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Table S1. Proportional Abundance, and Absolute Abundance of Penile Bacteria from the 266 Men Included in the HIV Seroconversion Cohort

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Table S1. Proportional Abundance, and Absolute Abundance of Penile Bacteria from the 266 Men Included in the HIV Seroconversion Cohort Table S1. Proportional abundance, and absolute abundance of penile bacteria from the 266 men included in the HIV Seroconversion Cohort. All men were uncircumcised. Proportional Abundance Absolute Abundance (16S copies/swab) Genus Median Q#1 Q#3 Median Q#1 Q#3 Prevotella 0.155 0.059 0.279 2.78E+07 9.78E+05 3.14E+08 Peptoniphilus 0.077 0.038 0.119 1.52E+07 1.66E+06 8.69E+07 Peptoniphilaceae<0.97*† 0.049 0.013 0.125 7.81E+06 2.97E+05 1.39E+08 Porphyromonas 0.032 0.010 0.067 4.47E+06 2.36E+05 9.88E+07 Finegoldia 0.029 0.005 0.104 3.37E+06 7.02E+05 2.07E+07 Corynebacterium 0.027 0.004 0.119 2.74E+06 7.12E+05 1.19E+07 Anaerococcus 0.025 0.008 0.061 4.38E+06 7.03E+05 2.10E+07 Dialister 0.018 0.002 0.045 1.76E+06 7.01E+04 3.40E+07 Lactobacillus 0.002 0.001 0.004 2.46E+05 3.33E+04 2.33E+06 Gardnerella 0.001 0.000 0.003 5.72E+04 9.27E+03 8.40E+05 Ezakiella 0.004 0.001 0.016 3.59E+05 2.59E+04 1.11E+07 Clostridiales incertae sedis XIII<0.97*† 0.003 0.000 0.010 3.80E+05 1.32E+04 1.10E+07 Mobiluncus 0.001 0.000 0.011 2.24E+05 1.18E+04 6.54E+06 Firmicutes<0.97*‡ 0.005 0.001 0.016 4.55E+05 1.76E+04 1.55E+07 Murdochiella 0.004 0.001 0.015 6.34E+05 2.70E+04 1.10E+07 Campylobacter 0.004 0.000 0.013 4.19E+05 1.69E+04 1.25E+07 Negativicoccus 0.003 0.000 0.018 3.83E+05 2.54E+04 6.11E+06 Saccharofermentans<0.97* 0.001 0.000 0.009 9.49E+04 7.09E+03 5.02E+06 Peptostreptococcus 0.004 0.000 0.027 2.13E+05 1.69E+04 1.38E+07 Proteobacteria<0.97*‡ 0.001 0.000 0.010 9.69E+04 7.26E+03 3.90E+06 Porphyromonas<0.97* 0.001 0.000 0.005 1.08E+05 4.03E+03 3.46E+06 Staphylococcus 0.000 0.000 0.004 8.00E+04 1.63E+04 3.13E+05 Clostridiales incertae sedis XI<0.97*† 0.001 0.000 0.003 1.04E+05 3.67E+03 2.42E+06 Escherichia/Shigella 0.000 0.000 0.002 3.52E+04 1.44E+04 1.32E+05 Pyramidobacter 0.000 0.000 0.003 2.85E+04 1.32E+03 1.19E+06 Peptococcus 0.001 0.000 0.002 1.17E+05 4.66E+03 2.49E+06 Streptococcus 0.000 0.000 0.002 2.59E+04 4.76E+03 2.32E+05 Jonquetella 0.000 0.000 0.001 1.60E+04 1.68E+03 3.01E+05 Actinomyces 0.000 0.000 0.001 6.25E+04 4.49E+03 5.74E+05 Bacteroidia<0.97*§ 0.000 0.000 0.003 2.93E+04 1.75E+03 2.05E+06 Varibaculum 0.000 0.000 0.002 4.50E+04 3.14E+03 8.46E+05 Sneathia<0.97* 0.000 0.000 0.002 2.56E+04 1.96E+03 4.25E+05 Veillonella 0.000 0.000 0.002 3.19E+04 2.70E+03 4.58E+05 Murdochiella<0.97* 0.000 0.000 0.002 2.30E+04 1.48E+03 8.33E+05 Fusobacterium 0.000 0.000 0.002 2.96E+04 1.71E+03 5.29E+05 Prevotellaceae<0.97*† 0.000 0.000 0.002 1.97E+04 1.23E+03 7.41E+05 Atopobium 0.000 0.000 0.001 1.30E+04 8.36E+02 2.31E+05 Spirochaetes<0.97*‡ 0.000 0.000 0.001 1.21E+04 4.03E+02 5.16E+05 Parvibacter<0.97* 0.000 0.000 0.000 1.28E+04 3.50E+02 2.21E+05 Bacteroidetes<0.97*‡ 0.000 0.000 0.001 7.90E+03 4.00E+02 2.65E+05 Peptostreptococcaceae<0.97*† 0.000 0.000 0.001 2.55E+04 3.88E+02 4.84E+05 Olsenella 0.000 0.000 0.001 8.59E+03 0.00E+00 2.18E+05 Porphyromonadaceae<0.97*† 0.000 0.000 0.001 9.35E+03 0.00E+00 8.89E+05 Dietziaceae<0.97*† 0.000 0.000 0.001 8.35E+03 0.00E+00 1.43E+05 Moryella 0.000 0.000 0.001 1.46E+04 0.00E+00 7.18E+05 Olsenella<0.97* 0.000 0.000 0.001 1.65E+04 0.00E+00 3.07E+05 Clostridia<0.97*§ 0.000 0.000 0.001 8.37E+03 0.00E+00 4.45E+05 Stomatobaculum<0.97* 0.000 0.000 0.000 4.55E+03 0.00E+00 2.74E+05 Acinetobacter 0.000 0.000 0.001 5.04E+03 0.00E+00 4.73E+04 Howardella<0.97* 0.000 0.000 0.000 1.83E+04 0.00E+00 3.59E+05 Facklamia 0.000 0.000 0.000 1.09E+04 0.00E+00 1.28E+05 Saccharibacteria incertae sedis 0.000 0.000 0.001 3.52E+03 0.00E+00 8.27E+04 Enterorhabdus<0.97* 0.000 0.000 