Fig. 4 |. Prominent public clonotypes in gaGCs of GF and Oligo-MM¹²-colonized mice.

(a) CDR_H3 aa sequence logos for B cells bearing public V_H1–47/J_H4 or J_H2 rearrangements of 11 or 12 aa length (left) or V_H1–12/J_H3, 7 aa length (right), sequenced from GF gaGCs. (b) frequency across mice/samples of B cells fitting public clonotype criteria or carrying other V_H1–47 or V_H1–12 rearrangements. Each bar represents one sample. Data are for 7 GF mice (GF1–7) and 3 Oligo-MM¹²-colonized mice (MM¹²1–3). D, duodenal; I, ileal; C, cecal colonic mLN; P, Peyer’s patch. (c) Circos plots showing distribution of V_H1–47 and V_H1–12 public clonotypes in a second cohort of sex and age-matched SPF, GF, and Oligo-MM¹²-colonized mice. Each segment represents pooled mLN and PP GC B cells from one mouse, with clones ordered clockwise from largest to smallest. Only clones containing identical CDR_H3s are linked (see Online Methods for full description). Gated as in Extended Data Fig. 9b; all samples were sequenced in a single experiment. (d) Circos plot as in (c) showing all public IgH clonotypes shared across mice housed under the indicated conditions. Lines connect clonotypes with the same V_H/CDR_H3/J_H aa sequence. Left, all clones; right, only clones spanning ≥ 30 total wells. In (c, d), only clones found in at least 2 wells from the same mouse were linked.