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  • Review Article
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Redefining bacterial populations: a post-genomic reformation

Nature Reviews Genetics volume 3, pages 462–473 (2002)Cite this article

Key Points

  • This review discusses how bacterial populations have been historically defined and classified, and how these definitions have been refined with the development of molecular tools and whole-genome sequencing.

  • We discuss the impact of horizontal gene transfer and how the increased awareness of this process is influencing our understanding of bacterial population structures.

  • We focus on the recent development of DNA microarray technology and its use as a method for high-throughput genome-wide strain comparisons. We give details of the current achievements and limitations of this technique to assess the extent of genetic variability through a discussion of the current literature. We describe the application of this technology to characterize isolates of Helicobacter pylori, Streptococcus pneumoniae, and Salmonella enterica and S. bongori species.

  • We propose how the information garnered from comparative genomic microarray analyses can provide important insight into the molecular basis of the relationships that exist between bacteria and their hosts.

Abstract

Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host–pathogen relationships.

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Figure 1: Dendrogram of Helicobacter pylori strains grouped using the CLUSTER program.
Figure 2: Distribution of strain-specific variation observed in two bacterial species.

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Acknowledgements

We thank our colleagues G. Dougan and S. Baker from the Imperial College of Science, Technology and Medicine, London, for Salmonella strains and sharing data; A. Covacci, Chiron-Biocine, Italy; J. Gordon, Washington University, Missouri; J. Parsonette, Stanford University, California; R. Peek Jr, Vanderbilt University, Tennessee; J. Solnick, University of California at Davis, for providing H. pylori clinical isolates; L. McGee from the Pneumococcal Diseases Research Unit at the South African Institute for Medical Research, Johannesburg, for the S. pneumoniae strains; and A. Kawale and S. Censini for technical assistance, C. Kim for developing analytical tools for microarray analysis and thoughtful discussion, and S. Reid, J. R. Fitzgerald and members of the Falkow Laboratory for critical reviews of the manuscript.

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  1. Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Fairchild D 037, Stanford, 94305-5402, California, USA

    Elizabeth A. Joyce, Kaman Chan & Stanley Falkow

  2. Division of Human Biology, Frederick Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, 98109, Washington, USA

    Nina R. Salama

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Corresponding author

Correspondence to Elizabeth A. Joyce.

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FURTHER INFORMATION

CLUSTER program

Genome Entry Database at NCBI

Multilocus sequence typing

NCBI GenBank Database

Salmonella.org

Salmonella Reference Collections B and C

Supplementary Table 6 from REF. 44

The Institute for Genomic Research (TIGR)

Glossary

CONJUGATION

The transfer of DNA from a donor cell to a recipient cell that is mediated by direct cell–cell contact.

TRANSFORMATION

The uptake of DNA by a bacterium from the surrounding environment.

TRANSDUCTION

Virus- or phage-mediated introduction into a cell of a DNA fragment that is derived from a different cell.

ARCHAEA

A kingdom of unicellular microorganisms, many members of which can survive extreme environmental conditions, such as temperatures >100 °C, extremely alkaline or acid environs, and highly osmotic conditions.

RIBOTYPING

A technique used to determine genetic and evolutionary relationships between organisms. Oligonucleotide probes targeted to highly conserved domains of coding sequences of ribosomal RNA are amplified and the products are visualized by gel electrophoresis banding patterns are compared with known species and strains to determine organism relatedness.

ATROPHIC GASTRITIS

Chronic inflammation of the stomach, accompanied by atrophy of the mucous membrane and destruction of the peptic glands.

DUODENUM

The first portion of the small intestine, extending from the pylorus (the posterior end of the stomach) to the jejunum (the next portion of the small intestine).

ADENOCARCINOMA

A form of malignant cancer that arises from the glandular epithelium.

SEROVAR/SEROTYPE

A group of intimately related microorganisms distinguished by a common set of antigenic determinants that are expressed on the cell surface.

CHEMOKINES

Small molecules that have a central role in inflammatory responses and trigger migration and activation of phagocytic cells and lymphocytes.

CLUSTER ANALYSIS

A mathematical algorithm that organizes a set of items according to their similarity. For example, genes can be clustered according to their similarity in pattern of expression.

INSERTION SEQUENCES

Small, mobile nucleotide sequences found in the genomes of many bacterial populations.

ADHESIVE FIMBRIAE

Hair-like structures that project from the surface of some bacteria. They are involved in adhesion of bacterial cells to surfaces, and can be important in bacterial virulence.

OTITIS MEDIA

Infection and inflammation of the middle ear space and ear drum.

GRAM REACTION

A differential stain that separates bacteria into two groups, Gram positive and Gram negative, on the basis of the biochemical composition of their cell wall.

DIPLOCOCCUS

Any of a variety of encapsulated bacteria (as the pneumococcus) that usually occur in pairs.

CAPSULE

A thick gel-like material generally composed of hydrophilic polysaccharide that surrounds the cell wall of Gram-positive or Gram-negative bacteria. It can contribute to pathogenicity by inhibiting phagocytosis of the bacteria by the macrophages of the host.

ENTEROBACTERIACEAE

A large family of Gram-negative bacilli that inhabit the large intestine of mammals.

AGGLUTINATED

The aggregation of particulate antigen by antibodies.

TISSUE TROPISM

Tissue-specific bacterial adherence and colonization due to a restricted distribution of receptor structures on certain host-cell surfaces and not on others.

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Joyce, E., Chan, K., Salama, N. et al. Redefining bacterial populations: a post-genomic reformation. Nat Rev Genet 3, 462–473 (2002). https://doi.org/10.1038/nrg820

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