0.000 2.94E+03 0.00E+00 1.16E+05 Parvimonas 0.000 0.000 0.001 3.54E+03 0.00E+00 2.38E+05 Sutterella 0.000 0.000 0.001 3.06E+03 0.00E+00 3.01E+05 Succiniclasticum<0.97* 0.000 0.000 0.000 2.23E+03 0.00E+00 1.73E+05 Synergistetes<0.97*‡ 0.000 0.000 0.001 3.60E+03 0.00E+00 3.73E+05 Micrococcus 0.000 0.000 0.000 2.30E+03 0.00E+00 1.75E+04 Ruminococcaceae<0.97*† 0.000 0.000 0.000 3.23E+03 0.00E+00 1.57E+05 Arcanobacterium 0.000 0.000 0.000 2.92E+03 0.00E+00 1.80E+05 Sneathia 0.000 0.000 0.000 1.34E+03 0.00E+00 5.78E+04 Sphingobacteriia<0.97*§ 0.000 0.000 0.000 1.30E+03 0.00E+00 7.58E+04 Megasphaera<0.97* 0.000 0.000 0.000 1.20E+03 0.00E+00 3.61E+04 Candidatus Saccharibacteria<0.97*‡ 0.000 0.000 0.000 1.95E+03 0.00E+00 1.21E+05 Mycoplasma 0.000 0.000 0.000 1.41E+03 0.00E+00 1.01E+05 Barnesiella<0.97* 0.000 0.000 0.000 7.43E+02 0.00E+00 3.44E+05 Eremococcus<0.97* 0.000 0.000 0.000 1.11E+03 0.00E+00 2.01E+04 Granulicatella 0.000 0.000 0.000 5.45E+02 0.00E+00 3.61E+04 Gemella 0.000 0.000 0.000 6.41E+02 0.00E+00 1.45E+04 Eubacteriaceae<0.97*† 0.000 0.000 0.000 5.02E+02 0.00E+00 5.77E+04 Dialister<0.97* 0.000 0.000 0.000 9.47E+01 0.00E+00 5.61E+04 Oribacterium<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 8.06E+04 Pseudomonas 0.000 0.000 0.000 0.00E+00 0.00E+00 8.43E+03 Aerococcus 0.000 0.000 0.000 0.00E+00 0.00E+00 1.17E+04 Peptostreptococcaceae incertae sedis<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 2.19E+04 Shuttleworthia<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 1.35E+04 Dermabacter<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 1.07E+04 Lachnospiracea incertae sedis<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 1.49E+04 Flavonifractor<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 2.69E+04 Treponema<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 1.02E+04 SR1 genera incertae sedis 0.000 0.000 0.000 0.00E+00 0.00E+00 1.57E+04 Bacteroidales incertae sedis<0.97*† 0.000 0.000 0.000 0.00E+00 0.00E+00 1.39E+04 Enterobacter<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 2.18E+03 Helcococcus 0.000 0.000 0.000 0.00E+00 0.00E+00 3.16E+03 Neisseria 0.000 0.000 0.000 0.00E+00 0.00E+00 2.28E+03 Bacteroides 0.000 0.000 0.000 0.00E+00 0.00E+00 2.49E+03 Chryseobacterium 0.000 0.000 0.000 0.00E+00 0.00E+00 1.55E+03 Comamonas 0.000 0.000 0.000 0.00E+00 0.00E+00 9.95E+02 Treponema 0.000 0.000 0.000 0.00E+00 0.00E+00 2.64E+03 Eubacterium 0.000 0.000 0.000 0.00E+00 0.00E+00 7.70E+03 Haemophilus<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 8.55E+02 Citrobacter<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 3.83E+02 Megasphaera 0.000 0.000 0.000 0.00E+00 0.00E+00 7.21E+02 Desulfovibrio<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 6.98E+02 Haemophilus 0.000 0.000 0.000 0.00E+00 0.00E+00 3.92E+02 Selenomonas<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 2.74E+02 Aeromonas 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Alloprevotella 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Fretibacterium 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Klebsiella 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Morganella 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Tenericutes<0.97*‡ 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Sphingobacterium 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Cytophagia<0.97*§ 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Cloacibacillus<0.97* 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Lactobacillales<0.97*¶ 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 Proteiniphilum 0.000 0.000 0.000 0.00E+00 0.00E+00 0.00E+00 *Genetic near neighbour, with <0.97% sequence similarity †Classified at the level of Family ¶Classified at the level of Order §Classified at the level of Class ‡Classified at the level of Phylum #Q, quartile Table S2.
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