should realize, as mentioned earlier in this section, that the bacterial species is not at all equiv- alent to that of plants and animals. In summary, the genetic de?nition of a species, if not perfect, appears to be both reliable and stable. DNA relatedness studies have already resolved many instances of confusion concerning which strains belong to a given species, as well as for resolving taxonomic problems at the species level. It has not been replaced as the current reference standard. It should remain the standard, at least until another approach has been compared to it and shown to be comparable or superior. Subspecies A species may be divided into two or more sub- species based on consistent phenotypic variations or on geneti- cally determined clusters of strains within the species. There is evidence that the subspecies concept is phylogenetically valid on the basis of frequency distribution of D T m values. There are pres- ently essentially no guidelines for the establishment of subspecies, which, although frequently useful, are usually designated at the pleasure of the investigator. Subspecies is the lowest taxonomic rank that is covered by the rules of nomenclature and has of?cial standing in nomenclature. Infrasubspeci?

In 1987, 60% of species descriptions included DNA re- latedness studies, 10% were described on the basis of serologic tests, and 30% did not use these approaches. In 1993, 75% of species descriptions included DNA relatedness data, 8% used serology, and 3% used neither method. In the remaining 14%, 16S rRNA sequence analysis was the sole basis for speciation. As 16S rRNA sequence data have accumulated, the utility of this extremely powerful method for phylogenetic placement of bac- teria has become evident (Woese, 1987; Ludwig et al., 1998b). The number of taxonomists using 16S rRNA sequencing is or soon will be greater than the number using DNA hybridization (Stackebrandt and Goebel, 1994), and many of them were cre- ating species solely or largely on the basis of 16S rRNA sequence analysis. It soon became evident, however, that 16S rRNA se- quence analysis was frequently not sensitive enough to differ- entiate between closely related species (Fox et al., 1992; Stacke- brandt and Goebel, 1994). Stackebrandt and Goebel (1994) con- cluded that the genetic de?nition of 70% relatedness with 5% or less divergence within related sequences continues to be the best means of creating species. They concluded that 16S rRNA sequence similarity of less than 97% between strains indicates that they represent different species, but at 97% or higher 16S rRNA sequence similarity, DNA relatedness must be used to de- termine whether strains belong to different species. In view of these perceived problems, it has been recommended that the best solution to the species problem in the absence of a “gold standard”, which has not been provided by DNA relatedness, is a pragmatic polyphasic (consensus) tax- onomy that integrates all available data. For many other species only one or a few strains were tested—usually because that was the total number of strains available.

It is true that the 70% relatedness and 5% divergence values chosen to represent strains of a given species are arbitrar y, and that there is a “gray area” around 70% for some species. None- theless, these values were chosen on the basis of results obtained from multiple strains, usually 10 or more, of some 600 species studied in a number of different reference laboratories. There are few, if any cases, in which the species de?ned in this manner have been shown to be incorrect. The DNA relatedness approach has standardized the means of de?ning species by providing a single, universally applicable criterion. Since it has been successful, one must believe that it generates species that are compatible with the needs and beliefs of most bacteriologists. There are two areas in which genomo- species have actually or potentially caused problems. One of these is where two or more genomospecies cannot be separated phe- notypically. In this case it has been recommended that these genomospecies not be formally named (Wayne et al., 1987). Al- ternatively, especially if a name already exists for one of the ge- nomospecies, the others can be designated as subspecies. In this way there is no confusion at the species level and, one can, if one wishes, distinguish between the genomospecies using a ge- netic technique. The other “problem” is with nomenspecies that were split or lumped, usually on the basis of pathogenicity or phytopathogenic host range. These include species in the genera Bordetella, Mycobacterium, Brucella, Shigella, Klebsiella, Neisseria, Yer- sinia, Vibrio, Clostridium, and Erwinia. In some of these cases ( Kleb- siella, Erwinia ) the classi?cation has been changed and is now In the others, changes have not yet been proposed or, as in the case of Yersinia pestis and Y ersinia pseudotuberculosis, which are the same genomospecies, the change was rejected by the Judicial Commission because of possible danger to public health if there was confusion regarding Y.

