Redefining bacterial populations: a post-genomic reformation

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. Access through your

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BEING VIEWED BY OTHERS HORIZONTAL GENE TRANSFER AND ADAPTIVE EVOLUTION IN BACTERIA Article 12 November 2021 HOTSPOTS OF GENETIC CHANGE IN _YERSINIA PESTIS_ Article Open access 04 January

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references 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. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * 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 * Division of Human Biology, Frederick Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, 98109, Washington, USA Nina R. Salama Authors * Elizabeth A. Joyce View

author publications You can also search for this author inPubMed Google Scholar * Kaman Chan View author publications You can also search for this author inPubMed Google Scholar * Nina R.

Salama View author publications You can also search for this author inPubMed Google Scholar * Stanley Falkow View author publications You can also search for this author inPubMed Google

Scholar CORRESPONDING AUTHOR Correspondence to Elizabeth A. Joyce. RELATED LINKS RELATED LINKS 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. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Issue

Date: 01 June 2002 * DOI: https://doi.org/10.1038/nrg820 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable

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