Major changes occured from adaptation to the caecal environment with up regulation of genes required for energy generation and carbohydrate metabolism/transport, while amino acids and nucleotide metabolism, translation, replication and cell wall biogenesis genes were among the down regulated genes.Fumarate respiratory and osmotic response genes were selected from the up regulated genes and were mutated and tested in the lab for their inhibitory effect and for competitive growth under anaerobic and osmotic environments showing variable responses. Association between chicken colonisation phenotype and gene mutation indicated that genes associated with osmolarity was more important than tri carboxylic acid (TCA) associated genes in their contribution to the colonisation phenotype.There is considerable scope for improvement in inactivated vaccines through a more rational approach. An inactivated vaccine prepared by formalising S.
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