PMC:3317825 / 12074-14612
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3317825","sourcedb":"PMC","sourceid":"3317825","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3317825","text":"Phylogeny\nThe 491 orthologous genes were used to infer phylogenetic relationships of the 28 Staphylococcus strains. The phylogenetic tree inferred from concatenated genes (Figure 1), as well as the majority rule consensus of the individual gene trees (Additional file 2, Figure S1) demonstrated that the vast majority of genes supported the monophyly of the 16 S. aureus strains (98%), the monophyly of the two S. epidermidis strains (99%), and the monophyly of the clade of S. aureus and S. simiae (81%), supporting previous suggestions that S. simiae is the putative sister group to S. aureus [11]. Of the 491 gene trees, 486, 491, and 322 (99%, 100%, and 65.6%) supported these three nodes with bootstrap support in excess of 70%, and none had a strongly supported conflicting signal compared to that topology.\nFigure 1 Phylogenetic tree inferred from concatenated genes. Maximum likelihood tree obtained from a concatenated nucleotide sequence alignment of the orthologous core genes for the 28 Staphylococcus strains and Macrococcus caseolyticus JCSCS5402 (outgroup). The horizontal bar at the base of the figure represents 0.1 substitutions per nucleotide site. The percentages of genes that support the branches of the tree are indicated. The most basal Staphylococcus lineage in our phylogenetic trees was S. pseudintermedius, followed by S. carnosus. Although support for these two nodes involved only 217 and 156 (44% and 32%) of the 491 gene trees, there were only a few instances of genes that had a strongly supported conflicting signal compared to that topology. Only 37 and 17 (7.5% and 3.5%) of the 491 genes had a conflicting evolutionary history for these two nodes with bootstrap support in excess of 70%, while 107 and 56 (21.8% and 11.4%) supported these two nodes with bootstrap support in excess of 70%. Staphylococcus species which are indigenous to humans include S. aureus, S. epidermidis, S. caprae, S. capitis, S. warneri, S. hominis, S. haemolyticus, S. lugdunensis, and S. saprophyticus [61]. S. carnosus has not been isolated from human skin or mucosa, and its natural habitat is unknown despite its natural occurrence in meat and fish products [26]. S. pseudintermedius is a coagulase-positive species from animals [62], and M. caseolyticus is typically isolated from animal skin and food such as milk and meat [13]. Although species indigenous to animals may be found occasionally on humans by recent contact [61,63], our phylogeny suggests that human adaptation evolved after the split of S. carnosus.","divisions":[{"label":"Title","span":{"begin":0,"end":9}},{"label":"Figure caption","span":{"begin":814,"end":1248}}],"tracks":[{"project":"2_test","denotations":[{"id":"22272658-16166694-10678880","span":{"begin":596,"end":598},"obj":"16166694"},{"id":"22272658-8118787-10678881","span":{"begin":2021,"end":2023},"obj":"8118787"},{"id":"22272658-19060169-10678882","span":{"begin":2180,"end":2182},"obj":"19060169"},{"id":"22272658-16014483-10678883","span":{"begin":2251,"end":2253},"obj":"16014483"},{"id":"22272658-19074389-10678884","span":{"begin":2347,"end":2349},"obj":"19074389"},{"id":"22272658-8118787-10678885","span":{"begin":2446,"end":2448},"obj":"8118787"},{"id":"22272658-17050817-10678886","span":{"begin":2449,"end":2451},"obj":"17050817"}],"attributes":[{"subj":"22272658-16166694-10678880","pred":"source","obj":"2_test"},{"subj":"22272658-8118787-10678881","pred":"source","obj":"2_test"},{"subj":"22272658-19060169-10678882","pred":"source","obj":"2_test"},{"subj":"22272658-16014483-10678883","pred":"source","obj":"2_test"},{"subj":"22272658-19074389-10678884","pred":"source","obj":"2_test"},{"subj":"22272658-8118787-10678885","pred":"source","obj":"2_test"},{"subj":"22272658-17050817-10678886","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93c8ec","default":true}]}]}}