c Ranks Ranks below subspecies, such as biovars, serovars, phagovars, and pathovars, are often used to indicate groups of strains that can be distinguished by some spe- cial character, such as antigenic makeup, reactions to bacterio- phage, etc. Such ranks have no of?cial standing in nomenclature, but often have great practical usefulness. A list of some common infrasubspeci?c categories is given in T able 3. Genus All species are assigned to a genus, which can be functionally de?ned as one or more species with the same general phenotypic characteristics, and which cluster together on the basis of 16S rRNA sequence. In this regard, bacteriologists con- form to the binomial system of nomenclature of Linnaeus in which the organism is designated by its combined genus and species names. There is not, and perhaps never will be, a satis- factory de?nition of a genus, despite the fact that most new genera are designated substantially on the basis of 16S rRNA sequence analysis. In almost all cases, genera can be differenti- ated phenotypically, although a considerable degree of ?exibility in genus descriptions is often needed. Considerable subjectivity continues to be involved in designating genera, and considerable reclassi?cation, both lumping and splitting, is still occurring at the genus level. Indeed, what is perceived to be a single genus by one systematist may be perceived as multiple genera by an- other. Higher Taxa Classi?catory relationships at the familial and higher levels are even less certain than those at the genus level, and descriptions of these taxa are usually much more general, if they exist at all. Families are composed of one or more genera that share phenotypic characteristics and that should be consis- tent from a phylogenetic standpoint (16S rRNA sequence clus- tering) as well as from a phenotypic basis. M AJOR DEVELOPMENTS IN BACTERIA L CLASSIFICATION A century elapsed between Antony van Leeuwenhoek’s discovery of bacteria and Mu.

A less detailed treatment of early clas- si?cations can be found in the sixth edition of the Manual,i n which post-1923 developments were emphasized. Two primary dif?culties beset early bacterial classi?cation sys- tems. First, they relied heavily upon morphologic criteria. For example, cell shape was often considered to be an extremely important feature. Thus, the cocci were often classi?ed together in one group (family or order). In contrast, contemporary schemes rely much more strongly on 16S rRNA sequence simi- larities and physiological characteristics. For example, the fer- mentative cocci are now separated from the photosynthetic cocci, which are separated from the methanogenic cocci, which are in turn separated from the nitrifying cocci, and so forth; with the 16S rRNA sequences of each group generally clustered together. Secondly, the pure culture technique which revolutionized bac- teriology was not developed until the latter half of the 19th cen- tury. In addition to dispelling the concept of “polymorphism”, this technical development of Robert Koch’ s laborator y had great impact on the development of modern procedures in bac- terial systematics. Pure cultures are analogous to herbarium spec- imens in botany. However, pure cultures are much more useful because they can be (a) maintained in a viable state, (b) sub- cultured, (c) subjected inde?nitely to experimental tests, and (d) shipped from one laborator y to another. A natural outgrowth of the pure culture technique was the establishment of type strains of species which are deposited in repositories referred to as “culture collections” (a more accurate term would be “strain collections” ). These type strains can be obtained from culture collections and used as reference strains to duplicate and extend the observations of others, and for direct comparison with new isolates.

