Bacterial genus and species

Bacterial genus and species DEFAULT

Research can be hard enough without worrying about how to use microbial nomenclature or scientific names of bacteria accurately. Writing bacteria names in a research article can be a big challenge for scientists, as the guidelines change to reflect new discoveries. Moreover, Latin names may be confusing.  In the first article of this series, we discussed effective tips on writing scientific names of plants and animals. This article will give you an overview of the biggest issues researchers encounter in using microbial nomenclature and some tips to keep you on track.

How are Bacteria Named?

The International Committee on Systematics of Prokaryotes (ICSP) has created guidelines that explain the proper nomenclature or naming system for bacteria. This system is known as the Bacteriological Code. A bacterium has a binomial name that consists of two parts: the genus name, which indicates which genus it belongs to and the species epithet.

Related: Go on a reading marathon and learn the important aspects of academic writing. Check out this section now!

When referring to a bacterium in a paper, the writer should underline or italicize the names in the text. After writing the complete name of a microorganism in the first mention, the genus name can be shortened to just the capital letter.

  • For example, Moraxella bovis can be written M. bovis.

The ICSP recommends spelling out the entire name of any bacteria again in the summary of your publication.

When discussing unnamed species, the abbreviation “sp.” is used to refer to a single unnamed species.  Whereas “spp.” written after a genus refers to more than one unnamed species.

  • For example, Moraxella sp. would be used to discuss one unnamed species of Moraxella.

Bacteria are often divided into subspecies, which are indicated by subdivisions such as biovar, chemoform, chemovar, cultivar, morphovar, pathovar, serovar, and state.

These subdivisions should be written in plain text preceding an additional italicized or underlined name. For example, “Rhizobium leguminosarum biovar viciae” would be correctly written as Rhizobium leguminosarum biovar viciae.

Common Issues in the Use of Microbial Nomenclature

However, there are some common issues that researchers encounter when using microbial nomenclature. The first, as you might have guessed, is that different types of bacteria might appear to be the same when their names are abbreviated.

M. bovis could indicate Moraxella bovis, Mycoplasma bovis, or Mycobacterium bovis.

In this case, the author should simply take care to either avoid using abbreviations if they might be confused, or be sure to clearly state which bacterium is being discussed.

Other issues that researchers encounter with microbial nomenclature are more complex. While the Bacteriological Code is often interpreted as the “official” list of valid names for bacteria, the Code only provides guidelines on how bacteria should be named. This allows for disagreement, discovery, and evolution in scientific research. For example, one group of researchers might classify a bacterium to genus A. Similarly, another group of researchers might conduct different research and conclude that the same bacterium belongs to genus B. Continuing with our previous example of the bovis species, one bacterium might be referred to as A bovis in one article and B bovis in another.

How Do I know If the Microbial Nomenclature I’m Using is Valid?

Many researchers mistakenly believe that the most recently published name is the “correct” name. In fact, as we saw above, this is not the case. A name must be published in an article in the International Journal of Systematic and Evolutionary Microbiology. It may also be published elsewhere if announced in the Validation Lists. Microbial nomenclature is, in other words, a matter of scientific judgment and consensus.

For example, Helicobacter pylori was immediately accepted as a replacement for Campylobacter pylori by the scientific community, whereas Tatlockia micdadei has not generally been accepted as a replacement for Legionella micdadei.

Finally, the ICSP does not give specific guidelines for how to indicate taxa after subspecies, such as strain designation. Strain designation should follow the genus and species and is generally a combination of numbers and letters.

For example, you might write Helicobacter pylori K164:K7, with K164:K7 indicating the specific strain of bacteria used in your work.

When you are in doubt about the correct usage microbial nomenclature in your writing, your first stop should be The International Code of Nomenclature of Bacteria (1990 Revision). Stay up to date on relevant publications in your field and be aware of any disagreements or new discoveries regarding the classification of bacteria. Finally, remember that valid names are a matter of scientific judgment and consensus.

Was this article helpful? What other problems or issues have you encountered in using microbial nomenclature in your writing? Let us know in the comments!

Manuscript drafting tips

Sours: https://www.enago.com/academy/write-scientific-names-in-a-research-paper-bacteria/

Defining bacterial species in the genomic era: insights from the genus Acinetobacter

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BMC Microbiologyvolume 12, Article number: 302 (2012) Cite this article

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Abstract

Background

Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data.

Results

In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species.

Conclusion

We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical.

Background

In the early eighteenth century, Linnaeus provided the first workable hierarchical classification of species, based on the clustering of organisms according to their phenotypic characteristics [1]. In The Origin of Species[2], Darwin added phylogeny to taxonomy, while also emphasizing the arbitrary nature of biological species: “I look at the term species as one arbitrarily given for the sake of convenience to a set of individuals resembling each other.” The reality and utility of the species concept continues to inform the theory and practice of biology and a stable species nomenclature underpins the diagnosis and monitoring of pathogenic microorganisms [3–5].

Traditional taxonomic analyses of plants and animals rely on morphological characteristics. However, this approach cannot easily be applied to unicellular microorganisms. In the latter half of the twentieth century, it became clear that bacteria could be grouped into taxonomic clusters based on stable phenotypic characters (e.g. cellular morphology and composition, growth requirements and other metabolic traits) that could be measured reliably in the laboratory. In the 1960s and 1970s, Sneath and Sokal exploited improved technical and statistical methods to develop a numerical taxonomy, which revealed discrete phenotypic clustering within many bacterial genera [6].

Such phenotypic approaches soon faced competition from genotypic approaches, such as DNA base composition (mol% G+C content) [7] and whole-genome DNA-DNA hybridization (DDH); the latter remains the gold standard in bacterial taxonomy [8]. Within this framework, Wayne et al.[8] recommended that “a species generally would include strains with approximately 70% or greater DNA-DNA relatedness”. However, few laboratories now perform DNA-DNA hybridization assays as these are onerous and technically demanding when compared to the rapid and easy sequencing of small signature sequences, such as the 16S ribosomal RNA gene. This shift has led to an updated species definition: “a prokaryotic species is considered to be a group of strains that are characterized by a certain degree of phenotypic consistency, showing 70% of DNA–DNA binding and over 97% of 16S ribosomal RNA (rRNA) gene-sequence identity” [9].

Most recently, whole-genome sequencing has delivered new taxonomic metrics—for example, average nucleotide identity (ANI), calculated from pair-wise comparisons of all sequences shared between any two strains. ANI exhibits a strong correlation with DDH values [10], with an ANI value of ≥ 95% corresponding to the traditional 70% DDH threshold [10].

Despite the ready availability of genome sequence data, microbial taxonomy remains a conservative discipline. When defining a bacterial species, most modern microbial taxonomists use a polyphasic approach, whereby a bacterial species represents “a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity with respect to many independent characteristics, and is diagnosable by a discriminative phenotypic property” [11]. Although the polyphasic approach is pragmatic and widely applicable, it has drawbacks. It relies on phenotypic information, which in turn relies on growth, usually in pure culture, in the laboratory, which may not be achievable for many bacterial species [12]. It also relies on techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern genome sequencing [4, 13, 14].

We, like others, are therefore driven to consider whether, in the genomic era, bacterial taxonomy could, and should, abandon phenotypic approaches and rely exclusively on analyses of genome sequence data [4, 10, 14–18]. However, such an approach brings fresh conceptual and methodological challenges. Several forces shape the evolution of bacterial genomes: the steady accumulation of point mutations or small insertions/deletions (indels), potentially giving rise to a tree-like phylogeny; the influence of homologous recombination in some lineages, obscuring such diversification; and the key role of gene gain/loss, particularly the pervasive influence of horizontal gene transfer, which, if substantial, could obliterate phylogenetic signals. These forces act with different strength on different parts of the genome and on different bacterial lineages. For example, sequences from a single gene such as the 16S rRNA gene have been shown to fail to capture the true genome-wide divergence between two strains [19–21]. Additionally, it may be expected that the various novel sequence-based metrics would be affected differently by different evolutionary forces. This raises potential problems with the consistency of classification (results may or may not be consistent across the metrics) and backwards compatibility (classification may or may not correspond to already named species within a genus). In this work, we wished to explore these issues on a well-characterized and important bacterial genus, Acinetobacter.

The genus Acinetobacter was first proposed by Brisou and Prévot in 1954 [22]; however, it was not until Baumann et al.[23] published their comprehensive study based on nutritional and biochemical properties that this designation became more widely accepted. In 1974 the genus was listed in Bergey’s Manual of Systematic Bacteriology with the description of a single species, A. calcoaceticus. To date, there are 27 species described in the genus (http://www.bacterio.cict.fr/a/acinetobacter.html). To fall within genus Acinetobacter, isolates must be Gram-negative, strictly aerobic, non-fermenting, non-fastidious, non-motile, catalase-positive, oxidase-negative and have a DNA G+C content of 38-47% [24]. Some isolates within the genus are naturally competent resulting in intra-species recombination [25–27]. Environmental isolates, such as A. calcoaceticus PHEA-2 and Acinetobacter oleivorans DR1, have attracted interest because they are able to metabolize a diverse range of compounds [28–30]. However, most research on the genus has focused on clinical isolates, particularly from the species A. baumannii. This species has shown an astonishing ability to acquire antibiotic resistance genes and some strains are now close to being untreatable [31, 32]. Worryingly, the incidence of serious infections caused by other Acinetobacter species is also increasing [33]. Genotypic approaches have suggested that A. baumannii forms a complex—the A. baumannii/calcoaceticus or ACB complex—with three other species A. calcoaceticus, A. nosocomialis and A. pittii. However, it remains very difficult, if not impossible, for a conventional reference laboratory to distinguish these species on phenotypic grounds alone [34]. Techniques such as AFLP and amplified 16S rRNA gene restriction analysis (ARDRA) can be used to identify species within the Acinetobacter genus and the ACB complex [35–38]; however, these techniques are too laborious to be carried out in a routine laboratory [24].

Given the general difficulty in defining bacterial species and the ready availability of genome sequence data, we sought to evaluate a range of novel genotypic and genome-based metrics for species delineation. In light of discussed obstacles and the on-going public health concern, we believe that genus Acinetobacter provides a timely test case to evaluate the validity and robustness of these sequence-based approaches. In pursuit of this goal, we generated a diverse and informative set of thirteen new draft genome sequences, representing ten species, and we analyzed the whole-genome sequences from a total of 38 strains belonging to the genus.

Results and discussion

General genome characteristics

The genomes of thirteen Acinetobacter strains, including seven type strains, were sequenced to draft quality using 454 sequencing (Table 1). The A. bereziniae strain was found to have the largest genome size within the genus (~ 5 Mb), while the strain with the smallest genome (~2.9 Mb) belonged to the species A. parvus, which is known to have a reduced metabolic repertoire compared to other Acinetobacter species [39]. These thirteen genomes were considered alongside twenty-five other publicly available genome sequences from the genus Acinetobacter (see Additional file 1).

