Seven years after the publication of the first microbial genome sequence — that of Haemophilus influenzae — the roster of microbial genomes has topped 100. Despite early fears that whole-genome sequencing might be economically justified only for human pathogens, this list represents a gratifyingly broad range of microbial phenotypes — soil bacteria and photosynthesizers, thermophiles and halophiles, animal and plant pathogens, and more. At least 12 prokaryotic phyla are represented, as are a few eukaryotes — enough to allow a meaningful examination of the Tree of (microbial) Life.

In the early days of molecular phylogenetics (the mid-1960s to the early 1990s), it was thought that sequencing was the path to enlightenment — more sequences of more genes could only improve the depth and resolution of our knowledge of life's history. But instead, our 100-genome world is riven by seemingly irreconcilable conflicts; ambiguities and discrepancies are the norm, rather than the exception. Some of modern biology's fundamental tenets — notably the darwinian–mendelian model of parent-to-offspring ('vertical') gene flow — have once again, at least for microbes, been thrown into doubt. Lateral (horizontal) gene flow — in which genes are transmitted across, rather than along, branches in family trees — is no longer an explanation of last resort, but a competitive model for the origin of microbial biodiversity.

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