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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
  1. A. Nasal vestibule. Fourteen host variants were associated at a q < 0.05 with the relative abundance of 10 genera. rs111354832 is associated with an unclassified genus of family Micrococcaceae in the summer and in the combined sample. B. Nasopharynx. Twenty-three host variants were associated at a q < 0.05 with the relative abundance of 14 genera. At this site, 2 SNPs (rs1653301 and rs7702475) are associated with more than one bacterium. rsIDs presented for dbSNP142. aGenome-wide significant result (p < 5 × 10−8). Alleles presented as minor/major. Direction of effect is presented for the minor allele. RA relative abundance, Chr chromosome. Gene labels 1–4 correspond to genes previously reported in either the Bonder [55] or Goodrich [19] GWAS. 1, Goodrich (fecal; unclassified genus of family Clostridiaceae); 2, Bonder (fecal; PWY-6948_sitosterol_degradation_to_androstenedione); 3, Goodrich (fecal; genus Blautia)