Strictly anaerobic, cellulolytic bacteria offer the potential to convert lignocellulosic biomass derived from forestry or agricultural waste-streams to alternative fuels such as ethanol and hydrogen (H₂). Current yields of ethanol and H₂ during cellulose fermentation, however, are very low. If biofuel production via direct cellulose fermentation to become practical, yields of ethanol or H₂ must be increased. Effective strategies to increase ethanol or H₂ production can only be developed through detailed knowledge of the relationships between genome content, gene and gene product expression, pathway utilization, and end-product synthesis patterns. Comparative bioinformatic analyses of mesophilic and thermophilic cellulolytic bacteria for which complete genome sequence data is available, in combination with metabolic data, suggests that genome content alone cannot predict which metabolic pathways will be utilized, and that genome content does not necessarily tell us about carbon and electron flux and end-product synthesis patterns.