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. Author manuscript; available in PMC: 2021 Jul 13.
Published in final edited form as: Cell Host Microbe. 2019 Nov 13;26(5):650–665.e4. doi: 10.1016/j.chom.2019.10.011

Figure 1: Rapid recovery during antibiotic administration in a human microbiota across antibiotics, with common trajectories of collapse and recovery but cage-specific end points.

Figure 1:

See also Figures S1 and S4.

(A) Schematic of humanization of germ-free mice, antibiotic treatment, and sampling.

(B,F) Culturable anaerobic and aerobic fecal densities in humanized mice treated for 5 days with (B) 20 mg streptomycin daily (n = 15), and (F) 3 mg ciprofloxacin twice daily (n = 14). Bacterial loads recovered during treatment (colored area). Error bars: S.E.M.

(C,G) Family-level composition in feces was similar in (C) streptomycin-treated and (G) ciprofloxacin-treated humanized mice (colored bars denote treatment period).

(D,H) Relative abundance of Bacteroides, S24-7, and Bacteroidetes in (D) streptomycin-treated and (H) ciprofloxacin-treated humanized mice.

(E,I) PCoA of community composition in humanized mice during (E) streptomycin or (I) ciprofloxacin treatment reveal a conserved trajectory. Analyses used weighted UniFrac distances.

(J) PCoA of humanized mice during ciprofloxacin treatment in two cages uncovered cage-specific differences.

(K) Family-level composition from the two cages in (H) revealed stochasticity of S24-7 recovery.