Strain‐specific genomic regions of Ruminococcus flavefaciens FD‐1 as revealed by combinatorial random‐phase genome sequencing and suppressive subtractive hybridization

Abstract

Summary Two closely related strains of the Gram‐positive, cellulolytic ruminal bacterium Ruminococcus flavefaciens were compared at the genomic level by suppressive subtractive hybridization. The two strains investigated in this study differ by 1.94% in their respective 16S rDNA genes. Three hundred and eighty‐four PCR‐amplified products were cloned and then screened for their strain identity by dot blot hybridization. Based on redundancy percentages of the clones sequenced, 9.5% of the genome of the R. flavefaciens FD‐1 strain is not present in the JM1 strain. The majority of identities of individual cloned subtracted products (642 bp average length) bore no relation to deposited sequences in GenBank (42% of the subtracted library), whereas of those with putative assigned functions 7% are loosely associated with fibre‐degradation, 6% with insertion elements, transposons and phage‐like ORFs, 5% with cell membrane associated proteins and 3% with signal transduction. Subtracted sequences were then supplemented with the draft (2 × coverage) genome sequence of R. flavefaciens FD‐1 to indicate potential regions of rearrangement within the genome, including a novel insertion sequence.

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