Extended Data Figure 6. Specificity of targeting and temporal variation in the prevalence of IgA-targeted or nontargeted taxa.

Specificity values from the indicator species analysis were calculated across all time points for the 30 OTUs identified as consistently IgA-targeted or not targeted in Figure 1a. Prevalence of the taxa, defined as detection in either the IgA+ or IgA- fraction, was plotted alongside the percentage of samples in which a given taxon had a positive or negative IgA index (n=4,186 IgA index values analyzed). The results reveal a group of OTUs that increased in prevalence over the course of the first two years of postnatal life and had very high ‘specificity’ for either the IgA⁺ or IgA⁻ fraction (i.e., across the population of fecal samples, the majority of 16S rRNA reads for a given OTU were detected in one of the two fractions). This group included R. torques OTU C.6 and C. nexile OTU 4436046 that were IgA targeted in the majority of twins (when they are detectable in their microbiota), as well as Ruminococcus sp. ce2 OTU C.39 which was IgA-negative in most of the children. A second group of OTUs becomes more prevalent with age but members had much weaker, albeit statistically significant, association with one or the other sorted fraction (e.g., R. gnavus OTU C.4 and B. vulgatus OTU C.15). A third group of OTUs was highly specific for a given sorted fraction but were only detected in a minority (≤20%) of children. This latter group included two strongly IgA-targeted OTUs assigned to A. muciniphila (OTU 588471 and OTU 4306262). Intriguingly, these two OTUs co-occurred just once among the 176 BugFACS samples in which A. muciniphila was detected (P<0.0001, chi-squared test).