Table 2 QTL mapping results of nasal microbiome relative abundance
From: Host genetic variation in mucosal immunity pathways influences the upper airway microbiome
A. Nasal vestibule | |||||||||
Bacteria genus (phylum/class/order/family) | Mean RA | rsID | Chr | Start | Alleles | Gene(s) | p | q | Beta |
Summer | |||||||||
Dermacoccus (Actinobacteria/Actinobacteria/Actinomycetales/Dermacoccaceae) | 7.9 × 10−5 | rs67386870 | 5 | 126156219 | A/C | LMNB1 | 2.46 × 10−7 | 0.016 | −1.10 |
rs77536542 | 5 | 168583325 | G/A | SLIT3 (1,2) | 6.35 × 10−8 | 0.005 | −1.27 | ||
rs117042385a | 19 | 5530692 | T/C | ZNRF4, TINCR | 1.61 × 10−8 | 0.002 | −1.16 | ||
rs28362459 | 19 | 5844792 | A/C | FUT3 | 9.47 × 10−7 | 0.047 | −0.81 | ||
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales/Micrococcaceae) | 4.1 × 10−4 | rs111354832 | 4 | 7136504 | –/CAT | FLJ36777, SORCS2 | 5.99 × 10−8 | 0.015 | −0.74 |
Winter | |||||||||
Kocuria (Actinobacteria/Actinobacteria/Actinomycetales/Micrococcaceae) | 5.2 × 10−4 | rs12713689a | 2 | 70427457 | G/A | C2orf42, TIA1 | 2.10 × 10−8 | 0.005 | −0.91 |
Aerococcus (Firmicutes/Bacilli/Lactobacillales/Aerococcaceae) | 2.2 × 10−4 | rs10505338 | 8 | 119755490 | A/G | SAMD12-AS1, TNFRSF11B | 2.02 × 10−7 | 0.038 | −0.81 |
Lactobacillus (Firmicutes/Bacilli/Lactobacillales/Lactobacillaceae) | 1.4 × 10−3 | rs4142162 | 13 | 81127842 | G/A | SPRY2, LINC00377 | 1.45 × 10−7 | 0.017 | −0.77 |
Combined | |||||||||
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales/Intrasporangiaceae) | 9.2 × 10−5 | rs11085969 | 19 | 15792546 | A/G | CYP4F12 | 5.84 × 10−8 | 0.005 | −0.91 |
Microbispora (Actinobacteria/Actinobacteria/Actinomycetales/Micrococcaceae) | 5.5 × 10−4 | rs2891405 | 12 | 113152097 | G/A | MIR1302-1, RPH3A | 1.50 × 10−7 | 0.038 | −0.81 |
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales/Micrococcaceae) | 3.5 × 10−4 | rs111354832a | 4 | 7136504 | –/CAT | FLJ36777, SORCS2 (2) | 3.45 × 10−8 | 0.017 | −0.77 |
Peptoniphilus (Firmicutes/Clostridia/Clostridiales/Tissierellaceae) | 8.9 × 10−5 | rs9865782 | 3 | 113652774 | A/G | GRAMD1C | 1.17 × 10−7 | 0.005 | −0.91 |
Paracoccus (Proteobacteria/Alphaproteobacteria/Rhodobacterales/Rhodobacteraceae) | 6.5 × 10−5 | rs9953410 | 18 | 29532946 | C/A | TRAPPC8, RNF125 | 2.21 × 10−7 | 0.038 | −0.81 |
Enterobacter (Proteobacteria/Gammaproteobacteria/Enterobacteriales/Enterobacteriaceae) | 6.4 × 10−5 | rs11042877 | 11 | 10576232 | A/C | MRVI1-AS1 | 3.86 × 10−7 | 0.017 | −0.77 |
rs12446497 | 16 | 7341674 | A/G | RBFOX1 | 5.84 × 10−7 | 0.005 | −0.91 | ||
B. Nasopharynx | |||||||||
Bacteria species (phylum/class/order/family) | Mean RA | rsID | Chr | Start | Alleles | Gene(s) | p | q | Beta |
Summer | |||||||||
Aerococcus (Firmicutes/Bacilli/Lactobacillales/Aerococcaceae) | 6.5 × 10−4 | rs7702475a | 5 | 58088523 | A/G | RAB3C | 3.97 × 10−8 | 0.010 | 0.77 |
Unclassified genus (Firmicutes/Bacilli/Lactobacillales/Aerococcaceae) | 5.3 × 10−4 | rs11888528 | 2 | 120118764 | C/T | C2orf76 | 1.43 × 10−7 | 0.038 | 0.79 |
