Table 1. Analysis of clone libraries and classification of taxonomic OTUs.
| Sample | Hum_01 | Hum_04 | Hum_07 | Hum_08 | Hum_10 | Graz_12 | Graz_13 | Rgbg_1 | Rgbg_3 | Rgbg_F | Rgbg_F | Rgbg_3_ PMA | CR5 | CR8 | Classification | ||
| Sample type | Human skin, wipe | Human skin, wipe | Human skin, wipe | Human skin, wipe | Human skin, wipe | ICU, BiSKit | ICU, BiSKit | ICU, wipe | ICU, wipe | ICU, wipe | ICU, wipe | ICU, wipe, PMA | CR ISO5, BiSKit | CR ISO8, BiSKit | |||
| Detection method | Nested PCR | Nested PCR | Direct PCR | Nested PCR | Nested PCR | Nested PCR | Nested PCR | Direct PCR | Direct PCR | Nested PCR | Direct PCR | Direct PCR | Nested PCR | Nested PCR | |||
| Coverage | 90.5% | 100.0% | 98.1% | 93.8% | 97.7% | 97.6% | 97.9% | 100.0% | 97.4% | 100.0% | 97.2% | 95.1% | 86.5% | 94.9% | |||
| OTU ID, Acc. No | # of clones screened | 42 | 46 | 53 | 32 | 44 | 41 | 48 | 45 | 39 | 45 | 36 | 41 | 37 | 39 | Phylum | Genus |
| CR5_31_CC, JX865688 | – | – | – | – | – | – | 97.92% | – | – | – | 2.78% | – | – | – | Euryarchaeota | Halococcus | |
| CR8_2_DB, JX865696 | – | – | – | 12.50% | – | – | – | – | – | – | – | – | – | – | Euryarchaeota | unclassified Halobacteriaceae | |
| CR5_8_CD, JX865692 | – | – | – | 3.13% | – | – | – | – | – | – | – | – | – | – | Euryarchaeota | unclassified Halobacteriaceae | |
| FlD_6_EA, JX865727 | – | – | – | – | – | – | – | – | – | – | 8.33% | – | – | – | Euryarchaeota | unclassified Halobacteriaceae | |
| Zi1DN_20_FE, JX865743 | – | – | 11.32% | – | – | – | – | – | – | – | – | – | – | – | Euryarchaeota | Methanomethylovorans | |
| Gr13_H02, JX865738 | – | – | - | – | – | – | – | – | 7.69% | – | – | – | – | – | Euryarchaeota | Methanosarcina | |
| Gr13_H08, JX865739 | – | – | 3.77% | – | – | – | – | – | – | – | – | – | – | – | Euryarchaeota | Methanosarcina | |
| MM_2_BA, JX865665 | – | – | – | – | – | – | – | – | 15.38% | – | – | – | – | – | Euryarchaeota | Methanosarcina | |
| MM_6_BE, JX865673 | – | – | – | – | – | – | – | 8.89% | – | – | – | – | – | – | Euryarchaeota | Methanosarcina | |
| Zi3D_28_BC, JX865756 | – | – | – | – | – | – | – | – | – | – | – | – | – | 51.28% | Euryarchaeota | unclassified Euryarchaeota | |
| CMD_28_CE, JX865701 | – | – | 1.89% | – | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| FL_41_AC, JX865715 | – | – | – | – | – | – | – | – | – | – | – | 2.44% | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| Zi3D_26_BA, JX865755 | – | – | – | – | – | – | – | – | – | – | – | – | – | 30.77% | Thaumarchaeota | Candidatus Nitrososphaera | |
| AA_15_AE, JX865655 | 2.38% | – | – | – | 2.27% | – | – | 42.22% | – | – | 22.22% | 51.22% | – | 2.56% | Thaumarchaeota | Candidatus Nitrososphaera | |
| AF_14_AB, JX865661 | 2.38% | – | 9.43% | 34.38% | – | – | – | 44.44% | 5.13% | – | – | – | 2.70% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD_41_EA, JX865706 | – | 26.09% | 28.30% | – | – | 2.44% | – | – | 64.10% | - | 33.33% | 19.51% | 10.81% | 2.56% | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR5_14_EA, JX865684 | – | – | – | – | – | – | – | – | – | 100.00% | - | 19.51% | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR5_4_BB, JX865690 | – | – | – | – | – | 21.95% | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR8_1_AA, JX865693 | – | – | – | 3.13% | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR8_10_CA, JX865694 | – | – | – | 12.50% | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| FLD_48_FD, JX865726 | – | – | 3.77% | - | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| Gr12_E3, JX865735 | – | – | – | – | – | – | – | – | – | – | – | – | 5.41% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| Gr13_C7, JX865736 | – | – | 5.66% | – | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| Zi3P_15_CA, JX865760 | – | – | – | – | – | 68.29% | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD_3_CB, JX865702 | – | – | 22.64% | – | – | – | – | – | – | – | 19.44% | 4.88% | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD_40_CA, JX865705 | – | – | – | – | – | – | – | – | – | – | – | – | 2.70% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| AA_1_AA, JX865653 | 2.38% | – | – | – | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| AA_10_CA, JX865654 | 2.38% | – | – | – | – | – | – | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD2_17_AC, JX865709 | – | – | – | – | – | – | – | – | – | – | – | – | 8.11% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD2_30_FC, JX865710 | – | – | 13.21% | 28.13% | – | 7.32% | – | 4.44% | 2.56% | – | – | 2.44% | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD2_35_CD, JX865711 | – | – | – | – | – | – | – | – | – | – | – | – | 2.70% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR5_12_AB, JX865683 | – | – | – | – | – | – | – | – | – | – | – | – | 2.70% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CR5_47_DB, JX865691 | – | – | – | – | – | – | 2.08% | – | – | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| MM_13_DD, JX865663 | 90.48% | 73.91% | - | 6.25% | 97.73% | – | – | – | – | – | – | – | 37.84% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| MM_8_EC, JX865674 | – | – | – | – | – | – | – | – | – | – | 13.89% | – | 8.11% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| CMD_38_DA, JX865704 | – | – | – | – | – | – | – | – | – | – | – | – | 2.70% | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| Gr12_D2, JX865733 | – | – | – | – | – | – | – | – | 5.13% | – | – | – | – | – | Thaumarchaeota | Candidatus Nitrososphaera | |
| MM_32_DC, JX865670 | – | – | – | – | – | – | – | – | – | – | – | – | – | 12.82% | Thaumarchaeota | Candidatus Nitrososphaera | |
| Zi3D_12_CB, JX865752 | – | – | – | – | – | – | – | – | – | – | – | – | 16.22% | - | unclassified Archaea | unclassified Archaea | |
Abbreviations: ICU (intensive care units); CR (clean room).doi:10.1371/journal.pone.0065388.t001