Alpha diversity estimate coefficient P value No. of OTUs shannon chao PD_whole_tree

Transcription

1 Supplementary Table 1. Paired differences between swab-1 and swab-2 in estimates of alpha diversity. Swab-1 mean Swab-2 paired Student t test P value paired Wilcoxon signed-rank test No. of unique OTUs Shannon's index chao PD_whole_tree Supplementary Table 2. Linear regression comparison of alpha diversity estimates with duration of time between swab-1 and swab-2. Alpha diversity estimate coefficient P value No. of OTUs shannon chao PD_whole_tree

2 Supplementary Table 3. Antibiotic use and anal microbial alpha diversity among HIV-positive participants. Alpha diversity Recent antibiotic use a estimate no (n=19) yes (n=6) P(wilcoxon) No. of unique OTUs Shannon s index Chao PD_whole_tree a Trimethoprim-sulfamethaxazole within 3 months. Clarithromycin data also were collected, but no recent use was reported. Supplementary Table 4. Contemporaneous plasma HIV load and anal microbial alpha diversity at swab-2 among HIVpositive participants.* Alpha diversity estimate coefficient P value observed_species -1.23E shannon -4.36E chao1 3.44E PD_whole_tree 5.08E * HIV load data were available for 13 of the 25 HIV-positive participants at swab-2. 26

3 Supplementary Table 5. Association of anal microbial beta diversity (weighted and unweighted UniFrac distance) with HIV status, T-cell counts, sexual activities, and smoking, and antibiotic use. Swab-1 a Swab-2 a unweighted weighted unweighted weighted HIV status T-cells/μL CD4 count CD8 count Unprotected sexual activity b No. of new male partners No. of male partners Anal intercourse, insertive Anal intercourse, receptive Anilingus, insertive Anilingus, receptive Fisting, insertive Fisting, receptive Fellatio, insertive Fellatio, receptive Smoking Cigarettes per day Antibiotic use TMP-SMX, clarithromycin none none TMP-SMX, Trimethoprim-sulfamethaxazole. a P-values, as calculated by Adnois method in QIIME. b As reported previously,[8] specific activities within the previous 12 months were reported in ordinal categories (0=none, 1=1-4 times, 2=5-9 times, 8=more than 200 times). 27

4 Supplementary Figure 1 28

5 Supplementary Figure relative abundance % I II Cluster HIV swab f_prevotellaceae_g_prevotella f_bacteroidaceae_g_bacteroides f_ruminococcaceae_g_faecalibacterium f_clostridiaceae_g_finegoldia f_streptococcaceae_g_streptococcus o_clostridiales_f_clostridiaceae f_lachnospiraceae_g_blautia f_ruminococcaceae_g_oscillospira f_lachnospiraceae_g_roseburia o_clostridiales_f_lachnospiraceae o_clostridiales_f_ruminococcaceae f_lachnospiraceae_g_.ruminococcus. f_veillonellaceae_g_phascolarctobacterium f_clostridiaceae_g_peptoniphilus f_ruminococcaceae_g_ruminococcus f_clostridiaceae_g_anaerococcus o_clostridiales_f_lachnospiraceae.1 f_.paraprevotellaceae._g_.prevotella. f_coriobacteriaceae_g_collinsella f_corynebacteriaceae_g_corynebacterium f_lachnospiraceae_g_coprococcus f_veillonellaceae_g_megasphaera f_enterobacteriaceae_g_escherichia o_fusobacteriales_f_fusobacteriaceae f_bifidobacteriaceae_g_bifidobacterium f_lachnospiraceae_g_dorea o_clostridiales_f_peptostreptococcaceae f_alcaligenaceae_g_sutterella o_clostridiales_f_ruminococcaceae.1 f_veillonellaceae_g_mitsuokella c_clostridia_o_clostridiales f_veillonellaceae_g_anaerovibrio f_peptostreptococcaceae_g_peptostreptococcus o_clostridiales_f_veillonellaceae f_clostridiaceae_g_clostridium f_lachnospiraceae_g_lachnospira f_.coprobacillaceae._g_catenibacterium f_campylobacteraceae_g_campylobacter c_bacteroidia_o_bacteroidales f_succinivibrionaceae_g_succinivibrio c_clostridia_o_clostridiales.1 o_bacteroidales_f_s24.7 f_bifidobacteriaceae_g_gardnerella f_erysipelotrichaceae_g_.eubacterium. f_porphyromonadaceae_g_porphyromonas f_veillonellaceae_g_acidaminococcus f_veillonellaceae_g_dialister o_coriobacteriales_f_coriobacteriaceae f_porphyromonadaceae_g_parabacteroides p_firmicutes_c_clostridia f_actinomycetaceae_g_actinomyces f_enterococcaceae_g_enterococcus p_firmicutes_c_clostridia.1 o_bacteroidales_f_rikenellaceae f_staphylococcaceae_g_staphylococcus o_lactobacillales_f_streptococcaceae f_actinomycetaceae_g_mobiluncus f_veillonellaceae_g_veillonella f_carnobacteriaceae_g_granulicatella o_clostridiales_f_catabacteriaceae f_actinomycetaceae_g_arcanobacterium f_lactobacillaceae_g_lactobacillus f_lachnospiraceae_g_lachnobacterium o_coriobacteriales_f_coriobacteriaceae.1 f_peptococcaceae_g_peptococcus f_.paraprevotellaceae._g_paraprevotella f_fusobacteriaceae_g_fusobacterium f_leptotrichiaceae_g_sneathia c_bacteroidia_o_bacteroidales.1 c_alphaproteobacteria_o_rf32