Full size table

A. ursingiiDSM 16037 genome characteristics

The species A. ursingii was first described by Nemec et al. in 2001 [40]. We have genome sequenced the type strain DSM 16037, which was isolated from a blood culture taken from an inpatient in Prague, Czech Republic in 1993 [40]. In the genome we identified 3252 good-quality CDSs (minimum length 50 codons of which less than 2% are stop codons); 270 of these do not have homologs in any of the other 37 Acinetobacter strains in this study. Depth of coverage was generally consistent, apart from two contigs which showed 3.5 times greater-than-average coverage. Scrutiny of the larger of these two contigs (9.4 kb) identified CDSs that are predicted to encode plasmid replication and mobilization proteins. This contig also contains homologs of sul1 and uspA genes, which are often associated with A. baumannii resistance islands [41].

A. lwoffiiNCTC 5866 genome characteristics

A. lwoffii was first described by Audureau in 1940 under the name Moraxella lwoffii[22], but was later moved to genus Acinetobacter by Baumann et al.[23]. In 1986, Bouvet and Grimont emended the description of the species to designate strain NCTC 5866 the type strain [42]. We identified 3005 good-quality CDSs in the NCTC 5866 genome, of which 229 do not have homologs in any of the Acinetobacter genomes examined in this study. Investigation of these CDSs revealed two putative prophages, ca. 44.5 and 25.6 kb. Interestingly, many of the CDSs found in these two putative prophages are also present in a recently sequenced environmental Acinetobacter strain P8-3-8 (not included in this study) isolated from the intestine of a blue-spotted cornetfish caught in Vietnam [43].

Among the remaining strain-specific CDSs, we identified fourteen that are nearly identical to tra genes found in PHH1107, a low GC content plasmid isolated from pig manure [44]. The tra homologs are distributed on two contigs, one of which has a GC content (37%) lower than the genome mean (43%).

A. parvusDSM 16617 genome characteristics

Strain DSM 16617 is the type strain for A. parvus isolated from the ear of an outpatient from Pribram, Czech Republic in 1996 [45]. We identified 2681 good-quality CDSs in the DSM 16617 genome, 179 of which do not have homologs in any of the remaining 37 genomes. Analysis with Prophinder [46] identified one 39kb putative prophage containing phage-related genes homologs to putative phage-related genes found in A. baumannii and A. oleivorans DR1. We identified an 8kb contig with 2.5 times higher than average depth of coverage, which contains homologs to phage related genes.

A. bereziniaeLMG 1003 genome characteristics

Strain LMG 1003 is the type strain for A. bereziniae, a recently named species by Nemec et al., which has been isolated from various human, animal and environmental sources [47]. We identified 4480 good-quality CDSs in the genome, with 1061 strain-specific CDSs (no homologs in the rest of the 37 genomes). This is a considerably higher percentage, 24%, than in other Acinetobacter strains (see Additional file 1). Many of the strain-specific CDSs form clusters of four or more CDSs, with the largest cluster containing 49 consecutive CDSs, of which 45 are strain-specific. Twenty-one CDSs in this cluster have no significant similarity to proteins in the non-redundant protein database.

Depth of coverage analysis revealed several contigs with higher than average value. One such contig has 5 times greater coverage compared to the rest of the genome, which suggests it is a mobile element. It contains a CDS homologous to the sul1 gene often found in A. baumannii resistance islands [41].

A. radioresistensDSM 6976 genome characteristics

A. radioresistens strain DSM 6976 was isolated in 1979 from cotton sterilized by γ-radiation and is the type strain for the species [48]. We identified 2964 good-quality CDSs in the genome, of which 188 do not have homologs in any of the remaining 37 genomes.

A comparison with two previously sequenced A. radioresistens, SK82 and SH164, reveals that the three strains share 2458 CDSs (about 83% of the average number of CDSs in these three strains), 43 of which were not found in the remaining 35 Acinetobacter genomes. Among these there is a homolog of the metE gene, and two genes involved in the degradation of benzoate, an aromatic compound which is known to support the growth of a number of A. radioresistens[49]. Though the three strains are quite similar, we identified 143 CDSs in DSM 6976 which are absent in SK82 and SH164, but do have homologs in other Acinetobacter genomes. Within this group there is a genomic island containing nine genes related to fructose metabolism and a cluster of four CDSs predicted to encode for type IV pilin proteins.

Phylogenetic relationships within genus Acinetobacter

Stackebrandt and Goebel suggested that bacterial species can be delineated using 16S rRNA gene sequences: according to their criteria, when two aligned sequences exhibit ≥ 97% identity, the isolates from which they originate are deemed to belong to the same species [50]. However, when we extracted 16S rRNA gene sequences from the Acinetobacter genomes in this study, we found that these criteria gave inconsistent results. For example, the 16S rRNA genes from the type strains of A. baumannii and A. radioresistens exhibit 97% sequence identity, suggesting they should be in the same species. Similarly, sequences from the type strains of A. calcoaceticus and A. lwoffii show 97.6% identity, again suggesting they should be classified in the same species. Recent studies by Keswani and Whitman [51] and Stackebrandt and Ebers [52] have suggested a revised cut-off value of ≈ 99% 16S rRNA identity for species delineation. We found that even using this stricter cut-off, we were not able to find evidence for delineating the type strains of A. calcoaceticus and A. pittii (99.3%), and the type strain of A. pittii from A. nosocomialis strains NCTC 8102 and RUH2624 (99.5%). Furthermore, when a phylogenetic tree is constructed from 16S rRNA sequence data, the monophyly of the ACB complex was not preserved and the confidence values for most branches fall below 70% (Figure 1). Similar problems with using 16S rRNA gene sequences to resolve species have been reported in other genera [11, 21].

Phylogenetic tree based on the 16S rRNA gene sequences. The tree was built for 37 Acinetobacter isolates (A. baumannii 6014059 was excluded as only partial 16S sequence was identified) and rooted at midpoint. Outgoing branches of a node are depicted in black if bootstrap support (100 replicates) at the node is ≥ 70%; in grey otherwise. The tree is significantly divergent from previous published results, e.g. the monophyly of the ACB complex is not preserved.

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Given the highly conserved nature of the 16S rRNA gene sequences, we attempted to reconstruct a phylogeny based on more comprehensive gene set -- the core genome of the genus. We found 911 orthologous coding sequences (CDSs) present in all thirty-eight strains, representing around a quarter of the average number of CDSs per strain. However, concerned that naïve use of this dataset might lead to problems due to homologous recombination, we selected a subset of 127 single-copy CDSs that showed with no signs of recombination according to three different measures (see Methods). These were concatenated, aligned and used to derive a phylogenomic tree (Figure 2). Interestingly, a tree constructed with no recombination filtering was nearly identical to the tree based on recombination-free CDSs (see Additional file 2).

Phylogenetic tree based on 127 CDSs present in all 38 strains. The 127 CDSs used for this tree are present in all strains, have no paralogs and show no signs of recombination. The tree is rooted at midpoint. Outgoing branches of a node are depicted in black if bootstrap support (100 replicates) at the node is ≥ 70%; in grey otherwise.

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This core genome tree generally supports the monophyletic status of the named species within the genus, with three exceptions: A. baumannii NCTC 7422 belongs in a deep-branching lineage with the A. parvus type strain DSM 16617, A. nosocomialis NCTC 10304 clusters within A. baumannii and A. calcoaceticus PHEA-2 is closer to the three A. pittii strains than to the other two A. calcoaceticus strains. The first two strains have been genome-sequenced as part of this study and our results suggest they have been misclassified in the culture collection. PHEA-2 is an isolate from industrial wastewater that was genome-sequenced by Xu et al.[53]. Our core genome tree and comparisons of 16S rRNA gene sequences show PHEA-2 to be closer to the three A. pittii strains than to the other two A. calcoaceticus strains, suggesting it too has been misclassified. Interestingly, the previously unclassified strain DR1 sits closest to the two A. calcoaceticus strains, while ATCC 27244 is closest to the species A. haemolyticus.

Once such reclassifications are taken into account, our core genome phylogenetic tree is consistent with the currently accepted genus taxonomy and also supports the monophyly of the ACB complex and of each of its four constituent species. Within A. baumannii, two lineages, international clones I and II, previously identified by comparative cell envelope protein profiling, ribotyping and AFLP genomic fingerprinting [53] are present as monophyletic groups in our tree. The tree obtained from the core genome is similar to a tree obtained from a recently described approach based on 42 ribosomal genes [15] (see Additional file 3).

Rapid genomic approaches to species delineation

Phylogenetic approaches are processor-intensive. We therefore evaluated genetic relatedness among the 38 strains using three rapid distance-based oligonucleotide and gene content approaches that avoid time-consuming calculations: the previously mentioned ANI, as well as K-string [54] and genome fluidity [55] approaches.

ANI relies on the identification of alignable stretches of nucleotide sequence in genome pairs, followed by a scoring and averaging of sequence identity, ignoring any divergent regions. The topology of the dendogram based on ANI analysis (Figure 3) is congruent with our core genome phylogenetic tree, confirming the misclassifications and new relationships already identified, while also showing the two international clones as separate lineages within A. baumannii.

The Average Nucleotide Identity (ANI) dendogram for the 38 strains. The vertical dashed line represents the 95% species cutoff value proposed by Goris et al. (10).

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The K-string composition approach [54] is based on oligopeptide content analysis of predicted proteomes. The divergence dendogram for K=5 (see Additional file 4) generally agrees with the results from the phylogenetic tree and ANI dendogram at species level. However, the major problem is that the K-string approach places A. baumannii SDF outside the ACB complex, probably reflecting the considerable difference in gene repertoires between this drug-sensitive strain and all other genome-sequenced A. baumannii strains.

Genome fluidity provides a measure of the dissimilarity of genomes evaluated at the gene level [55]. A dendogram based on genomic fluidity (see Additional file 5) significantly differs from the results obtained with other techniques: A. baumannii SDF again sits outside the ACB complex, A. nosocomialis strains NCTC 8102 and RUH2624 now sit within the A. baumannii clade and PHEA-2 sits not with the A. pittii strains but with DR1 and the other A. calcoaceticus strains. We also performed pair-wise comparison of the gene content of the 38 strains, calculating the amount of the CDSs shared by each pair of strains (see Additional file 6). While strains from the same species generally share at least 80% of their CDSs, we found strains from different species exhibiting similar ratios. For example, A. calcoaceticus RUH2202 shares more than 80% of its CDS repertoire with DR1 and various A. nosocomialis, A. baumannii, A. pittii strains; PHEA-2 and DR1 share 88.1% of their CDSs. Based on gene content only, A. baumannii SDF is distinct from all other A. baumannii strains in our study (sharing at most 71.6% of its CDSs), which explains its placement in the K-string and genomic fluidity dendograms (see Additional files 4 and 5, respectively). These results indicate a potentially significant level of horizontal gene transfer among Acinetobacter species and illustrate an inability to delineate species based on gene content comparison only.

