Table 2. Comparison of bacterial diversity between HIV SN and HIV+ on EFV and PI-based regimens.

Groups	Chao1	Observed species	PD_whole_tree	Shannon
HIV SN	1174.78 ± 357.48	727.14 ± 228.15	41.16 ± 9.26	5.70 ± 0.77
HIV+ EFV	859.09 ± 254.71	532.61 ± 170.11	30.03 ± 7.66	4.95 ± 0.84
HIV+ PI	797.73 ± 195.90	495.51 ± 123.81	30.52 ± 5.96	4.69 ± 0.73
HIV SN vs HIV+ EFV	0.0225	0.0375	0.0075	0.042
HIV SN vs HIV+ PI	0.012	0.021	0.006	0.018
HIV+ EFV vs HIV+ PI	0.459	0.499	0.848	0.38

Bacterial diversity values are given as mean ± standard deviation at a rarefaction depth of 25,025 sequences per sample and correspond to the first three rows. Alpha diversity was compared between HIV SN and HIV+ EFV and HIV+ PI by means of a non-parametric t-test using the compare_alpha_diversity.py script of QIIME. P values were FDR-corrected for multiple comparisons and are shown in the last three rows. Abbreviation: PD_whole_tree: Faith´s phylogenetic diversity, HIV SN: HIV seronegative, HIV+ EFV: HIV-infected individuals on EFV-based and HIV+ PI: HIV-infected individuals on a PI-based regimen.