Testing culture purity in prokaryotes: criteria and challenges.

Переведенное название: Тестирование чистоты культуры прокариот: критерии и проблемы.

Результат исследований: Научные публикации в периодических изданияхстатья

Выдержка

Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer’s personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by ‘culturomics’ will overcome this obstacle.
Язык оригиналаанглийский
Номер статьиDOI 10.1007/s10482-018-1054-4
Страницы (с-по)1509-1521
Число страниц13
ЖурналAntonie van Leeuwenhoek
Том111
Номер выпуска9
DOI
СостояниеОпубликовано - 17 авг 2018

Ключевые слова

  • Culturomics Metagenomics Pure (axenic) culture Species in prokaryotes Uncultivable bacteria Whole genome sequencing

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title = "Testing culture purity in prokaryotes: criteria and challenges.",
abstract = "Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer’s personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by ‘culturomics’ will overcome this obstacle.",
keywords = "Culturomics Metagenomics Pure (axenic) culture Species in prokaryotes Uncultivable bacteria Whole genome sequencing",
author = "Дмитриева, {Елена Юрьевна} and Пиневич, {Александр Васильевич} and Пиневич, {Агния Александровна} and Андронов, {Евгений Евгеньевич} and Першина, {Елизавета Владимировна}",
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T1 - Testing culture purity in prokaryotes: criteria and challenges.

AU - Дмитриева, Елена Юрьевна

AU - Пиневич, Александр Васильевич

AU - Пиневич, Агния Александровна

AU - Андронов, Евгений Евгеньевич

AU - Першина, Елизавета Владимировна

PY - 2018/8/17

Y1 - 2018/8/17

N2 - Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer’s personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by ‘culturomics’ will overcome this obstacle.

AB - Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer’s personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by ‘culturomics’ will overcome this obstacle.

KW - Culturomics Metagenomics Pure (axenic) culture Species in prokaryotes Uncultivable bacteria Whole genome sequencing

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DO - 10.1007/s10482-018-1054-4

M3 - Article

VL - 111

SP - 1509

EP - 1521

JO - Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology

JF - Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology

SN - 0003-6072

IS - 9

M1 - DOI 10.1007/s10482-018-1054-4

ER -