These findings suggest that ANI analyses provide results that are compatible with traditional and phylogenetic classifications, whereas K-string and genome fluidity approaches appear to be too strongly influenced by the effects of horizontal gene transfer to be consistent with previously accepted approaches.

Defining species in Acinetobacteron the basis of whole-genome analyses

The congruence of the phylogenetic tree and ANI dendogram with each other and with existing species definitions provides confidence that these techniques are fit for purpose in delineating species in the absence of phenotypic data. Furthermore, as Goris et al. suggest, the ANI approach provides a handy numerical cut-off at 95% identity to demarcate species boundaries, which corresponds to the 70% DDH value [10]. When we applied this cut-off to our dataset, we were able to classify 37 of the strains into thirteen previously named species.

In line with the likely misclassification of strains, we observed that A. nosocomialis NCTC 10304 shares phylogenetic history and exhibits pair-wise ANI values greater than 95% with all 14 sequenced A. baumannii strains, thus confirming it should be designated A. baumannii NCTC 10304. Similar arguments apply for A. calcoaceticus PHEA-2 (new designation A. pittii PHEA-2) and A. sp. ATCC 27244 (A. haemolyticus ATCC 27244). However, the strain NCTC 7422 appears to be distinctive enough to represent new species. While the traditional polyphasic approach to taxonomy demands additional phenotypic characterization before these species can be named, on the basis of the analyses presented here, we propose the species name Acinetobacter bruijnii sp. nov. (N. L. gen. masc. n. bruijnii, of Bruijnius, named after Nicolaas Govert de Bruijn, Dutch mathematician) for strain NCTC 7422 and all future strains that are monophyletic and show ≥ 95% ANI to this strain.

It is interesting to note that our results based on core genome and ANI analyses differ from those based on AFLP patterns [56]; notably in the latter A. haemolyticus and A. junii do not cluster together nor does the cluster form a sister branch to the ACB complex; also A. johnsonii does not appear on the same deep-branch as A. lwoffii. This observation suggests that although AFLP is adept at species resolution, it appears to be unsuitable for phylogenetic analysis.

Several recent studies report alternative genomic approaches to bacterial taxonomy and species identification. These include in silico multilocus sequence analysis (MLSA), average amino acid identity (AAI) and ribosomal multilocus sequence typing (rMLST), which have been used to delineate species in the genera Neisseria, Vibrio and Mycoplasma[17, 18, 57]. Although MLSA can be used to infer phylogeny, this approach suffers from arbitrariness in choice of in genes which varies from one taxon to the next. Our proposed approach, core-genome phylogeny, can be considered an extension of MLSA and rMLST. However, as it is based on all shared CDSs in a given genus, it makes use of all potentially informative sequence sites. ANI, like AAI, measures pair-wise similarities between genome sequences but provides better resolution of species and sub-species [58, 59].

Conclusions

The aim of this study has been to determine, using the genus Acinetobacter as a test case, whether genome sequence data alone are sufficient for the delineation and even definition of bacterial species. To this end, we explored the applicability of two broad approaches: sequence-based phylogenies for single and multiple gene and distance-based methods that include gene content comparisons (K-string and genomic fluidity) and whole-genome sequence similarities (ANI). We have found that a phylogenetic analysis of the genus Acinetobacter based on 16S rRNA gene sequences provides unreliable and uninformative results. By contrast, a core genome phylogenetic tree provides robust, informative results that are backwards compatible with the existing taxonomy.

Among the distance metrics, we found that approaches using gene content (K-string and genomic fluidity) led to anomalous conclusions, e.g., placing the SDF strain outside of the A. baumannii cluster, presumably because they are affected by horizontal gene transfer. In contrast, the easy-to-compute ANI results are congruent with the core genome phylogeny and traditional approaches. Using the core genome phylogeny and ANI approach, we found three misclassifications, one of which represents new species. These findings illustrate the need to genome-sequence all strains archived in culture collections, which is likely to become technically and economically feasible in the near future.

We believe a combination of core genome phylogenetic analysis and ANI provides a feasible method for bacterial species delineation, in which species are defined as monophyletic groups of isolates that exhibit at least 95% pair-wise ANI to each other. This approach combines a theoretically rigorous approach (sequence phylogeny) with a pragmatic metric (ANI) that provides a numerical cut-off that is backwards compatible and has been shown to be applicable to a diverse group of bacteria [10, 60].

Our sequence-based approach has several desirable characteristics. Firstly, it is capable of resolving the inconsistency in classification of genomospecies. For example, our results confirm the recent assignment of genomospecies 3 and 13TU to Latin binomials A. pittii and A. nosocomialis, respectively. Secondly, it provides a scalable and uniform approach that works for both culturable and non-culturable species, solving the problem in classifying non-culturable organisms, in an era when whole-genome sequences of such organisms can be recovered relatively easily via metagenomics or single-cell genomics. Thirdly, our approach is faster and cheaper than traditional taxonomic methods, as well as being easily replicable and transferable among research institutions. Finally a method that combines phylogeny and pragmatism falls in line with Darwin’s vision of classification, as stated in the conclusion of Origin of Species: “Our classification will come to be, as far as they can be so made, genealogies…” [2].

Methods

Strain selection and growth conditions

Details of Acinetobacter strains used in this study are listed in Additional file 1. Acinetobacter baumannii W6976 and W7282 were provided by Drs. Mike Hornsey and David Wareham at Barts and The London NHS Trust, whilst the remaining strains were obtained from the UK, German and Belgium culture collections. Sequenced isolates were cultured in Nutrient broth or Tryptic soy medium at 25°C or 30°C. DNA was extracted from single colony cultures using Qiagen 100/G Genomic-tips and quantified using Quant-iT PicoGreen dsDNA kits (Invitrogen). DNA was stored at 4°C.

Genomic sequencing and annotation

DNA from thirteen isolates was sequenced by 454 GS FLX pyrosequencing (Roche, Branford, CT, USA) according to the standard protocol for whole-genome shotgun sequencing, producing an average of 450bp fragment reads. Draft genomes were assembled from flowgram data using Newbler 2.5 (Roche). The resulting contigs were annotated using the automated annotation pipeline on the xBASE server [61]. The genome sequences of the thirteen newly sequenced strains have been deposited in GenBank as whole genome shotgun projects (Table 1).

Ortholog computation

We computed the set of all orthologs within the 38 strains in our study with OrthoMCL [62] which performs a bidirectional best hit search in the amino-acid space, followed by a subsequent clustering step (percentMatchCutoff = 70, evalueCutoff = 1e-05, I = 1.5). Predicted are 7,334 clusters of orthologous groups (COGs) containing 124,870 coding sequences (CDSs), which represents 95.7% of all good-quality CDSs (length at least 50 codons of which less than 2% are stop codons).

Core genome phylogenetic tree construction

Using the orthologs data, we extracted the genus core genome, i.e. the set of COGs which are present in each of the 38 strains (911 COGs). We filtered this set to exclude COGs containing paralogs and obtained a set of 827 single-copy COGs. The nucleotide gene sequences of each single-copy COG were aligned using MUSCLE 3.8.31 [63] with default parameters and the alignments were trimmed for quality, leading and trailing blocks using GBlocks 0.91b [64] with default parameters. After excluding 8 COGs with trimmed length < 50 bp, we screened the remaining 819 COGs for possible evidence of recombination using the PHI [65], MaxChi [66] and Neighbour similarity score [67] tests implemented in PhiPack (http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar) using 1000 permutations, window size = 50 bp and p-value < 0.05. To facilitate a more robust phylogeny construction, we selected only the 127 recombination-free COGs for which none of the three tests found evidence of recombination. The trimmed alignments of the 127 COGs were concatenated and used to build the tree by the approximately maximum-likelihood FastTree 2 [68] with 100 bootstrap replicates (created using SEQBOOT program from the PHYLIP package [69]. The resulting tree was visualized using FigTree (http://tree.bio.ed.ac.uk/software/figtree) and rooted at the mid-point.

The trees based on the 16S, the 819 single-copy COGs (no recombination filtering) and the 42 ribosomal genes were built in the same manner – multiple alignment of the nucleotide sequences with MUSCLE, trimming with GBlocks, and constructing bootstrapped trees (100 replicates) with FastTree 2, rooting them at mid-point.

Average nucleotide identity (ANI)

The ANI analysis was based on whole-genome data using the method proposed by Goris et al.[10]. Briefly, for each genome pair, one of the genomes was chosen as a query and split into consecutive 500 bp fragments. These were then used to interrogate the second genome, designated the reference, using BLASTn [70] (X = 150, q = -1 F= F). For each query, the hit with the highest bit-score was selected and if the alignment exhibited at least 70% identity and over 70% of the query fragment length, the hit was retained for further evaluation. The ANI score was computed as the mean identity of the retained hits. Based on the pair-wise ANI values, we compiled a distance matrix to represent the ANI divergence (which is defined as 100% - ANI) between the strains and used it to compute the ANI divergence dendogram with the hierarchical clustering package hcluster 0.2.0 adopting the complete linkage algorithm (http://pypi.python.org/pypi/hcluster).

Gene repertoire comparison (K-string and genomic fluidity)

K-string analysis was based on the method proposed by Qi et al.[54]; for each proteome, its composition vector was computed by extracting the frequency of overlapping amino acid strings of length K and filtering out the random mutation background using a Markov model. The divergence between two genomes was computed by calculating the cosine function of the angle between the pair’s composition vectors. The dendogram based on the pair-wise K-string distances was built as for ANI. The pair-wise genomic fluidity for each pair of genomes was computed using the ortholog data as suggested by Kislyuk et al.[55]. The dendogram was built as for ANI and K-string.

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Sours: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-12-302
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The Taxonomic Scheme

Bacterial taxonomy is the rank-based classification of bacteria.

Learning Objectives

Outline the factors that play a role in the classification of bacterial taxonomy

Key Takeaways

Key Points

  • Bacterial species differ amongst each other based on several characteristics, allowing for their identification and classification.
  • Gram staining results are most commonly used as a classification tool.
  • In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.

Key Terms

  • bacteria: A type, species, or strain of bacterium.
  • taxonomy: the academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Each group is given a rank and groups of a given rank can be aggregated to form a super group of higher rank and thus create a hierarchical classification.
  • Gram stain: Gram staining (or Gram’s method) is a method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).It is based on the chemical and physical properties of their cell walls. Primarily, it detects peptidoglycan, which is present in a thick layer in Gram positive bacteria. A Gram positive results in a purple/blue color while a Gram negative results in a pink/red color.

