Extended Data Fig. 3: Defined community mixing experiment (M2).
From: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome
(a) An outline of the process for producing the fecal mixing library. Zymo Gut Microbial Standard and Zymo High Concentration Spike-in are separately embedded at equal cell ratios at 1x or 3x concentration replicates. They are then combined during the cryofracturing step, and are then size sorted, amplified and sequenced in aliquots of 10,000 particles, of average size ~50μm, which were used for further analysis (b) Histograms of particle sizes for the replicates. (c) Scatterplots of technical (amplification) and biological (concentration) replicates, using both the relative abundance based on summed reads, and ASV prevalence among particles, which is the percentage of particles an ASV is found (excluding the Spike-in). (d) Scatterplot of ASV relative abundance and prevalence compared to absolute reference provided by the manufacturer. SAMPL-seq abundances are averaged between replicates (excluding Spike-in). (e) Histograms of the ASV per particle distribution by concentration (excluding Spike-in). (f) Barplot of the multiplet rate of each replicate, grouped by concentration. (g) Plot showing mixing rates of two defined communities (M1A and M1B), with each colored dot corresponding to a classified particle. (h) Heatmap of particles clustered by Bray-Curtis similarity and the Ward’s method.
