Strain, clone and species: comments on three basic concepts of bacteriology

Dijkshoorn, Lenie; Ursing, Björn M.; Ursing, Jan

doi:10.1099/0022-1317-49-5-397

Cited by 105 publications

(74 citation statements)

References 18 publications

(25 reference statements)

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“…There are population density increases followed by cell death, in other words, cycles of local invasion and recess, that spread the cells far from their initial parent cell (7,23) and which, as a consequence, modify local diversity by shuffling clones. Our results suggest that a clone can spread at a distance of at least 1 cm, which is obviously an underestimation since we only explored a volume of 1 cm 3 . The distance between cells of a given clone could be the result of clonal spreads or relicts of former colonization.…”

Section: Discussionmentioning

confidence: 88%

“…Bacteria are naturally clonal due to binary fission; however, due to the occurrence of horizontal gene transfer, the genetic structure of populations is likely to range from strictly clonal (organized in a clone-like manner) to panmictic (12,16,17,27). Clonal multiplication and mating take place at a short spatial scale in the soil matrix and, when repeated isolates from a strain are sampled, the starting point in space and time and also the further development of bacterial spread and growth are unknown (3). Many population genetic studies among conspecific bacteria have used pooled collections of strains from widely separated locations and different sampling times.…”

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confidence: 99%

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Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

Vogel

Normand²,

Thioulouse

et al. 2003

Appl Environ Microbiol

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The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 m in diameter were sampled with spatial coordinates in 1 cm 3 of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10 3 agrobacteria g ؊1 ), a high genetic diversity was maintained. In two independent microsamples (500 m in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.

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Section: Discussionmentioning

confidence: 88%

mentioning

confidence: 99%

Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

Vogel

Normand²,

Thioulouse

et al. 2003

Appl Environ Microbiol

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“…We note that despite a large body of work on strain-level phenotypic characterization and genetic comparisons from microbial isolates, a clear definition of the concept of "strain" is still lacking (Dijkshoorn et al 2000;Konstantinidis et al 2006). Genomes differing by just one or a few nucleotides could be defined as different strains, but such limited genetic differences may not result in any phenotypic changes (e.g., synonymous mutations) and would lead to the differentiation of strains in just a few microbial generations.…”

Section: Resultsmentioning

confidence: 99%

Microbial strain-level population structure and genetic diversity from metagenomes

et al. 2017

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Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant reconstruction within species-specific marker genes. It identified primarily subject-specific strain variants (<5% inter-subject strain sharing), and we determined that a single strain typically dominated each species and was retained over time (for >70% of species). Microbial population structure was correlated in several distinct ways with the geographic structure of the host population. In some cases, discrete subspecies (e.g., for Eubacterium rectale and Prevotella copri) or continuous microbial genetic variations (e.g., for Faecalibacterium prausnitzii) were associated with geographically distinct human populations, whereas few strains occurred in multiple unrelated cohorts. We further estimated the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal microbes, providing a comprehensive strain-level genetic overview of the gut microbial diversity.

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“…Following the standard nomenclature of microbiology, we refer to the viruses used as strains, because these have been isolated, grown as pure cultures in vitro, and characterized to the point of genome sequencing (31). Twenty passaged HSV-1 strains were provided by Hiroshi Sakaoka, as DNA isolated from infected cell lysates.…”

Section: Viruses and Sequencingmentioning

confidence: 99%

Evolution and Diversity in Human Herpes Simplex Virus Genomes

Szpara

Gatherer

Ochoa

et al. 2014

J Virol

197

280

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gHerpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide. Herpes simplex virus 1 (HSV-1; species Human herpesvirus 1, genus Simplexvirus, subfamily Alphaherpesvirinae, family Herpesviridae, order Herpesvirales) is among the most successful human pathogens in terms of its global distribution, longevity in the host, and mild symptoms among the great majority of those exposed (1-4). HSV-1 is a large, enveloped DNA virus that infects lytically at epithelial surfaces and establishes a lifelong, latent infection in sensory neurons. HSV-1 infection produces a wide range of symptoms, ranging from few or none in many seropositive individuals to periodic lesions on epithelial surfaces in a significant proportion of people and to lethal encephalitis as an extreme manifestation in a few. There is no vaccine at present (5, 6). Studies in animal models have characterized the ways in which genetic variation between viral strains can influence the symptoms of pathology, including lesion severity and rates of reactivation from latency. The most recent phase III vaccine trial for HSV failed to provide protection from infection (7, 8), and one contributing factor to this failure may well be variation among HSV isolates found in the field.Based on early restriction fragment length polymorphism (RFLP) analyses, HSV-1 has been described as more diverse than HSV-2 (9-11). In contrast to both HSV-1 and HSV-2, the related human alphaherpesvirus, varicella-zoster virus (VZV), has relatively low interstrain diversity (12-15). Decades of research comparing RFLP bands, polypeptide size, and PCR-based sequence analysis have revealed that HSV-1 strains vary between individuals, over sequential isolates from the s...

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Strain, clone and species: comments on three basic concepts of bacteriology

Cited by 105 publications

References 18 publications

Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

Relationship between Spatial and Genetic Distance in Agrobacterium spp. in 1 Cubic Centimeter of Soil

Microbial strain-level population structure and genetic diversity from metagenomes

Evolution and Diversity in Human Herpes Simplex Virus Genomes

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