Taxonomic Systems

Bacterial taxonomy is the rank-based classification of bacteria. In the scientific classification established by Carl von Linné, each distinct species is assigned to a genus using a two-part binary name (for example, Homo sapiens). This distinct species is then in turn placed within a lower level of a hierarchy of ranks. These ranks range in ascending scale from family to suborder, and upward to order, subclass, class, division/phyla, kingdom and domain.

In the currently accepted scientific classification of Life, there are three domains of microorganisms: the Eukaryotes, Bacteria and Archaea, The different disciplines of study refer to them using differing terms to speak of aspects of these domains, however, though they follow similar principles. Thus botany, zoology, mycology, and microbiology use several different conventions when discussing these domains and their subdivisions. In zoology, for example, there are type specimens, whereas in microbiology there are type strains.

Historical Challenges of Classification

Despite there being little agreement on the major subgroups of the Bacteria, gram staining results were commonly used as a classification tool. As an example, Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. Until the advent of molecular phylogeny the Kingdom Prokaryotae was divided into four divisions, a classification scheme still formally followed by Bergey’s manual of systematic bacteriology.The various species differ amongst each other based on several characteristics determined by gram staining, which allowed their identification and classification. Major groups of this system include: Gracilicutes (gram negative); Firmacutes (gram positive); Mollicutes (gram variable, e.g. Mycoplasma); and Mendocutes (uneven gram stain, “metlynogenic bacteria” now known as the Archaea).

Molecular Classification

In the Molecular era of classification, Carl Woese, who is regarded as the forerunner of the molecular phylogeny revolution, argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two billion years ago, and that co-evolution may have been occurring between members of these groups. It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are “extreme environments” in archaeal terms, and organisms that live in cooler environments appeared only later. Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote’s only surviving meaning is “not a eukaryote”, limiting its value.

With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were erroneously believed to be relics of ancient bacteria. Thus, though Woese identified three primary lines of descent the Archaebacteria, the Eubacteria and the Urkaryotes, the latter now represented by the nucleocytoplasmic component of the Eukaryotes. these lineages were formalised into the rank Domain (regio in Latin) which divided Life into 3 domains: the Eukaryota, the Archaea and the Bacteria. This scheme is still followed today.

In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.

image

Prokaryote phylogeny diagram: Phylogenetic tree showing the relationship between the archaea and other forms of life. Eukaryotes are colored red, archaea green and bacteria blue.

The Diagnostic Scheme

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.

Learning Objectives

Outline the various types of diagnostic methods used to diagnose a microbial infection

Key Takeaways

Key Points

  • Diagnosis of infectious disease is nearly always initiated by medical history and physical examination.
  • Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.
  • Diagnostic methods include: Microbial culture, microscopy, biochemical tests and molecular diagnostics.

Key Terms

  • Diagnosis: Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation.
  • infectious: Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs and/or symptoms of disease) resulting from the infection, presence, and growth of pathogenic biological agents in an individual host organism.
  • pathogens: A pathogen or infectious agent (colloquially known as a germ) is a microorganism (in the widest sense, such as a virus, bacterium, prion, or fungus) that causes disease in its host. The host may be an animal (including humans), a plant, or even another microorganism.

The Challenge of Diagnosis

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified. The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is benign.

Primary and Opportunistic Pathogens

Among the almost infinite varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depends upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. Clinicians therefore classify infectious microorganisms or microbes according to the status of host defenses – either as primary pathogens or as opportunistic pathogens.

An Orderly Process

Diagnosis of infectious disease is nearly always initiated by taking a medical history and performing a physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype. Other techniques, such as X-rays, CAT scans, PET scans or NMR, are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.

Diagnostic methods include microbial culture, microscopy, biochemical tests and molecular diagnostics:

  • Microbiological culture is a principal tool used to diagnose infectious disease. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium.
  • Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques.
  • Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species, the detection of fermentation products is commonly used in bacterial identification. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media.
  • Molecular diagnostics using technologies based upon the polymerase chain reaction ( PCR ) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids in order to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known, if they are not already.

The Species Concept in Microbiology

The number of species of bacteria and archaea is surprisingly small, despite their early evolution, genetic, and ecological diversity.

Learning Objectives

Describe the concept of polyphasic species

Key Takeaways

Key Points

  • The differences in species concepts between the Bacteria and macro-organisms, the difficulties in growing/characterising in pure culture (a prerequisite to naming new species, vide supra), and extensive horizontal gene transfer blurring the distinction of species makes differentiation difficult.
  • The most commonly accepted definition is the polyphasic species definition, which takes into account both phenotypic and genetic differences.
  • A quicker diagnostic threshhold is to separate species as less than 70% DNA -DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity.

Key Terms

  • bacteria: Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet.
  • species: In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring.
  • DNA hybridization: Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily.
image

Biological classification: The hierarchy of biological classification’s eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.

Judging Species in an Asexual Context

Bacteria divide asexually and for the most part do not show regionalisms. In other words, “Everything is everywhere. ” Accordingly, the concept of species which works best for animals, becomes entirely a matter of judgement.

The approximately 5000 species of bacteria and archaea constitute a surprisingly small number, considering their relatively early evolution, genetic diversity, and ability to reside in all ecosystems on Earth. The reason for this numerical peculiarity lies in the differences in species concepts between the bacteria and macro-organisms and in the difficulties in growing and characterizing in pure culture (a prerequisite to naming new species, vide supra). In addition, the extensive amount of horizontal gene transfer among microorganisms results in the blurring of the distinctions between species among microorganisms.

The most commonly accepted definition is the polyphasic species definition,which takes into account both phenotypic and genetic differences. However, a quicker diagnostic ad hoc threshhold to separate species is less than 70% DNA-DNA hybridization, which corresponds to less than 97% 16S DNA sequence identity. It has been noted that if this were applied to animal classification the order of Primates would be considered a single species.

The International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) is a peer-reviewed journal that acts as the official international forum for the publication of new prokaryotic taxa. If a species is published in a different peer review journal, the author can submit a request to IJSEM with the appropriate description. If the information is correct, the new species will be featured in the Validation List of IJSEM.

Classification and Nomenclature

Nomenclature is the set of rules and conventions that govern the names of taxa.

Learning Objectives

Recognize the factors involved with general classification and nomenclature used for microorganism classification

Key Takeaways

Key Points

  • The names ( nomenclature ) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code).
  • Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms.
  • Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter, with the exception of epithets for species and subspecies.

Key Terms

  • nomenclature: binomial nomenclature (also called binominal nomenclature or binary nomenclature) is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just “binomial”), a binomen or a scientific name; more informally it is also called a Latin name.
  • prokaryotes: ( /proʊkæri.oʊts/, pro-kah-ree-otes or /proʊkæriəts/, pro-kah-ree-əts) a group of organisms whose cells lack a cell nucleus (karyon), or any other membrane-bound organelles. Most prokaryotes are unicellular organisms, although a few such as myxobacteria have multicellular stages in their life cycles.
  • Bacteriological code: The International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank. As such it is one of the Nomenclature Codes of biology.

Nomenclature is the set of rules and conventions which govern the names of taxa. It is the application of formal rules for naming organisms. Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype. Despite there being no official and complete classification of prokaryotes, the names (nomenclature) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code), a book which contains general considerations, principles, rules, and various notes and advises in a similar fashion to the nomenclature codes of other groups.

image

International Journal of Systematic and Evolutionary Microbiology (IJSEM): The IJSEM covers the naming of new bacteria and how they fit evolutionarily.

The taxa which have been correctly described are reviewed in Bergey’s manual of Systematic Bacteriology, which aims to aid in the identification of species and is considered the highest authority. An online version of the taxonomic outline of bacteria and archaea is available. Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter with the exception of epithets for species and subspecies. Despite it being common in zoology, tautonyms (e.g. Bison bison) are not acceptable and names of taxa used in zoology, botany or mycology cannot be reused for bacteria (Botany and Zoology do share names).

For bacteria, valid names must have a Latin or Neolatin name and can only use basic latin letters (w and j inclusive, see History of the Latin alphabet for these), consequently hyphens, accents and other letters are not accepted and should be translitterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be translitterated into the Latin alphabet.

Many species are named after people, either the discoverer or a famous person in the field of microbiology, for example Salmonella is after D.E. Salmon, who discovered it (albeit as “Bacillus typhi”). For the generic epithet, all names derived from people must be in the female nominative case, either by changing the ending to -a or to the diminutive -ella, depending on the name. For the specific epithet, the names can be converted into either adjectival form (adding -nus (m.), -na (f.), -num (n.) according to the gender of the genus name) or the genitive of the latinised name.

Many species (the specific epithet) are named after the place they are present or found (e.g. Borrelia burgdorferi). Their names are created by forming an adjective by joining the locality’s name with the ending -ensis (m. or f.) or ense (n.) in agreement with the gender of the genus name, unless a classical Latin adjective exists for the place. However, names of places should not be used as nouns in the genitive case.

For the Prokaryotes (Bacteria and Archaea) the rank kingdom is not used (although some authors refer to phyla as kingdoms). If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriological Code the name is formed by the addition of an appropriate suffix to the stem of the name of the type genus. For subclass and class the reccomendation from is generally followed, resulting in a neutral plural, however a few names do not follow this and instead keep into account Graeco-Latin grammar (e.g. the female plurals Thermotogae, Aquificae, and Chlamydiae, the male plurals Chloroflexi, Bacilli, and Deinococci, and the Greek plurals Spirochaetes, Gemmatimonadetes, and Chrysiogenetes).

Phyla are not covered by the Bacteriological Code, however, the scientific community generally follows the Ncbi and Lpsn taxonomy, where the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria, and Proteobacteria, whose names do not stem from a genus name. The higher taxa proposed by Cavalier-Smith are generally disregarded by the molecular phylogeny community (vide supra).

Sours: https://courses.lumenlearning.com/boundless-microbiology/chapter/classification-of-microorganisms/

Bacterial Library

USMS Bacterial Library

Bacteria are prokaryotic (no organized nucleus), single-celled (0.2-10 um) organisms.

Bacteria are divided into five basic groups based on morphology (shape): coccus, bacillus, spiral, coryneform, and filamentous. When bacteria are Gram-stained, they may be further classified as Gram-positive, Gram-negative, or Gram-variable depending on the ability of their cell walls to hold a specific type of stain. Gram-positive bacteria stain blue-purple and Gram-negative bacteria stain red.

Bacterial names are based on the binomial system: the first name is the genus, the second name is the species. When written, the genus name is capitalized and the species name is not. Both genus and species names are italicized (e.g., Escherichia coli).  A genus is a group of related species.  A species is a group of microorganisms that have similar genotypic and phenotypic characteristics.

Sours: https://www.usmslab.com/microbiology-lab-resources-library/bacterial-library/

Genus and species bacterial

Bacterial taxonomy

Bacterial taxonomy is the taxonomy, i.e. the rank-based classification, of bacteria.

