Fig. 1.
Sequential changes in the relative abundance of two members of the 15-member artificial human gut microbiota and correlation with the appearance of two previously undescribed phages. (A) Relative abundance plot for each bacterial species as a function of time for either the live p-VLP or the heat-killed p-VLP treatment groups. Mean values ± SEM are shown (n = 5 mice). The color key next to the plot indicates the identity of each bacterial species. (B and C) Plots of the relative abundance (fraction of the total community; mean ± SEM; n = 5 animals per treatment group) of B. caccae and B. ovatus in the fecal microbiota of gnotobiotic mice as a function of time before and after gavage with live purified VLPs pooled from the fecal microbiota of five human donors or a control heat-killed version of the same p-VLP preparation (time of gavage indicated by the upward pointing arrow; t = 0 on the x axis refers to the time of introduction of the 15-member artificial community into germ-free animals). The change in abundance of these Bacteroides spp. occurs in a reproducible sequence among individually caged mice that received live but not heat-killed p-VLPs. (D and E) Changes in the abundance of two phages, derived from the p-VLP sample, in the fecal microbiota of recipient gnotobiotic mice. Differences in the time course of change in bacterial and viral abundances are highlighted by the gray shading (lighter for B. caccae and ϕHSC01). Insets in D and E are assembled genome sequences for ϕHSC01 and ϕHSC02. The location of genes on the positive strand (green) and negative strand (red) are shown; those that have significant sequence similarity to known viral genes are colored blue (blastp E-value <10−5; Dataset S1). The inner plot represents GC skew based on 200-bp windows (yellow, G/C ratio is greater than the average for the genome; purple, ratio is lower than the average).