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The 16S rRNA gene is conserved across all bacteria and as such is routinely targeted in PCR surveys of bacterial diversity. PCR primer design aims to amplify as many different 16S rRNA gene sequences from as wide a range of organisms as possible, though there are no suitable 100% conserved regions of the gene, leading to bias. In the gastrointestinal tract, bifidobacteria are a key genus, but are often under-represented in 16S rRNA surveys of diversity. We have designed modified, 'bifidobacteria-optimised' universal primers, which we have demonstrated detection of bifidobacterial sequence present in DNA mixtures at 2% abundance, the lowest proportion tested. Optimisation did not compromise the detection of other organisms in infant faecal samples. Separate validation using fluorescence in situ hybridisation (FISH) shows that the proportions of bifidobacteria detected in faecal samples were in agreement with those obtained using 16S rRNA based pyrosequencing. For future studies looking at faecal microbiota, careful selection of primers will be key in order to ensure effective detection of bifidobacteria. [ABSTRACT FROM AUTHOR]

We have investigated the use of a natural transformation protocol to introduce mutations into Actinobacillus pleuropneumoniae serotypes 1 and 5b. For both strains tested, we recovered 1 in 108 transformants during culture in rich medium, a result that was independent of the growth phase. This low frequency of transformation of A. pleuropneumoniae did not increase when bacteria were grown under conditions known to be optimal for induction of competence in Haemophilus influenzae. Using linearised plasmid DNA containing a kanamycin cassette inserted into the sodC gene of A. pleuropneumoniae serotype 1, we showed that natural transformation can be used as a simple method for introducing allele replacements into this bacterium, and can be used to transfer mutations from one serotype to another. [Copyright &y& Elsevier]

APXIVA is an RTX toxin of Actinobacillus pleuropneumoniae that is a candidate antigen to differentiate infected from vaccinated animals (DIVA). Insertion of ISApl1 into the apxIVA gene is known to compromise an APXIVA-based DIVA approach, as is potentially a TGG to TGA mutation in the apxIVA gene. ISApl1 was found in 63/349 (18.1%) A. pleuropneumoniae isolates from England and Wales including serovars 2, 3, 6-8 and 12. No ISApl1 insertions into apxIVA were found. Only two serovar 3 isolates contained the TGG to TGA mutation. We conclude that an ApxIVA-based DIVA approach would potentially be viable in England and Wales., (Copyright 2010 Elsevier Ltd. All rights reserved.)