In the scientific classification established by Carl Linnaeus,[1] each species has to be assigned to a genus (binary nomenclature), which in turn is a lower level of a hierarchy of ranks (family, suborder, order, subclass, class, division/phyla, kingdom and domain). In the currently accepted classification of life, there are three domains (Eukaryotes, Bacteria and Archaea),[2] which, in terms of taxonomy, despite following the same principles have several different conventions between them and between their subdivisions as they are studied by different disciplines (botany, zoology, mycology and microbiology). For example, in zoology there are type specimens, whereas in microbiology there are type strains.

Diversity[edit]

Main article: Bacteria

Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. The various species differ amongst each other based on several characteristics, allowing their identification and classification. Examples include:

  • Phylogeny: All bacteria stem from a common ancestor and diversified since, and consequently possess different levels of evolutionary relatedness (see Bacterial phyla and Timeline of evolution)
  • Metabolism: Different bacteria may have different metabolic abilities (see Microbial metabolism)
  • Environment: Different bacteria thrive in different environments, such as high/low temperature and salt (see Extremophiles)
  • Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bilayers) or bilayer composition (see Bacterial cellular morphologies, Bacterial cell structure)

History[edit]

First descriptions[edit]

Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design.[3] He called them "animalcules" and published his observations in a series of letters to the Royal Society.[4][5][6]

Early described genera of bacteria include Vibrio and Monas, by O. F. Müller (1773, 1786), then classified as Infusoria (however, many species before included in those genera are regarded today as protists); Polyangium, by H. F. Link (1809), the first bacterium still recognized today; Serratia, by Bizio (1823); and Spirillum, Spirochaeta and Bacterium, by Ehrenberg (1838).[7][8]

The term Bacterium, introduced as a genus by Ehrenberg in 1838,[9] became a catch-all for rod-shaped cells.[7]

Early formal classifications[edit]

Main article: Monera

Tree of Life in Generelle Morphologie der Organismen(1866)[10]

Bacteria were first classified as plants constituting the class Schizomycetes, which along with the Schizophyceae (blue green algae/Cyanobacteria) formed the phylum Schizophyta.[11]

Haeckel in 1866 placed the group in the phylum Moneres (from μονήρης: simple) in the kingdom Protista and defines them as completely structureless and homogeneous organisms, consisting only of a piece of plasma.[10] He subdivided the phylum into two groups:[10]

  • die Gymnomoneren (no envelope)
    • Protogenes – such as Protogenes primordialis, now classed as a eukaryote and not a bacterium
    • Protamaeba – now classed as a eukaryote and not a bacterium
    • Vibrio – a genus of comma shaped bacteria first described in 1854[12])
    • Bacterium – a genus of rod shaped bacteria first described in 1828, that later gave its name to the members of the Monera, formerly referred to as "a moneron" (plural "monera") in English and "eine Moneren"(fem. pl. "Moneres") in German
    • Bacillus – a genus of spore-forming rod shaped bacteria first described in 1835[13]
    • Spirochaeta – thin spiral shaped bacteria first described in 1835[13]
    • Spirillum – spiral shaped bacteria first described in 1832[14]
    • etc.
  • die Lepomoneren (with envelope)
    • Protomonas – now classed as a eukaryote and not a bacterium. The name was reused in 1984 for an unrelated genus of Bacteria[15]
    • Vampyrella – now classed as a eukaryote and not a bacterium

The classification of Ferdinand Cohn (1872) was influential in the nineteenth century, and recognized six genera: Micrococcus, Bacterium, Bacillus, Vibrio, Spirillum, and Spirochaeta.[7]

The group was later reclassified as the Prokaryotes by Chatton.[16]

The classification of Cyanobacteria (colloquially "blue green algae") has been fought between being algae or bacteria (for example, Haeckel classified Nostoc in the phylum Archephyta of Algae[10]).

in 1905, Erwin F. Smith accepted 33 valid different names of bacterial genera and over 150 invalid names,[17] and Vuillemin, in a 1913 study,[18] concluded that all species of the Bacteria should fall into the genera Planococcus, Streptococcus, Klebsiella, Merista, Planomerista, Neisseria, Sarcina, Planosarcina, Metabacterium, Clostridium, Serratia, Bacterium, and Spirillum.

Cohn[19] recognized four tribes: Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil[20] recognized the kingdom Monera with two phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae (three orders), Myxobacteriae (one order), and Spirochetae (one order). Bisset[21] distinguished 1 class and 4 orders: Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales. Walter Migula's system,[22] which was the most widely accepted system of its time and included all then-known species but was based only on morphology, contained the three basic groups Coccaceae, Bacillaceae, and Spirillaceae, but also Trichobacterinae for filamentous bacteria. Orla-Jensen[23] established two orders: Cephalotrichinae (seven families) and Peritrichinae (presumably with only one family). Bergey et al.[24] presented a classification which generally followed the 1920 Final Report of the Society of American Bacteriologists Committee (Winslow et al.), which divided class Schizomycetes into four orders: Myxobacteriales, Thiobacteriales, Chlamydobacteriales, and Eubacteriales, with a fifth group being four genera considered intermediate between bacteria and protozoans: Spirocheta, Cristospira, Saprospira, and Treponema.

However, different authors often reclassified the genera due to the lack of visible traits to go by, resulting in a poor state which was summarised in 1915 by Robert Earle Buchanan.[25] By then, the whole group received different ranks and names by different authors, namely:

Furthermore, the families into which the class was subdivided changed from author to author and for some, such as Zipf, the names were in German and not in Latin.[29]

The first edition of the Bacteriological Code in 1947 sorted out several problems.[30][example needed]

A. R. Prévot's system[31][32]) had four subphyla and eight classes, as follows:

  • Eubacteriales (classes Asporulales and Sporulales)
  • Mycobacteriales (classes Actinomycetales, Myxobacteriales, and Azotobacteriales)
  • Algobacteriales (classes Siderobacteriales and Thiobacteriales)
  • Protozoobacteriales (class Spirochetales)

Main article: Kingdom (biology) § Summary

Informal groups based on Gram staining[edit]

Despite there being little agreement on the major subgroups of the Bacteria, Gram staining results were most commonly used as a classification tool. Consequently, until the advent of molecular phylogeny, the Kingdom Prokaryotae was divided into four divisions,[41] A classification scheme still formally followed by Bergey's manual of systematic bacteriology for tome order[42]

  • Gracilicutes (gram-negative)
    • Photobacteria (photosynthetic): class Oxyphotobacteriae (water as electron donor, includes the order Cyanobacteriales=blue-green algae, now phylum Cyanobacteria) and class Anoxyphotobacteriae (anaerobic phototrophs, orders: Rhodospirillales and Chlorobiales
    • Scotobacteria (non-photosynthetic, now the Proteobacteria and other gram-negative nonphotosynthetic phyla)
  • Firmacutes [sic] (gram-positive, subsequently corrected to Firmicutes[43])
    • several orders such as Bacillales and Actinomycetales (now in the phylum Actinobacteria)
  • Mollicutes (gram variable, e.g. Mycoplasma)
  • Mendocutes (uneven gram stain, "methanogenic bacteria", now known as the Archaea)

Molecular era[edit]

"Archaic bacteria" and Woese's reclassification[edit]

Main article: Archaea

Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms.[45][46] However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria.[47] In any case, it is thought that viruses and archaea began relationships approximately two billion years ago, and that co-evolution may have been occurring between members of these groups.[48] It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared only later.[49] Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote's only surviving meaning is "not a eukaryote", limiting its value.[50]

With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were (erroneously) believed to be relics of ancient bacteria[51] thus Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, identified three primary lines of descent: the Archaebacteria, the Eubacteria, and the Urkaryotes, the latter now represented by the nucleocytoplasmic component of the Eukaryotes.[52] These lineages were formalised into the rank Domain (regio in Latin) which divided Life into 3 domains: the Eukaryota, the Archaea and the Bacteria.[2]

Subdivisions[edit]

Main article: Bacterial phyla

In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several additions are still used today.[53][54]

Opposition[edit]

While the three domain system is widely accepted,[55] some authors have opposed it for various reasons.

One prominent scientist who opposes the three domain system is Thomas Cavalier-Smith, who proposed that the Archaea and the Eukaryotes (the Neomura) stem from Gram positive bacteria (Posibacteria), which in turn derive from gram negative bacteria (Negibacteria) based on several logical arguments,[56][57] which are highly controversial and generally disregarded by the molecular biology community (c.f. reviewers' comments on,[57]e.g. Eric Bapteste is "agnostic" regarding the conclusions) and are often not mentioned in reviews (e.g.[58]) due to the subjective nature of the assumptions made.[59]

However, despite there being a wealth of statistically supported studies towards the rooting of the tree of life between the Bacteria and the Neomura by means of a variety of methods,[60] including some that are impervious to accelerated evolution—which is claimed by Cavalier-Smith to be the source of the supposed fallacy in molecular methods[56]—there are a few studies which have drawn different conclusions, some of which place the root in the phylum Firmicutes with nested archaea.[61][62][63]

Radhey Gupta's molecular taxonomy, based on conserved signature sequences of proteins, includes a monophyletic Gram negative clade, a monophyletic Gram positive clade, and a polyphyletic Archeota derived from Gram positives.[64][65][66] Hori and Osawa's molecular analysis indicated a link between Metabacteria (=Archeota) and eukaryotes.[67] The only cladistic analyses for bacteria based on classical evidence largely corroborate Gupta's results (see comprehensive mega-taxonomy).

James Lake presented a 2 primary kingdom arrangement (Parkaryotae + eukaryotes and eocytes + Karyotae) and suggested a 5 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, Halobacteria, and Eubacteria) based on ribosomal structure and a 4 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, and Photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (Photocyta), methanogenesis (Methanobacteria), and sulfur respiration (Eocyta).[68][69][70] He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria.[71]

Authorities[edit]

See also: International Code of Nomenclature of Bacteria and LPSN

Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms.[72]

Nomenclature authority[edit]

Main article: Bacteriological Code

Despite there being no official and complete classification of prokaryotes, the names (nomenclature) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria (Bacteriological Code), a book which contains general considerations, principles, rules, and various notes, and advises[73] in a similar fashion to the nomenclature codes of other groups.

Classification authorities[edit]

Main article: Bergey's Manual of Systematic Bacteriology

The taxa which have been correctly described are reviewed in Bergey's manual of Systematic Bacteriology, which aims to aid in the identification of species and is considered the highest authority.[42] An online version of the taxonomic outline of bacteria and archaea (TOBA) is available [1].

Main article: LPSN

List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database which currently contains over two thousand accepted names with their references, etymologies and various notes.[74]

Description of new species[edit]

Main article: International Journal of Systematic and Evolutionary Microbiology

The International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) is a peer reviewed journal which acts as the official international forum for the publication of new prokaryotic taxa. If a species is published in a different peer review journal, the author can submit a request to IJSEM with the appropriate description, which if correct, the new species will be featured in the Validation List of IJSEM.

