genomes approaches 500, there seems to be no end to the ways in which genes can be arranged—on linear chromosomes or circular, on one or many, tightly compacted or (in many eukaryotic microbes) separated by “junk” DNA 10 times their length. The number of genes in the genome of a free-living bacterium ranges from 500 to 10,000 or more; the largest bacterial genomes are more than twice the size of the smallest eukaryotic genomes. In contrast, the genomes of many parasitic or symbiotic microbes are highly reduced, with not nearly enough genes to support them independently of their hosts.

Even within a single clonal culture established from a single cell, there will probably be multiple forms of the genome. Many bacteria, especially pathogens, have elaborate mechanisms for rearranging their genes. The mechanisms serve as mutational switches, ensuring that as the microbe’s environment changes due to shifts in chemical, physical, or biological conditions, there will be variants in the population that can flourish. For example, no matter what defenses a host’s immune system mounts against the pathogen, there will be some resistant variants in the pathogen’s population. Variability is also achieved by exchange between genomes: recombination (similar to the genetic exchange that occurs in sexual reproduction) constantly reshuffles the variants (alleles) of genes in the population, generating new adaptive combinations. Plasmids, small and often self-transmissible packets of genes that encode environmentally relevant functions, are rife.

It is, however, the pervasiveness of lateral gene transfer between species that most profoundly challenges the notion that a single bacterial species has a single genome. Several natural processes—transport by viruses, bacterial “mating,” and the direct uptake of DNA from the environment—carry genetic information from one species to another. These processes are regulated and evolutionarily preserved; they are turned on when they are most likely to result in gene transfer, and genes that must function together are often transferred together, forming genomic “islands” (pathogenicity islands, symbiosis islands, or biodegradation islands). Genomic plasticity is an evolved strategy. No single sequence can be said to be the genome sequence of the bacterial species Escherichia coli. And the variations are decidedly not like the trivial differences that account for much of the 0.1% sequence variation among humans. When genomes of multiple strains of the same species (like E. coli K12, O157:H7, and another dozen now available) are compared, they differ up to 25% in genome size and in the number and kinds of genes they carry. Indeed, the genes that are shared by all sequenced E. coli strains amount to less than 40% of the genes present in the species as a whole (see Figure 2-1). Microbial genomicists have started to think in terms of microbial “species genomes” or pangenomes, which comprise a core of genes shared by all strains of a species and a library,

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