Methanosphaera stadtmanae has the most restricted energy metabolism of all methanogenic archaea. This human intestinal inhabitant can generate methane only by reduction of methanol with H 2 and is dependent on acetate as a carbon source. We report here the genome sequence of M. stadtmanae, which was found to be composed of 1,767,403 bp with an average G؉C content of 28% and to harbor only 1,534 protein-encoding sequences (CDS). The genome lacks 37 CDS present in the genomes of all other methanogens. Among these are the CDS for synthesis of molybdopterin and for synthesis of the carbon monoxide dehydrogenase/acetylcoenzyme A synthase complex, which explains why M. stadtmanae cannot reduce CO 2 to methane or oxidize methanol to CO 2 and why this archaeon is dependent on acetate for biosynthesis of cell components. Four sets of mtaABC genes coding for methanol:coenzyme M methyltransferases were found in the genome of M. stadtmanae. These genes exhibit homology to mta genes previously identified in Methanosarcina species. The M. stadtmanae genome also contains at least 323 CDS not present in the genomes of all other archaea. Seventythree of these CDS exhibit high levels of homology to CDS in genomes of bacteria and eukaryotes. These 73 CDS include 12 CDS which are unusually long (>2,400 bp) with conspicuous repetitive sequence elements, 13 CDS which exhibit sequence similarity on the protein level to CDS encoding enzymes involved in the biosynthesis of cell surface antigens in bacteria, and 5 CDS which exhibit sequence similarity to the subunits of bacterial type I and III restriction-modification systems.There are two types of methanogenic archaea, those belonging to the order Methanosarcinales, which contain cytochromes and which can use methanol, methyl amines, acetate, and/or CO 2 plus H 2 as methanogenic substrates, and those belonging to the orders Methanobacteriales, Methanomicrobiales, Methanococcales, and Methanopyrales, which are devoid of cytochromes and which can use CO 2 plus H 2 and/or formate only to fuel anaerobic growth (95, 102). The energy metabolism of both types of methanogens has been investigated in detail (17). However, there are still a few pertinent questions. For example, why is the growth yield on H 2 and CO 2 of methanogens lacking cytochromes considerably lower (Ͻ50%) than that of cytochrome-containing methanogens? The growth yield on H 2 and CO 2 of Methanobrevibacter arboriphilus is 1.3 g/mol methane, whereas that of Methanosarcina barkeri is 7.3 g/mol (101). Could the reason for this be that in cytochrome-containing methanogens two steps in the reduction of CO 2 to methane, methyl transfer from methyl-tetrahydromethanopterin (methyl-H 4 MPT) to coenzyme M and reduction of the heterodisulfide coenzyme M-S-S-coenzyme B (CoM-S-S-CoB) with H 2 , are coupled with energy conservation, whereas in methanogens without cytochromes only one step, the methyltransfer reaction, is coupled? Indeed, methanogens with cytochromes contain a heterodisulfide reductase (HdrDE) that is anchored via a cytoc...