TY - JOUR

T1 - Testing culture purity in prokaryotes

T2 - criteria and challenges

AU - Pinevich, Alexander V.

AU - Andronov, Eugeny E.

AU - Pershina, Elizaveta V.

AU - Pinevich, Agnia A.

AU - Dmitrieva, Helena Y.

N1 - Funding Information: Acknowledgements The work was supported by St. Petersburg State University Grant No 1.40.540.2017 (AVP), and Russian Scientific Foundation Grant No 14-26-00094P (EEA). We thank St. Petersburg State University research centres ‘‘Molecular and Cell Technologies’’ and ‘‘Culture Collection of Microorganisms’’ for technical assistance. We are grateful to Helena Kozhenkova for useful discussions. We especially thank the anonymous reviewers for their criticism and for offering valuable suggestions that have strongly improved the manuscript.

PY - 2018/9/1

Y1 - 2018/9/1

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

KW - Culturomics

KW - Metagenomics

KW - Pure (axenic) culture

KW - Species in prokaryotes

KW - Uncultivable bacteria

KW - Whole genome sequencing

KW - ESCHERICHIA-COLI

KW - IN-SITU HYBRIDIZATION

KW - GENOME SEQUENCING DATA

KW - PURE CULTURE

KW - MOLECULAR MARKERS

KW - MICROBIAL DIVERSITY

KW - SP-NOV

KW - UNCULTURABLE BACTERIA

KW - RPOB GENE

KW - 16S RIBOSOMAL-RNA

UR - http://www.scopus.com/inward/record.url?scp=85042618880&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/testing-culture-purity-prokaryotes-criteria-challenges

U2 - 10.1007/s10482-018-1054-4

DO - 10.1007/s10482-018-1054-4

M3 - Review article

C2 - 29488181

AN - SCOPUS:85042618880

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

ER -