Distribution[edit]

Main article: Culture collection

Microbial culture collections are depositories of strains which aim to safeguard them and to distribute them. The main ones being:[72]

Collection Acronym Name Location
ATCCAmerican Type Culture CollectionManassas, Virginia
NCTCNational Collection of Type CulturesPublic Health England, United Kingdom
BCCMBelgium Coordinated Collection of MicroorganismsGhent, Belgium
CIPCollection d'Institut Pasteur Paris, France
DSMZDeutsche Sammlung von Mikroorganismen und ZellkulturenBraunschweig, Germany
JCMJapan Collection of MicroorganismsSaitama, Japan
NCCBNetherlands Culture Collection of Bacteria Utrecht, Netherlands
NCIMB National Collection of Industrial, Food and Marine BacteriaAberdeen, Scotland
ICMPInternational Collection of Microorganisms from PlantsAuckland, New Zealand
CECTSpanish Type Culture CollectionValencia, Spain

Analyses[edit]

[icon]

This section needs expansion. You can help by adding to it. (May 2011)

Bacteria were at first classified based solely on their shape (vibrio, bacillus, coccus etc.), presence of endospores, gram stain, aerobic conditions and motility. This system changed with the study of metabolic phenotypes, where metabolic characteristics were used.[75] Recently, with the advent of molecular phylogeny, several genes are used to identify species, the most important of which is the 16S rRNA gene, followed by 23S, ITS region, gyrB and others to confirm a better resolution. The quickest way to identify to match an isolated strain to a species or genus today is done by amplifying it's 16S gene with universal primers and sequence the 1.4kb amplicon and submit it to a specialised web-based identification database, namely either Ribosomal Database Project[2], which align the sequence to other 16S sequences using infernal, a secondary structure bases global alignment,[76][77] or ARB SILVA, which aligns sequences via SINA (SILVA incremental aligner), which does a local alignment of a seed and extends it [3].[78]

Several identification methods exists:[72]

New species[edit]

The minimal standards for describing a new species depend on which group the species belongs to. c.f.[79]

Candidatus[edit]

Main article: candidatus

Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a Bacteriology Culture Collection. It is an interim taxonomic status for noncultivable organisms. e.g. "Candidatus Pelagibacter ubique"

Species concept[edit]

Main article: Species problem

Bacteria divide asexually and for the most part do not show regionalisms ("Everything is everywhere"), therefore the concept of species, which works best for animals, becomes entirely a matter of judgement.

The number of named species of bacteria and archaea (approximately 13,000)[80] is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The reason for this is the differences in species concepts between the bacteria and macro-organisms, the difficulties in growing/characterising in pure culture (a prerequisite to naming new species, vide supra) and extensive horizontal gene transfer blurring the distinction of species.[81]

The most commonly accepted definition is the polyphasic species definition, which takes into account both phenotypic and genetic differences.[82] However, a quicker diagnostic ad hoc threshold to separate species is less than 70% DNA–DNA hybridisation,[83] which corresponds to less than 97% 16S DNA sequence identity.[84] It has been noted that if this were applied to animal classification, the order primates would be a single species.[85] For this reason, more stringent species definitions based on whole genome sequences have been proposed.[86]

Pathology vs. phylogeny[edit]

Ideally, taxonomic classification should reflect the evolutionary history of the taxa, i.e. the phylogeny. Although some exceptions are present when the phenotype differs amongst the group, especially from a medical standpoint. Some examples of problematic classifications follow.

Escherichia coli: overly large and polyphyletic[edit]

Main article: Escherichia coli

In the family Enterobacteriaceae of the class Gammaproteobacteria, the species in the genus Shigella (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) from an evolutionary point of view are strains of the species Escherichia coli (polyphyletic), but due to genetic differences cause different medical conditions in the case of the pathogenic strains.[87] Confusingly, there are also E. coli strains that produce Shiga toxin known as STEC.

Escherichia coli is a badly classified species as some strains share only 20% of their genome. Being so diverse it should be given a higher taxonomic ranking.[88] However, due to the medical conditions associated with the species, it will not be changed to avoid confusion in medical context.

Bacillus cereus group: close and polyphyletic[edit]

Main article: Bacillus cereus

In a similar way, the Bacillus species (=phylum Firmicutes) belonging to the "B. cereus group" (B. anthracis, B. cereus, B . thuringiensis, B. mycoides, B. pseudomycoides, B. weihenstephanensis and B. medusa) have 99-100% similar 16S rRNA sequence (97% is a commonly cited adequate species cut-off) and are polyphyletic, but for medical reasons (anthrax etc.) remain separate.[89]

Yersinia pestis: extremely recent species[edit]

Main article: Yersinia pestis

Yersinia pestis is in effect a strain of Yersinia pseudotuberculosis, but with a pathogenicity island that confers a drastically different pathology (Black plague and tuberculosis-like symptoms respectively) which arose 15,000 to 20,000 years ago.[90]

Nested genera in Pseudomonas[edit]

Main article: Azotobacter

In the gammaproteobacterial order Pseudomonadales, the genus Azotobacter and the species Azomonas macrocytogenes are actually members of the genus Pseudomonas, but were misclassified due to nitrogen fixing capabilities and the large size of the genus Pseudomonas which renders classification problematic.[75][91][92] This will probably rectified in the close future.

Nested genera in Bacillus[edit]

Main article: Bacillus

Another example of a large genus with nested genera is the genus Bacillus, in which the genera Paenibacillus and Brevibacillus are nested clades.[93] There is insufficient genomic data at present to fully and effectively correct taxonomic errors in Bacillus.

Agrobacterium: resistance to name change[edit]

Main article: Agrobacterium

Based on molecular data it was shown that the genus Agrobacterium is nested in Rhizobium and the Agrobacterium species transferred to the genus Rhizobium (resulting in the following comp. nov.: Rhizobium radiobacter (formerly known as A. tumefaciens), R. rhizogenes, R. rubi, R. undicola and R. vitis)[94] Given the plant pathogenic nature of Agrobacterium species, it was proposed to maintain the genus Agrobacterium[95] and the latter was counter-argued[96]

Nomenclature[edit]

Main article: Binomial Nomenclature

See also: Latin grammar and Ancient Greek grammar

Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter with the exception of epithets for species and subspecies. Despite it being common in zoology, tautonyms (e.g. Bison bison) are not acceptable and names of taxa used in zoology, botany or mycology cannot be reused for Bacteria (Botany and Zoology do share names).

Nomenclature is the set of rules and conventions which govern the names of taxa. The difference in nomenclature between the various kingdoms/domains is reviewed in.[97]

For Bacteria, valid names must have a Latin or Neolatin name and can only use basic latin letters (w and j inclusive, see History of the Latin alphabet for these), consequently hyphens, accents and other letters are not accepted and should be transliterated correctly (e.g. ß=ss).[98] Ancient Greek being written in the Greek alphabet, needs to be transliterated into the Latin alphabet.

When compound words are created, a connecting vowel is needed depending on the origin of the preceding word, regardless of the word that follows, unless the latter starts with a vowel in which case no connecting vowel is added. If the first compound is Latin then the connecting vowel is an -i-, whereas if the first compound is Greek, the connecting vowel is an -o-.[99]

For etymologies of names consult LPSN.

Rules for higher taxa[edit]

For a comparison with other nomenclature codes, see Taxonomic rank § Terminations of names.

For the Prokaryotes (Bacteria and Archaea) the rank kingdom is not used[100] (although some authors refer to phyla as kingdoms[72])

If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriological Code the name is formed by the addition of an appropriate suffix to the stem of the name of the type genus.[73] For subclass and class the recommendation from[101] is generally followed, resulting in a neutral plural, however a few names do not follow this and instead keep into account graeco-latin grammar (e.g. the female plurals Thermotogae, Aquificae and Chlamydiae, the male plurals Chloroflexi, Bacilli and Deinococci and the greek plurals Spirochaetes, Gemmatimonadetes and Chrysiogenetes).[102]

Rank Suffix Example
Genus -ae (Elusimicrobiae)
Subtribe (disused) -inae (Elusimicrobiinae)
Tribe (disused) -eae (Elusimicrobiieae)
Subfamily -oideae (Elusimicrobioideae)
Family -aceae Elusimicrobiaceae
Suborder -ineae (Elusimicrobineae)
Order -ales Elusimicrobiales
Subclass -idae (Elusimicrobidae)
Class -ia Elusimicrobia
Phylum see text Elusimicrobia

Phyla endings[edit]

See also: Bacterial phyla

Phyla are not covered by the Bacteriological code,[102] however, the scientific community generally follows the Ncbi and Lpsn taxonomy, where the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria and Proteobacteria, whose names do not stem from a genus name. The higher taxa proposed by Cavalier-Smith[56] are generally disregarded by the molecular phylogeny community (e.g.[58]) (vide supra).

For the Archaea the suffix -archaeota is used.[103] For bacterial phyla it was proposed that the suffix -bacteria be used for phyla.[104]

Consequently for main phyla the name of the phyla is the same as the first described class:

Whereas for others where the -ia suffix for class is used regardless of grammar they differ:

An exception is the phylum Deinococcus–Thermus, which bears a hyphenated pair of genera—only non-accented Latin letters are accepted for valid names, but phyla are not officially recognised.[103] More recently it has been proposed to amend the Bacteriological Code to specify -aeota as the ending for bacterial phyla and that the names be derived from a type class within the phylum.[105] This would require the following changes:

Names after people[edit]

Main articles: List of bacterial genera named after personal names and List of bacterial genera named after mythological figures

Several species are named after people, either the discoverer or a famous person in the field of microbiology, for example Salmonella is after D.E. Salmon, who discovered it (albeit as "Bacillus typhi"[106]).[107]

For the generic epithet, all names derived from people must be in the female nominative case, either by changing the ending to -a or to the diminutive -ella, depending on the name.[99]

For the specific epithet, the names can be converted into either adjectival form (adding -nus (m.), -na (f.), -num (n.) according to the gender of the genus name) or the genitive of the latinised name.[99]

Names after places[edit]

Main articles: List of bacterial genera named after geographical names and List of bacterial genera named after institutions

Many species (the specific epithet) are named after the place they are present or found (e.g. Thiospirillum jenense). Their names are created by forming an adjective by joining the locality's name with the ending -ensis (m. or f.) or ense (n.) in agreement with the gender of the genus name, unless a classical Latin adjective exists for the place. However, names of places should not be used as nouns in the genitive case.[99]

Vernacular names[edit]

See also: Common name

Despite the fact that some hetero/homogeneus colonies or biofilms of bacteria have names in English (e.g. dental plaque or Star jelly), no bacterial species has a vernacular/trivial/common name in English.

