The short chain-fatty acids, other than acetate, that are produced in the Acidogenesis step are further converted to acetate, hydrogen gas and carbon dioxide by the acetogenic bacteria. β-oxidation is the mechanism of anaerobic oxidation of long chain fatty acids with as products hydrogen and acetate. The available H₂ and CO₂ is partly converted into acetate by the homoacetogenic bacteria. Both propionate and butyrate are important intermediates in anaerobic digestion, and then are converted by the hydrogen producing acetogenic bacteria into acetate and hydrogen (see table 1).

The acetogenic bacteria are obligate hydrogen producers and their metabolism is inhibited by hydrogen. Studies carried out with these bacteria have shown the narrow association between the H₂-producing acetogenic bacteria and the H₂-consuming methanogenic bacteria, thereby regulating the H₂ level in their Environment. This is of vital importance as these reactions are thermodynamically unfavorable (positive ΔGo’) unless the hydrogen partial pressure is maintained at an extremely low pressure. Methanogenic bacteria utilize molecular hydrogen in the usual anaerobic digester so rapidly that the hydrogen partial pressure can be kept as low as 10^-4 atm which is enough to ensure the active performance of the hydrogen producing acetogenic bacteria. This means that the degradation of higher fatty acids depends largely on the activity of methanogenic bacteria. Microbial association in which a H₂-producing organism can grow only in the presence of H₂-consuming organism are called syntrophic association. The coupling of formation and use of H₂ is called interspecies hydrogen transfer (HTS).