Genomics against flatulence

In the past several months, eukaryotic genome sequencing has brought us the complete genome of the tiny green alga Ostreococcus ‘lucimarinus’ (Palenik et al., 2007) and a draft genome of the mosquito Aedes aegypti (Nene et al., 2007). Given that the genome sequence of another Ostreococcus species, Ostreococcus tauri, has been sequenced less than a year ago (Derelle et al., 2006), the availability of the O. lucimarinus genome opens a possibility to study the evolution of this unicellular planktonic organism and its adaptation to the life in the surface layer of the sea. There has been also exciting news from archaeal and bacterial genome sequencing. The list of recently sequenced genomes (Table 1) includes bacteria that inhabit a variety of ecological niches and degrade numerous environmental contaminants, as well as two g-proteobacteria with near-minimal gene sets. Archaea (archaebacteria) are generally viewed as freeliving organisms capable of surviving at extremely high temperatures, salt concentrations and extreme pH values. The discoveries, primarily in the past several years, of various mesophilic archaea have done little to shatter the perception of archaea as exotic organisms with little relevance to everyday human life. Indeed, there are no known human pathogens among the Archaea. Nevertheless, archaea play a key role in human gut, accounting for one of its activities that usually goes unmentioned, namely, production of gas. Some of this gas, consisting largely of methane and hydrogen, makes it all the way back the gastrointestinal tract and shows up in human breath. Most of the gas, however, is released from the large intestine the natural way, by some estimates, up to 0.5 l day-1 (see McKay et al., 1985; Suarez et al., 1997). Although the excreted gas has a complex and variable chemical composition, its methane component is produced by methanogenic bacteria, which, as we now know, are actually not bacteria but archaea. Isolation of methanogens from human feces was first reported almost 40 years ago (Nottingham and Hungate, 1968). The isolated organism was similar to the ruminal methanogen Methanobacterium ruminantium, described by Paul H. Smith and Robert E. Hungate (1958) several years earlier. The culture counts, estimated from serial dilutions, were in the range of 2 ¥ 10 to 2 ¥ 10 organisms g-1. In the spirit of the time, the validity of the latter figure is discussed in the article (which is freely available on line at the Journal of Bacteriology website http://jb.asm.org/cgi/reprint/96/6/2178 or through PubMed Central) with the following details: