MGV

1 Summary table before filtering duplication

	time	gel	Number of samples	Mean	Median	SD
1	0	Gel	28	6725.900	3680.5	7204.986
2	0	No gel	28	9132.704	8427.0	5962.919
3	24	h	26	8521.962	7751.5	5669.882
4	5	Gel	28	5547.864	2675.5	6111.219
5	5	No gel	29	8127.179	7932.0	4367.264
Full Table

	gel	Number of samples	Mean	Median	SD	IQR1	IQR3
1	Gel	70	6515.815	3724.0	6613.201	201.0	11448.5
2	h	28	8729.357	7751.5	6215.736	4367.5	11182.5
3	No gel	66	8617.333	8099.0	5094.618	4899.0	11733.0

	Number of samples	Mean	Median	SD	IQR1	IQR3
1	139	7742.163	8011	5876.105	2802	11325

SI Appendix, Table S2. Number of reads per sample type.

G0 – sample collected with lubrication and stored at -80°C within one hour of sampling.

N0 – sample collected without lubrication and stored at -80°C within one hour of sampling.

G5 - sample collected with lubrication and stored at -80°C within five hours of sampling.

N5 - sample collected without lubrication stored at -80°C within five hours of sampling.

G24 - sample collected 24 hours after first sampling stored at -80°C within one hour.

Rarefaction was adjusted to a minimum of 2000 reads.

2 Reads number

2.1 Summary statistics

time	n	pval	median	sd
Paired P-values gels Vs. No gel
0	27	0.009609835	4577.5	6612.864
5	28	0.003493442	6106.5	5403.185

gel	n	pval	median	sd
Paired P-values Immediate freeze Vs. 5 hours delay
Gel	28	0.7120570	985.0	6754.861
No gel	28	0.1817423	8172.5	5897.082

Figre 1a. Number of reads per sample type. 149 samples were included. Each point represents one sample, red dashed line represents the rarefaction threshold selected (2000 reads/sample). Red, blue and green circles represent samples collected with gel, without gel, and samples collected 24 hours after primary sample collection (in vivo) respectively. Between group read number comparison was performed using paired T test (paired on the patient ID). Boxes show median and interquartile range; whiskers extend from minimum to maximum values within each cohort.

3 Alpha diversity

Warning: Removed 14 rows containing non-finite values (`stat_boxplot()`).

Warning: Removed 13 rows containing non-finite values (`stat_signif()`).

Warning: Removed 14 rows containing non-finite values (`stat_summary()`).

Warning: Removed 14 rows containing missing values (`geom_point()`).

T test Paired alpha diversity for each group

Figure 1b. Alpha diversity, as quantified by Faith pd, is plotted versus sample type. Comparison within sample was performed using paired T test between gel and non gel samples. The number of samples in each group shown in the boxplot.

3.1 Summary statistics

4 PCoA - unweighted unifrac

Figure 2. Weighted Unifrac PCoA for all patient samples. Shapes represent three sequencing runs, Each color represents a different patient.

5 Clustering by microbial population resulted 3 main clusters

K-means clustering for Axis 1 and 2, k = 3

6 Heatmap

Figure 3. Heatmap showing the relative abundance of bacteria (rows) across samples (columns, sorted by Patient ID) across the 108(???) samples. Top color bars show the Patient ID, storage group??? (what colors??? Or should we remove this bar???) And gel treatment group (gel and no-gel represented by orange and green respectively????). *** need to replot this figure without the unreadable labels on the top.

7 Heatmap ordered by cluster

8 Most prevelant sequences

[1] 108