Before the development of computer-assisted numerical tax- onomy and subsequent taxonomic methods based on molecular biology, the traditional method of classifying bacteria was to char- acterize them as thoroughly as possible and then to arrange them according to the intuitive judgment of the systematist. Although the subjective aspects of this method resulted in classi?cations that were often drastically revised by other systematists who were likely to make different intuitive judgments, many of the ar- rangements have survived to the present day, even under scrutiny by modern methods. One explanation for this is that the system- atists usually knew their organisms thoroughly, and their intuitive judgments were based on a wealth of information. Their data, while not computer processed, were at least processed by an active mind to give fairly accurate impressions of the relationships existing between organisms. Moreover, some of the characteris- tics that were given great weight in classi?cation were, in fact, highly correlated with many characteristics. This principle of cor - relation of characteristics appears to have started with Winslow and Winslow (1908), who noted that parasitic cocci tended to grow poorly on ordinary nutrient media, were strongly Gram- positive, and formed acid from sugars, in contrast to saprophytic cocci which grew abundantly on ordinary media, were generally only weakly Gram-positive and formed no acid. This division of the cocci studied by the Winslows (equivalent to the present genus Micrococcus (the saprophytes) and the genera Staphylococcus and Streptococcus (the parasites) has held up reasonably well even to the present day. Other classi?cations have not been so fortunate. A classic ex- ample of one which has not is that of the genus “Paracolobactrum”. This genus was proposed in 1944 and is described in the Seventh Edition of Bergey’ s Manual in 1957.

It was created to contain certain lactose-negative members of the family Enterobacteriaceae. Because of the importance of a lactose-negative reaction in iden- ti?cation of enteric pathogens (i.e., Salmonella and Shigella ), the reaction was mistakenly given great taxonomic weight in classi- ?cation as well. However, for the organisms placed in “Paraco- lobactrum”, the lactose reaction was not highly correlated with other characteristics. In fact, the organisms were merely lactose- negative variants of other lactose-positive species; for example “Paracolobactrum coliform” resembled E. coli in ever y way except in being lactose-negative. Absurd arrangements such as this even- tually led to the development of more objective methods of clas- si?cation, i.e., numerical taxonomy, in order to avoid giving great weight to any single characteristic. Phylogenetic Classi?cations We have already discussed the im- pact of DNA relatedness at the species level. Unfortunately, this method is of marginal value at the genus level and of no value above the genus level because the extent of divergence of total bacterial genomes is too great to allow accurate assessment of relatedness above the species level. At the genus level and above, phylogenetic classi?cations, especially as based on 16S rRNA se- quence analysis, have revolutionized bacterial taxonomy (see Overview: A Phylogenetic Backbone and Taxonomic Framework for Procaryotic Systematics by Ludwig and Klenk). Of?cial Classi?cations A signi?cant number of bacteriologists have the impression that there is an “of?cial classi?cation” and that the classi?cation presented in Bergey’ s Manual represents this “of?cial classi?cation”. It is important to correct that misim- pression. A classi?cation that is of little use to bacteriologists, regardless of how ?ne a scheme or who devised it, will soon be ignored or signi?cantly modi?ed.

The editors of Bergey’ s Manual and the authors of each chapter make substantial efforts to provide a classi?cation that is as accurate and up-to-date as possible, how- ever it is not and cannot be “of?cial”. It also seems worthwhile to emphasize something that has often been said before, viz.Special methods noted by the committee that show great promise for taxonomists include sequencing of housekeeping genes, DNA pro?ling and the application of DNA arrays. Other recommendations were made to base the species description on more than a single strain, to follow guidelines established by the subcommittees of ICSP (Interna- tional Committee on Systematics of Prokaryotes) for minimal characterization of a species, and to recognize the importance of phenotypic properties for species identi?cation. Also, because electronic databases are an immensely important aid for the in- ternational community of bacterial systematists, the committee recommended the development of standards for electronic ex- change of taxonomic information. A CKNOWLEDGMENTS This chapter is dedicated to the memor y of John L. Johnson, a consum- mate scientist, trusted colleague and friend, whose search for truth was uncompromising and unhindered by personal ego. Strain: Historically, this has meant a microbial isolate, although the definition is not well-suited to microbial community studies.. Strain-level epidemiology of microbial communities and the human microbiome Article Full-text available Aug 2020 Yan Yan Long H. Nguyen Eric A. Franzosa Curtis Huttenhower The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome.