Chimerism

A total of 85 metagenomic libraries from the Tara Oceans project (54 (link)) were used to evaluate performance on real-world data (Data Set S1). For each library, only the first 10 million read pairs were used to control for the effect of library size on assembly quality. Different mapping settings were tested as described above. Assembly with SPAdes, Emirge, and Matam was performed as described above. The uchime_ref chimerism score (5 (link)) was calculated for each assembled SSU rRNA gene sequence with VSEARCH v2.5.0, using the filtered SILVA 132 SSU Ref NR99 database as reference. Code and results for the environmental metagenomes analyses are archived at https://doi.org/10.5281/zenodo.3909388.

We measured the efficacy of antimalarial compounds against P. yoelii or P. berghei in a ‘4-day test’ [60] as described previously [56] (link). We adapted this assay to measure the therapeutic efficacy against P. falciparum. Cohorts of age matched female (40 to 80, depending on the experiment) NOD^{scid/β2m−/−} were injected i.p. daily with hE throughout the experiment. When the mice reached ≥40% of chimerism in peripheral blood (7–9 days after initiation of injections), we infected them i.v. with 20·10⁶ parasites obtained from infected donors and the mice were randomly distributed in groups of n = 3 mice·group⁻¹ (day 0). Treatments were administered from day 3 until day 6 after infection. We measured the percentage of TER-119⁻YOYO-1⁺ (or SYTO-16⁺) hE in peripheral blood at day 7 after infection and recrudescence up to day 35 if the parasitemias were below our detection limit (0.01%). We determined the minimum size of each experimental group (n = 3) to detect a reduction of 50% in parasitemia in peripheral blood assuming Type I error α = 0.05 (confidence level) and Type II error β = 0.2 (power of the assay). This sample size was calculated upon the distribution of the decimal logarithm of the mean percentage of TER-119⁻YOYO-1⁺ parasitized hE, which is normally distributed (log parasitemia 0.334±0.01; n = 327 mice, P>0.2, Kolmogorov–Smirnov test of normality with Lilliefors' correction of significance) (Fig. 5D). The therapeutic efficacy of compounds was expressed as the effective dose (mg·Kg _bodyweight⁻¹) that reduces parasitemia by 90% with respect to vehicle treated groups (ED₉₀). All compounds and corresponding vehicles were administered orally at 20 ml·Kg⁻¹ or subcutaneously at 10 ml·Kg⁻¹, as appropriate. Chloroquine is included as quality control for each in vivo assay.