New feel for new phyla

Michael Y Galperin

doi:10.1111/j.1462-2920.2008.01699.x

Abstract

According to the dictionary, the Latin term ‘phylum’ comes from Greek phylon (ϕũλov), which means ‘race, tribe or clan’ and is unrelated to either philia (ϕiλiα) meaning ‘love, affection’ or to the ‘feel’, which comes from Old English felan ‘to touch’. These similarly sounding words illustrate a key problem of systematic microbiology: How can we extract useful information from short sequence fragments and not be swayed by superficial similarities? One of the most useful approaches has been binning together sequences from related microorganisms, even if the nature of these organisms remained unknown. This resulted in a number of candidate microbial phyla that still have no cultivated representatives (Hugenholtz et al., 1998). Extensive sequencing has been the only way to get a ‘feel’ of these organisms, find out at least some information about their physiology and distribution in the environment. The ultimate goal, of course, is to get a complete genome sequence of the previously uncharacterized organism and use the power of comparative genome analysis to deduce its features.

Highlights

The phylum Verrucomicrobia, first recognized as a separate bacterial lineage more than 20 years ago (Albrecht et al, 1987; Hedlund et al, 1997), remains poorly characterized
Genomes of two organisms (Akkermansia muciniphila and Opitutus terrae) have been completed and three more genomes released in the draft form (Bacterium Ellin514, 7.5 Mbp, GenBank accession number ABOX00000000, Opitutaceae bacterium TAV2, 4.9 Mbp, ABEA00000000; and Verrucomicrobium spinosum, 8.2 Mbp, ABIZ00000000)
Tubulin genes were missing in A. muciniphila and O. terrae genomes. These results argue against bacterial origin of tubulin and suggest that Prosthecobacter acquired tubulin genes through lateral gene transfer from some eukaryotic cells after its divergence from other verrucomicrobial lineages

Summary

Introduction

The phylum Verrucomicrobia, first recognized as a separate bacterial lineage more than 20 years ago (Albrecht et al, 1987; Hedlund et al, 1997), remains poorly characterized. A genome of one more member of Verrucomicrobia, an extremely acidophilic methanotroph Methylacidiphilum infernorum, has been sequenced at the University of Hawaii (Hou et al, 2008). Akkermansia muciniphila is a strictly anaerobic bacterium, originally isolated from a human fecal sample, that can use gastric mucin as carbon, energy and nitrogen source (Derrien et al, 2004).

Results

Conclusion