TABLE 1.
Summary of the endophytic data set from all peer-reviewed publications with prokaryotic 16S rRNA gene sequencesa
| Phylogenetic affiliationb | No. of sequences | % of sequences |
|---|---|---|
| Bacteria | 7,319 | |
| Acidobacteria | 53 | 0.72 |
| Actinobacteria | 1,461 | 19.88 |
| Armatimonadetes | 6 | 0.08 |
| Bacteroidetes | 462 | 6.29 |
| GOUTA4c | 1 | 0.01 |
| ODc | 6 | 0.08 |
| TM7c | 2 | 0.03 |
| Chlamydiae | 8 | 0.11 |
| Chlorobi | 5 | 0.07 |
| Chloroflexi | 3 | 0.04 |
| Cyanobacteria | 102 | 1.39 |
| Deinococcus-Thermus | 7 | 0.1 |
| Elusimicrobia | 1 | 0.01 |
| Firmicutes | ||
| Bacilli | 1,132 | 15.41 |
| Clostridia | 68 | 0.93 |
| Fusobacteria | 3 | 0.04 |
| Nitrospirae | 3 | 0.04 |
| Planctomycetes | 5 | 0.07 |
| Proteobacteria | ||
| Alpha- | 1,337 | 18.2 |
| Beta- | 736 | 10.02 |
| Delta- | 26 | 0.35 |
| Epsilon- | 3 | 0.04 |
| Gamma- | 1,878 | 25.56 |
| Spirochaetae | 3 | 0.04 |
| Tenericutes | 2 | 0.03 |
| Verrucomicrobia | 6 | 0.08 |
| Archaea | 29 | |
| Euryarchaeota | 23 | 0.31 |
| Thaumarcheota | 6 | 0.08 |
| Total | 7,348 |
a
Endophytic sequences with >300 bp were retrieved from peer-reviewed manuscripts available in the ISI Web of Science and PubMed databases (as of 1 March 2014).
b
Based on comparison with the small-subunit rRNA SILVA database (version 115) (372) by using the SINA aligner (364).
c
Candidate division phyla.