Ron-specific; ECF sigma factorcluster 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3Table 1. Nineteen genes form the specific phylogroup A MPEC core genome. These genes cluster into three loci, including two adjacent genes ymdE and ycdU, ten genes from the phenylacetic acid degradation operon (feaR, feaB, paaFGHIJKXY) and the seven genes of the ferric citrate uptake system (fecIRABCDE).Figure 5. The carriage of the genes surrounding ymdE and ycdU. These data shows that several genes between pgaD and ycdU are more abundant in MPEC genomes from phylogroup A than they are in the wider phylogroup A population. These genes comprise what appears to be a genome island, flanked by the core genes efeB/phoH, and ghrA/TAPI-2 chemical information ycdXYZ. Although pgaB and pgaA, along with ymdE and ycdU, are present in less than 446 of all phylogroup A (blue open circles), only ymdE and ycdU are also present in at least 65/66 MPEC genomes (red filled circles), qualifying these as MPEC-specific core.A (100 of MPEC), pgaA is found only in approximately 80 of all phylogroup A (90 in MPEC). This suggests that the pga locus is relatively unstable and prone to attrition in different genomes of both MPEC and other phylogroup A strains. The pga genes are responsible for the biosynthesis of biofilm polysaccharides31, and so these data suggest against a consistent role for biofilms in mastitis. Unlike this attrition of the pga genes, in MPEC, ymdE and ycdU are robustly co-maintained. The adjacent gene ycdT could also be considered a core MPEC gene, since it is present in 65/66 strains, however its abundance in other phylogroup A strains is sufficiently high that it can be captured in the core genome of sixty-six randomly sampled stains more than 0.015 of the time, so although we have not identified it as part of the specific MPEC core, both its distribution and proximity to ymdE and ycdU suggest that this gene could also contribute to the MPEC lifestyle. The ycdT gene is annotated in EPZ004777 web MG1655 as a membrane-anchored diguanylate cyclase. This type of gene regulates the turnover of the second messenger cyclic-di-GMP, which is known to affect behaviourScientific RepoRts | 6:30115 | DOI: 10.1038/srepwww.nature.com/scientificreports/Figure 6. Carriage of the paa region in MPEC compared with phylogroup A E. coli. The core MPEC genes are coloured green, whilst a region of the paa locus which has been deleted in several MPEC is coloured yellow. The ybdA gene, which in MG1655 is a pseudogene, is outlined in magenta – the carriage for this gene is for the full length composite sequence from the MG1655 genome rather than for each half separately.such as motility, virulence, and biofilm production in a wide range of bacterial species32, and its homologue in Yersinia species (hmsT) regulates the pga genes (termed hmsHFRS) in that genus33. However, evidence suggests that although ycdT is co-regulated with the pga genes, the function of this gene is not linked to the expression of the pga operon34,35. For the phenylacetic acid degradation locus which, in MG1655, consists of a seventeen gene locus encoded by feaRB-tynA-paaZABCDEFGHIJKXY36, we detected only ten of these (feaR, feaB, paaFGHIJKXY) to be components of the MPEC-specific core genome. We include the feaR, feaB, and tynA in the paa locus since these genes are involved in the metabolism of phenylethylamine to phenylacetic acid37,38, which provides substrate for the pathway encoded by the paa genes. We then analysed the distribution of the paa locus and s.Ron-specific; ECF sigma factorcluster 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3Table 1. Nineteen genes form the specific phylogroup A MPEC core genome. These genes cluster into three loci, including two adjacent genes ymdE and ycdU, ten genes from the phenylacetic acid degradation operon (feaR, feaB, paaFGHIJKXY) and the seven genes of the ferric citrate uptake system (fecIRABCDE).Figure 5. The carriage of the genes surrounding ymdE and ycdU. These data shows that several genes between pgaD and ycdU are more abundant in MPEC genomes from phylogroup A than they are in the wider phylogroup A population. These genes comprise what appears to be a genome island, flanked by the core genes efeB/phoH, and ghrA/ycdXYZ. Although pgaB and pgaA, along with ymdE and ycdU, are present in less than 446 of all phylogroup A (blue open circles), only ymdE and ycdU are also present in at least 65/66 MPEC genomes (red filled circles), qualifying these as MPEC-specific core.A (100 of MPEC), pgaA is found only in approximately 80 of all phylogroup A (90 in MPEC). This suggests that the pga locus is relatively unstable and prone to attrition in different genomes of both MPEC and other phylogroup A strains. The pga genes are responsible for the biosynthesis of biofilm polysaccharides31, and so these data suggest against a consistent role for biofilms in mastitis. Unlike this attrition of the pga genes, in MPEC, ymdE and ycdU are robustly co-maintained. The adjacent gene ycdT could also be considered a core MPEC gene, since it is present in 65/66 strains, however its abundance in other phylogroup A strains is sufficiently high that it can be captured in the core genome of sixty-six randomly sampled stains more than 0.015 of the time, so although we have not identified it as part of the specific MPEC core, both its distribution and proximity to ymdE and ycdU suggest that this gene could also contribute to the MPEC lifestyle. The ycdT gene is annotated in MG1655 as a membrane-anchored diguanylate cyclase. This type of gene regulates the turnover of the second messenger cyclic-di-GMP, which is known to affect behaviourScientific RepoRts | 6:30115 | DOI: 10.1038/srepwww.nature.com/scientificreports/Figure 6. Carriage of the paa region in MPEC compared with phylogroup A E. coli. The core MPEC genes are coloured green, whilst a region of the paa locus which has been deleted in several MPEC is coloured yellow. The ybdA gene, which in MG1655 is a pseudogene, is outlined in magenta – the carriage for this gene is for the full length composite sequence from the MG1655 genome rather than for each half separately.such as motility, virulence, and biofilm production in a wide range of bacterial species32, and its homologue in Yersinia species (hmsT) regulates the pga genes (termed hmsHFRS) in that genus33. However, evidence suggests that although ycdT is co-regulated with the pga genes, the function of this gene is not linked to the expression of the pga operon34,35. For the phenylacetic acid degradation locus which, in MG1655, consists of a seventeen gene locus encoded by feaRB-tynA-paaZABCDEFGHIJKXY36, we detected only ten of these (feaR, feaB, paaFGHIJKXY) to be components of the MPEC-specific core genome. We include the feaR, feaB, and tynA in the paa locus since these genes are involved in the metabolism of phenylethylamine to phenylacetic acid37,38, which provides substrate for the pathway encoded by the paa genes. We then analysed the distribution of the paa locus and s.