The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

  title={The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity},
  author={Christophe Fraser and Eric J. Alm and Martin F. Polz and Brian G. Spratt and William P. Hanage},
  pages={741 - 746}
The Bacteria and Archaea are the most genetically diverse superkingdoms of life, and techniques for exploring that diversity are only just becoming widespread. Taxonomists classify these organisms into species in much the same way as they classify eukaryotes, but differences in their biology—including horizontal gene transfer between distantly related taxa and variable rates of homologous recombination—mean that we still do not understand what a bacterial species is. This is not merely a… 

The Prokaryotic Species Concept and Challenges

This chapter presents the main concepts and operational definitions commonly used to designate microbial species and emphasizes how these different concepts accommodate the idiosyncrasies of prokaryotic genomics, in particular, the existence of a core- and a pangenome.

Biological Species Are Universal across Life’s Domains

It is shown that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes, and a single biological species definition based on gene flow is applicable to all cellular lifeforms.

Microbial systematics in the post-genomics era

Two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships are described.

Population Genomics Insights into Adaptive Evolution and Ecological Differentiation in Streptomycetes

It is demonstrated that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes and raising concerns of an underrated microbial diversity at the intraspecies level.

2 Quantitative and Theoretical Microbial Population Biology

The quest for bacterial and archaeal populations is one for defining and identifying fundamental players in ecology and evolution.

Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Analysis of the genomes of 119 strains of the marine actinomycete genus Salinispora reveals patterns of orthologous group distributions that reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population

Bioinformatics of Microbial Sequences

The immense and rapidly expanding quantity of genome sequence information has made it possible for DNA-based diagnostic and typing methods to be designed with precisely understood performances in relation to the population structure of the species or the likely gene content of an analytical sample.

Taxonomy and Phylogeny of Prokaryotes

Prokaryotic microorganisms correspond to two of the three domains of life: Archaea and Bacteria and their systematics is described in the “Bergey's Manual for Systematic Bacteriology, second edition” published in five volumes.



What are bacterial species?

  • F. Cohan
  • Biology, Environmental Science
    Annual review of microbiology
  • 2002
These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species, which is more like a genus than a species.

Microbial diversity and the genetic nature of microbial species

It is proposed that decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces.

Recombination and the Nature of Bacterial Speciation

It is suggested that the rate of recombination and its relation to genetic divergence have a strong influence on outcomes and it is proposed that a distinction be made between clonal divergence and sexual speciation.

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

This work introduces a sequence-based approach (“ecotype simulation”) to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the “Evolution Canyons” of Israel.

Re-evaluating prokaryotic species

The current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics are discussed and the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters are considered.

Recombination and the population structures of bacterial pathogens.

In many bacterial species, including Neisseria meningitidis, Streptococcus pneumoniae, and Staphylococcus aureus, evolutionary change at neutral (housekeeping) loci is more likely to occur by recombination than mutation and can result in the elimination of any deep-rooted phylogenetic signal.

Metagenomics: Application of Genomics to Uncultured Microorganisms

  • J. Handelsman
  • Biology
    Microbiology and Molecular Biology Reviews
  • 2004
Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community.

Convergence of Campylobacter Species: Implications for Bacterial Evolution

The nature of species boundaries in bacteria remains controversial. In particular, the mechanisms of bacterial speciation and maintenance in the face of frequent genetic exchange are poorly

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

It is suggested that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the ‘opportuni-troph’, exploiting spatially and temporally variable resources and the passive oligotroph, efficiently using low nutrient concentrations.