TABLE 2.
Overview of analyses for each of the four species examined at the strain level and for all species combined in aggregatea
| Adol | Long | Bifi | Anim | In aggregate | |||
|---|---|---|---|---|---|---|---|
| A | Marker gene-based phylogeny (StrainPhlAn) |
Longitudinal stability | Yes | Yes | Yes | No | Yes |
| Stability GG > stability AA/AG | No | No | NA | NA | No | ||
| Twin effect | No | No | No | No | No | ||
| B | % of shared marker-SNPs (MIDAS) |
Longitudinal stability | Yes | Yes | Yes | No | Yes |
| Stability GG > stability AA/AG | Yes | Yes | NA | NA | Yes | ||
| Twin effect | Yes | No | No | No | No | ||
| C | Synteny (all regions for each species in aggregate) |
No. of gene regions | 7 | 10 | 4 | 0 | 21 |
| Longitudinal stability | 6/7 | 4/10 | 2/4 | NA | Yes | ||
| Stability GG > stability AA/AG | 0/2 | 0/8 | 0/0 | NA | No | ||
| Twin effect | 4/7 | 0/8 | 1/4 | NA | No | ||
| D | Enriched in GG vs AA/AG (16S rRNA SVs) | Yes | Yes | Yes | No | Yes | |
Panels A to C show significance for our three strain-level approaches. StrainPhlAn results are based on best tree values from the RAxML hill-climbing algorithm. Within each panel, “longitudinal stability” refers to significantly greater similarity of Intra (same person over time) versus Unrelated (between unrelated people) comparison categories. “Stability GG > stability AA/AG” refers to greater mean “Intra” values for GG individuals than for AA/AG individuals (i.e., is there greater stability within lactase-nonpersistent than lactase-persistent individuals). Finally, “Twin effect” refers to greater similarity of Same Family (between twin siblings) than Unrelated comparison categories. Panel D shows significance of genotypic enrichment from 16S rRNA SV data across the broad TwinsUK data set (n = 1,680). In each panel, “yes” and “no” refer to significance of the statistical test as described in the main text, while “NA” indicates that 3 or fewer samples were available in at least one category. In panel C (synteny), the number of significant regions out of the total number of regions with sufficient comparisons is shown. P values are shown in Table S1, tabs 5 and 6. Species abbreviations are as follows: Adol, B. adolescentis; Long, B. longum; Bifi, B. bifidum; Anim, B. animalis.