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Figure 3 | Genome Biology

Figure 3

From: Temporal and technical variability of human gut metagenomes

Figure 3

Comparison of technical, temporal within-subject and between-subject variability at taxonomic and functional levels. (A,B) Spearman’s rank correlations of species profiles (A) and cluster of orthologous groups (COG) profiles (B) were highly correlated between different preservation methods (frozen versus RNALater (+4 to 10°C or RT for 1 week (1w) each), RNALater at +4 to 10°C versus RNALater at RT and frozen versus RNALater at +4°C, 24 h), less correlated between sampling time points (d7 versus d392), with lower correlation seen between subjects. Black bars represent group-wise medians. Relatively lower correlation between time points was apparent for the Alien samples (red squares), which were taken before and after antibiotics treatment (see main text). (C,D) Preservation-induced changes relative to between-subject variability was quantified by two-way ANOVA for species (C) and COGs (D), including only features with a relative abundance of at least 0.01% in three or more samples. In total, 7.3% and 5.33% of species and COGs, respectively, showed greater between-method variation than between-subject variation (features above the horizontal black line), but this was statistically significant for only 0.36% of COGs and none of the species tested (Benjamini-Hochberg false discovery rate, α = 0.05, Additional file 5). Vertical blue and green lines represent the threshold for statistical significance for d7 and d392, respectively. Percentages left and right of these lines identify the fractions of statistically significant and insignificant features with larger between-protocol variation for each time point, respectively.

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