For names in the singular form, plurals cannot be made (singulare tantum) as would imply multiple groups with the same label and not multiple members of that group (by analogy, in English, chairs and tables are types of furniture, which cannot be used in the plural form "furnitures" to describe both members), conversely names plural form are pluralia tantum. However, a partial exception to this is made by the use of vernacular names. However, to avoid repetition of taxonomic names which break the flow of prose, vernacular names of members of a genus or higher taxa are often used and recommended, these are formed by writing the name of the taxa in sentence case roman ("standard" in MS Office) type, therefore treating the proper noun as an English common noun (e.g. the salmonellas), although there is some debate about the grammar of plurals, which can either be regular plural by adding -(e)s (the salmonellas) or using the ancient Greek or Latin plural form (irregular plurals) of the noun (the salmonellae); the latter is problematic as the plural of - bacter would be -bacteres, while the plural of myces (N.L. masc. n. from Gr. masc. n. mukes) is mycetes.[108]

Customs are present for certain names, such as those ending in -monas are converted into -monad (one pseudomonad, two aeromonads and not -monades).

Bacteria which are the etiological cause for a disease are often referred to by the disease name followed by a describing noun (bacterium, bacillus, coccus, agent or the name of their phylum) e.g. cholera bacterium (Vibrio cholerae) or Lyme disease spirochete (Borrelia burgdorferi), note also rickettsialpox (Rickettsia akari) (for more see[109]).

Treponema is converted into treponeme and the plural is treponemes and not treponemata.

Some unusual bacteria have special names such as Quin's oval (Quinella ovalis) and Walsby's square (Haloquadratum walsbyi).

Before the advent of molecular phylogeny, many higher taxonomic groupings had only trivial names, which are still used today, some of which are polyphyletic, such as Rhizobacteria. Some higher taxonomic trivial names are:

  • Blue-green algae are members of the phylum Cyanobacteria
  • Green non-sulfur bacteria are members of the phylum Chloroflexi
  • Green sulfur bacteria are members of the Chlorobi
  • Purple bacteria are some, but not all, members of the phylum Proteobacteria
  • Purple sulfur bacteria are members of the order Chromatiales
  • low G+C Gram-positive bacteria are members of the phylum Firmicutes, regardless of GC content
  • high G+C Gram-positive bacteria are members of the phylum Actinobacteria, regardless of GC content
  • Rhizobacteria are members of various genera of proteobacteria
  • Rhizobia are members of the order Hyphomicrobiales
  • Lactic streptococci are members of the genus Lactococcus
  • Coryneform bacteria are members of the family Corynebacteriaceae
  • Fruiting gliding bacteria or myxobacteria are members of the order Myxococcales
  • Enterics are members of the order Enterobacteriales, although the term is avoided if they do not live in the intestines, such as Pectobacterium
  • Acetic acid bacteria are members of the family Acetobacteraceae

Terminology[edit]

  • The abbreviation for species is sp. (plural spp.) and is used after a generic epithet to indicate a species of that genus. Often used to denote a strain of a genus for which the species is not known either because has the organism has not been described yet as a species or insufficient tests were conducted to identify it. For example Halomonas sp. GFAJ-1
  • If a bacterium is known and well-studied but not culturable, it is given the term Candidatus in its name
  • A basonym is original name of a new combination, namely the first name given to a taxon before it was reclassified
  • A synonym is an alternative name for a taxon, i.e. a taxon was erroneously described twice
  • When a taxon is transferred it becomes a new combination (comb. nov.) or nomina nova (nom. nov.)
  • paraphyly, monophyly and polyphyly

See also[edit]

  • Branching order of bacterial phyla (Woese, 1987)
  • Branching order of bacterial phyla (Gupta, 2001)
  • Branching order of bacterial phyla (Cavalier-Smith, 2002)
  • Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
  • Branching order of bacterial phyla (Battistuzzi et al.,2004)
  • Branching order of bacterial phyla (Ciccarelli et al., 2006)
  • Branching order of bacterial phyla after ARB Silva Living Tree
  • Branching order of bacterial phyla (Genome Taxonomy Database, 2018)
  • Bacterial phyla, a complicated classification
  • List of Archaea genera
  • List of Bacteria genera
  • List of bacterial orders
  • List of Latin and Greek words commonly used in systematic names
  • List of sequenced archaeal genomes
  • List of sequenced prokaryotic genomes
  • List of clinically important bacteria
  • Species problem
  • Evolutionary grade
  • Cryptic species complex
  • Synonym (taxonomy)
  • Taxonomy
  • LPSN, list of accepted bacterial and archaeal names
  • Cyanobacteria, a phylum of common bacteria but poorly classified at present
  • Human microbiome project
  • Microbial ecology

References[edit]

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Sours: https://en.wikipedia.org/wiki/Bacterial_taxonomy
Genus and Species

VetBact

Nomenclature of bacteria

Introduction

Nomenclature of bacteria refers to naming and bacteria and other organisms are named according to the binomial system, which was introduced by Carl Linnaeus (1674-1748). This means that a bacterium has a species name, which is composed of a genus name that tells you to which genus it belongs and a species epithet which, together with the genus name, is unique to the bacterium. An example of this is Moraxella bovis, where the genus name indicates that the bacterium belongs to the genus Moraxella and the species epithet indicates that the bacterium has been isolated from cattle. The genus name and the species epithet form together the scientific name of the species, which is always written in italics. Bacterial names are international and Latin or latinized Greek are used to form the name. If misunderstandings cannot occur, you can abbreviate the genus name after it has been written for the first time in a text, e.g. M. bovis. However, note that there are also bacteria called Mycoplasma bovis and Mycobacterium bovis.

There are strict international rules for how bacteria should be named and these rules are published in a book named: "International Code of Nomemclature of Bacteria". In order to get a proposed name accepted, a scientific paper on the proposed species must be published and approved by an international taxonomy committee.

Trivial name

Trivial names are often used as a simplified way of naming a bacterial genus. A trivial name should neiter be written with capital first letter nor in italic. Examples of trivial names are: lactobacilli, mycobacteria, salmonella, staphylococci and streptococci. The scientific names for these groups are: genus Lactobacillus (or Lactobacillus spp.), genus Mycobacterium (or Mycobacterium spp.), genus Salmonella (or Salmonella spp.), genus Staphylococcus (or Staphylococcus spp.), genus Streptococcus (or Streptococcus spp.), respectively.

If you refer to a specific bacterial species, a trivial name refering to a complete genus should never be used.

Subspecies, biovars and serovars

Sometimes there is a need to divide bacterial species into subspecies, because they are too closely related to be regarded as different species, but too distantly related to be regarded as the same species. In this case a subspecies is introduced by adding a subspecies epithet and write subspecies (subsp. or ssp.) in front of it. An example of this is Streptococcus equi subsp. equi. When you divide a species into several subspecies, the original species always gets the same subspecies epithet as the species epithet.

There is often a need to divide species and subspecies in different biovars (bio­logi­cal variants) or different strains, but this is not strictly regulated, which means that researchers themselves can name their strains or biovars. One type of biovar is serovar (serological variant), by which various surface antigens can be identified with specific antibodies. Contact tracing and epidemiology is based on identification of different variants of the same bacterial species.

Serovar vs. serotype

Serovar and serotype are  synonyms and thus, interchangeable terms, but according to the Rules of the Bacteriological Code (1990 Revision), serovar is the preferred term. Serogroup is a group of bacteria containing a common antigen. A serogroup may contain several serotypes. Serogroup is not an official designation, but has been used to classify bacteria belonging to the genera Leptospira, Salmonella, Shigella and Streptococcus.

Salmonella nomenclature

A bacterial subspecies that occurs in several thousand different serovars is Salmonella enterica subsp. enterica. A common serovar is Dublin and if you you want to write the complete and correct name of the bacterium, it becomes Salmonella enterica subsp. enterica serovar Dublin. Please note that the name of the sero­var is capitalized, but not italicized. If the name appears in several places in the text, you can write S. enterica subsp. enterica serovar Dublin. However, because even this abbreviated writing is rather lengthy, it has been agreed that it is acceptable to simply write Salmonella Dublin, except on the first occurrance in a text, where the name must be given in full.

You can read more about naming of salmonellas on VetBact at Salmonella spp. and Salmonella enterica.

Updated: 2020-12-14.

Sours: https://www.vetbact.org/displayextinfo/59

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Scientific Nomenclature

Italics are used for bacterial and viral taxa at the level of family and below. All bacterial and many viral genes are italicized. Serovars of Salmonella enterica are not italicized.

For organisms other than bacteria, fungi, and viruses, scientific names of taxa above the genus level (families, orders, etc.) should be in roman type.

Because abbreviations for restriction endonucleases are derived from the name of the organism (usually bacteria) from which they are isolated, they should be italicized.

SmaI was isolated from Serratia marcescens.

Taq polymerase, which is used in PCRs, was isolated from Thermus aquaticus.

Use italics for genus and species in virus names.

A/Cygnus cygnus/Germany/R65/2006

Italicize species, variety or subspecies, and genus when used in the singular. Do not italicize or capitalize genus name when used in the plural.

Listeria monocytogenes is

…listeria are; salmonellae; mycobacteria

The genus Salmonella consists of only 2 species: S. enterica (divided into 6 subspecies) and S. bongori. Most salmonellae encountered in EID will be serotypes (serovars) belonging to S. enterica. Put the genus and species in italics, followed by initially capped serotype in Roman (e.g., Salmonella enterica serotype Paratyphi). The genus shorthand “S.” should never be used without a species name

Correct: S. enterica

Correct: S. enterica serovar Typhimurium

Correct: S. enterica ser. Typhimurium

Incorrect: Salmonella Typhimurium

Incorrect: S. Typhimurium

Serotypes belonging to other subspecies are designated by their antigenic formulae following the subspecies name (e.g., S. enterica subspecies diarizonae 60:k:z or S. IIIb 60:k:z).

For an article about 1 genus, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, P. putida, P. fluorescens, and P. denitrificans.

For an article about multiple genera that each have a different abbreviation, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, Streptococcus pyogenes, P. putida, and S. felis.

For an article about multiple genera, some of which have the same abbreviation, write out first mention of new species.  Abbreviate later.

We studied the relationship between Trypanosoma cruzi and Triatoma infestans.

We found the relationship between T. infestans and T. cruzi to be...

For an article about several species of the same genus, the genus must be spelled out only in the title and at first use in the abstract, text, tables, and figures. It may subsequently be abbreviated for other species.

We studied Pseudomonas aeruginosa, P. putida, and P. fluorescens.

However, if >1 genus begins with the same letter in an article, the full genus name must be spelled out the first time it is used with a new species. On subsequent mentions of a species, the genus may be abbreviated.

Ticks were discovered on Canis lupus, Canis latrans, Cerdocyon thous, and Chrysocyon brachyurus, but C. lupus hosted the greatest number of ticks.