Methylobacterium (Proteobacteria/Alphaproteobacteria/Rhizobiales/Methylobacteriaceae) | 4.3 × 10−4 | rs308961 | 3 | 12150014 | T/G | SYN2 | 8.12 × 10−7 | 0.034 | −0.70 |
rs10547084 | 4 | 37753111 | –/TCTC | RELL1,PGM2 | 4.93 × 10−7 | 0.031 | 0.77 | ||
rs67737950 | 4 | 40260058 | G/C | RHOH, LOC101060498 | 2.73 × 10−7 | 0.023 | 0.85 | ||
rs7702475 | 5 | 58088523 | A/G | RAB3C | 2.46 × 10−7 | 0.023 | 0.77 | ||
rs1278260 | 10 | 127731197 | C/A | ADAM12 | 6.21 × 10−7 | 0.031 | 0.95 | ||
Unclassified genus (Proteobacteria/Alphaproteobacteria/Caulobacterales/Caulobacteraceae) | 8.5 × 10−4 | rs927984 | 6 | 25412987 | T/C | LRRC16A | 2.78 × 10−7 | 0.036 | 0.94 |
rs1543603a | 6 | 25413922 | A/G | LRRC16A | 2.30 × 10−8 | 0.006 | 0.88 | ||
Winter | |||||||||
Mycobacterium (Actinobacteria/Actinobacteria/Actinomycetales/Mycobacteriaceae) | 2.2 × 10−4 | rs1802665 | 10 | 61788623 | G/T | ANK3 | 8.73 × 10−8 | 0.007 | −0.98 |
Gemella (Firmicutes/Bacilli/Gemellales/Gemellaceae) | 3.7 × 10−4 | rs17631306a | 1 | 111072322 | A/G | KCNA10, KCNA2 | 2.94 × 10−8 | 0.008 | 1.27 |
Unclassified genus (Firmicutes/Bacilli/Lactobacillales) | 5.7 × 10−4 | rs1153741 | 2 | 182860422 | G/A | PPP1R1C | 1.52 × 10−7 | 0.039 | −0.83 |
Combined | |||||||||
Gordonia (Actinobacteria/Actinobacteria/Actinomycetales/Gordoniaceae) | 1.1 × 10−4 | rs61925863 | 12 | 66694722 | C/G | IRAK3, HELB | 2.88 × 10−7 | 0.038 | −0.90 |
rs12435212a | 14 | 85483485 | G/T | LINC00911 | 1.93 × 10−8 | 0.005 | 0.88 | ||
Unclassified genus (Firmicutes/Clostridia/Clostridiales/Clostridiaceae) | 1.0 × 10−2 | rs9661504 | 1 | 205915667 | A/T | SLC26A9, FAM72C | 4.16 × 10−7 | 0.046 | −0.70 |
rs10232599 | 7 | 46035291 | G/A | IGFBP3, TNS3 | 1.14 × 10−7 | 0.029 | −0.67 | ||
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales) | 1.3 × 10−3 | rs12156316 | 8 | 41706484 | T/C | ANK1 | 8.16 × 10−7 | 0.042 | 0.58 |
rs10901086 | 9 | 134635034 | T/C | RAPGEF1, MED27 | 7.05 × 10−7 | 0.042 | 0.89 | ||
rs12244238 | 10 | 6083239 | G/A | IL2RA | 6.82 × 10−7 | 0.042 | −0.69 | ||
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales/Micrococcaceae) | 5.0 × 10−4 | rs3006458 | 1 | 153320372 | T/G | PGLYRP4 | 5.10 × 10−7 | 0.032 | −0.75 |
rs4774283 | 15 | 58114121 | T/G | GCOM1, ALDH1A2 | 2.56 × 10−7 | 0.032 | −0.57 | ||
rs4814474 | 20 | 16322199 | A/C | KIF16B | 9.3 5× 10−7 | 0.040 | 0.56 | ||
Rhodococcus (Actinobacteria/Actinobacteria/Actinomycetales/Nocardiaceae) | 6.4 × 10−5 | rs1653301a | 2 | 201076401 | A/G | C2orf47, SPATS2L | 1.45 × 10−8 | 0.004 | −0.82 |
Unclassified genus (Actinobacteria/Actinobacteria/Actinomycetales/Sporichthyaceae) | 1.5 × 10−4 | rs13128830 | 4 | 21455808 | T/C | KCNIP4 | 3.03 × 10−7 | 0.022 | 0.64 |
Unclassified genus (Proteobacteria/Alphaproteobacteria/Sphingomonadales/Sphingomonadaceae) | 5.1 × 10−3 | rs1653301 | 2 | 201076401 | A/G | C2orf47, SPATS2L (3) | 9.48 × 10−8 | 0.024 | −0.80 |