Bacteria

Italicize family, genus, species, and variety or subspecies. Begin family and genus with a capital letter. Kingdom, phylum, class, order, and suborder begin with a capital letter but are not italicized. If a generic plural for an organism exists (see Dorland’s), it is neither capitalized nor italicized.

Mycobacterium tuberculosis

family Mycobacteriaceae, order Actinomycetales

mycobacteria

Binary genus-species combinations are always used in the singular. Genus used alone (capitalized and italicized) is usually used in the singular, but it may be used in the plural (not italicized) if it refers to all species within that genus.

Salmonella enterica is…

Salmonellae are ubiquitous…

Do not use spaces for MRSA isolates.

Preferrred: USA300

Avoid: USA 300

Fungi

Use Valley fever, not Valley Fever, when referring coccidioidomycosis. The use of a lowercase “f” in “fever” is consistent with use in the Communicable Diseases Manual and with AMA style for Rift Valley fever.

Genes

Gene designations are generally italicized, which helps clarify whether the writer is referring to a gene or to another entity that might be confused with a gene. Style for genes varies according to organism.

There is no real consensus on style of depicting acronyms for Plasmodium genes, except that when referred to as genes, they are italicized; when referred to as proteins, they are not. The style is more dependent on the particular journal. In molecular microbiology the gene and species abbreviation, i.e., pf, is italicized and all of the term is in lowercase; pfmdr1, pfatp6, pvdhfr. This particular gene was presented in The Lancet as PfATPase6. The main idea is to be consistent throughout the manuscript.

Acronyms for Plasmodium genes are italicized when referring to a gene. When referring to a protein they are not italicized.

Many virus gene names are written in italics and are traditionally 3 letters, lowercase, although some will be written in all caps, roman. No definitive rules exist for naming such genes, and you will see them described in a variety of different ways.

src gene, myc gene, HA, NA

Bacteria gene names are always written in italics.

lacZ gene

Fungus gene names are generally treated the same as virus gene names (i.e., 3 italicized letters, lowercase). With a multigene family, a numeric notation is included. When different alleles of the same gene are noted, the terminology allows for a superscript.

Mitochondrial genes add an “mt” prefix to the 3- or 4-letter gene, which may or may not be in lowercase. Drug target genes are all capped, no italics.

msg1, msg2, msg3 (multigene)

xyz1 (different alleles of same gene)

mtLSU (mitochondrial genes)

DHPS and DHFR (drug target genes)

Cholera toxin gene is written as ctx, and cholera toxin gene subunit A is written as ctxA.

Insertion sequences are written as “IS” plus an italicized number (IS6110).

Human gene names are all caps and italicized. May be all uppercase Latin letters or a combination of uppercase letters and Arabic numbers, ideally no longer than 6 characters. Initial character is always a letter. No subscript, superscript, roman numerals, or Greek letters are used.

Similar gene names may exist for humans and mice. For example, AMA Manual of Style lists the following genes:

β2-microglobulin: B2m (mice) and B2M (humans)

CD5 antigen: Cd5 (mice) and CD5 (humans)

A list of human gene names is available at http://www.genenames.org/guidelines.html

Proteins

Proteins, the combinations of amino acids that make up plants and animals, including humans, often have the same name as a gene but are not italicized and always begin with a capital letter. For example, 1 of the outer surface proteins of Borreliaburgdorferi is named outer surface protein A. It is encoded by ospA (the gene), and the protein is OspA.

Proteins often have common names (e.g., β-galactosidase is the gene product of lacZ).

How to tell difference between proteins and genes? If a term is combined with 1 of the following words, it is probably describing a gene:

Promoter (e.g., P2 core promoter [of myc gene]); promoters are parts of genes, not proteins

Terminator, operator, attenuator sites

If term is combined with one of following words, it is probably describing a protein.

Repress—a protein represses, a gene doesn’t.

React—a protein reacts, a gene doesn’t

Heterodimerization

Elevated levels of ____ [A common usage error is for authors to write “elevated myc” when they mean: “elevated levels of myc.”]

Italicizing MMR is another common usage error. This term, which means “mismatch repair,” is never a gene, just an abbreviation for a process. But you may see “Mice with specific alterations in a number of MMR genes have been developed…”

Restriction Enzymes

Restriction enzymes are identified with a 3-letter designation of the bacterium from which they are isolated, plus a single-letter strain designation (as needed) and a roman numeral showing the order in which it was identified. The 3-letter bacterium designation should begin with a capital letter and is italicized; the rest of the enzyme name is set roman.

SmaI, EcoRI, BamHI

Viruses

Italics Use with Virus Names

A virus is not a species; a virus belongs to a species. Italicize species, genus, and family of a virus when used in a taxonomic sense. Note however, that it is fine to not mention taxonomy of a virus, especially one like dengue or polio that is well known.

Do not italicize a virus name when used generically. If you capitalize a virus name (other than one that has a proper name in it so that you must capitalize it), then you need to italicize it.

bovine kobuviruses, a kobuvirus, kobuviruses, but Kobuvirus spp.

The presence of West Nile virus was confirmed in mosquitoes and dead crows. (AMA Style Guide, p. 758).

Epidemic transmission of West Nile virus (WNV)…prompted aerial application.

The species West Nile virus is a member of the genus Flavivirus.

Family Bunyaviridae, genus Phlebovirus, species Rift Valley fever virus

Recent attention has been drawn to Toscana virus (family Bunyaviridae, genus Phlebovirus, species Sandfly fever Naples virus) in countries…

Acronyms Use with Virus names

It is permissible to use an acronym for a virus (e.g., WNV for West Nile virus), after defining it. However, do not abbreviate a species (including the species West Nile virus). In short, if you do italicize, don’t use an acronym.

Correct: West Nile virus (WNV; family Flaviviridae, genus Flavivirus) is transmitted to humans [here the virus is being transmitted, not the species name; so West Nile virus is roman type and may be abbreviated]. 

For viruses that begin with a Greek letter, write it out and close up space between the letter and the rest of the word.

            Betaherpesvirus

For human coronavirus, use the abbreviation hCoV. Be aware that there is a genus/species named Human coronavirus, which should be abbreviated as H. coronavirus, not hCoV.

For numbered echoviruses (e.g., echovirus 13), use the following format: E13 (do not use EV)

For hepatitis E virus, use the acryonym HEV.

Use a capital H for human virus abbreviations (e.g., HMPV, not hMPV), unless otherwise directed by author or precedent (see human coronavirus above).

For human enterovirus, use human EV, not HEV.  For numbered enteroviruses, use the following format: EV75.

For influenza virus, see separate section (i.e., following West Nile virus below).

For polyomaviruses, use the following:

KIPyV for KI polyomaviruses (formerly known as Karolinska Institute polyomavirus)

MCPyV, not MCV, for Merkel cell polyomavirus, and

WUPyV for WU polyomaviruses (formerly known as Washington University polyomavirus).

For West Nile virus, use WNV.

Influenza

On October 18, 2011, WHO published guidelines for the standardization of terminology of the pandemic A(H1N1)2009 virus (see http://www.who.int/influenza/gisrs_laboratory/terminology_ah1n1pdm09/en/index.html). The guidelines are intended to minimize confusion and differentiate the pandemic virus from the old seasonal A (H1N1) viruses circulating in humans before pandemic A(H1N1)2009 virus. In agreement with WHO guidelines, EID will use the following nomenclature for the pandemic A(H1N1)2009 virus:

influenza A(H1N1)pdm09 virus

 After a first mention of the full virus name, including the word “influenza,” it is sufficient to use “A(H1N1)pdm09”;  however, the word “virus,”  “infection,” or “outbreak” should be added to the name, as appropriate. If the term appears frequently, the abbreviation “pH1N1” may be used.

Examples of other influenza virus nomenclature used by EID:

avian influenza A(H7N9) virus

avian influenza A(H5N1) virus

As stated above for influenza A(H1N1)pdm09 virus, other influenza virus names can be shortened after a first mention that includes the word “influenza,” but, as appropriate, the word word “virus,”  “infection,” or “outbreak” should be added to the name. Examples: A(H7N9) virus, A(H7N9) infection, A(H7N9) outbreak.

The H and N subtype should always be in parentheses when it follows “influenza”: 

influenza virus A (H5N1) (for “influenza virus A subtype H5N1”)

A (H3N2)v (for “variant influenza A (H3N2)”)

When used alone, subtypes do not need parentheses but must be accompanied by the word “subtype.”

The H5N1 subtype is…

Different subtypes, such as H5N1…

Note: H5N1 is neither a virus, nor a disease; it is merely a subtype designation of influenza virus type A. If you want to drop anything later in the article, you may leave out the subtype designation. If only 1 virus is being studied, you can say in the Methods that influenza virus means influenza virus A subtype H5N1, and leave the subtype out from then on.

Influenza virus (H5N1) can have high or low pathogenicity. It is not redundant to include "highly pathogenic" in the title.

For information on this virus nomenclature style, adopted by several international organizations, see International Committee on Taxonomy of Viruses.

For influenza virus isolates, include the virus subtype, write out in full the host of origin (omit if human), include the site of isolation and strain number, and use the 4-digit year if the virus was isolated in 2000 or later. For viruses isolated during the 1900s, use the 2-digit year.

Incorrect: dk/Laos/3295/06

Correct: A/duck/Laos/3295/2006

Italicize genus and species of the host in isolate names.

A/Cygnus cygnus/Germany/R65/2006

The formal nomenclature for the designation of influenza viruses was revised and published by the World Health Organization (WHO). (WHO. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull.World Health Organ. 1980;58;585–9). The full and correct nomenclature includes the type of virus (A, B, or C), the host of origin (except for human), the geographic site of isolation, the strain number, the year of isolation (4-digit year for viruses isolated in 2000 or later; 2-digit year for viruses isolated during the 1900s), and the subtype (16 possible H and 9 possible N subtypes).

Thus a type A virus isolated in 1995 from a Mallard duck in Memphis Tennessee with a strain number of 123 and an H5N1 subtype is designated:

Influenza A/mallard/Memphis/123/95 (H5N1).

Site can be abbreviated in human viruses, as in the following for which PR (Puerto Rico) and FM (Fort Monmouth) are well known and not written out.

Influenza viruses used were A/PR/8/34 (H1N1), A/FM/1/47 (H1N1), and
A/Thailand/SP-83/2004 (H5N1).

When referring to avian influenza viruses that have low pathogenicity, use the term “low pathogenicity avian influenza” not “low pathogenic avian influenza.” If used 3 or more times, the term can be abbreviated as LPAI.

When referring to avian influenza viruses that have high pathogenicity, use the term “highly pathogenic avian influenza” not “high pathogenicity avian influenza.” If used ≥3 times, the term can be abbreviated as HPAI.

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Page created: February 04, 2010
Page updated: April 07, 2014
Page reviewed: April 07, 2014
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
Sours: https://wwwnc.cdc.gov/eid/page/scientific-nomenclature


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