TABLE A1.

Schematic overview of experiments and material within this study. A short explanation for each action is provided below

Process	Action	Material	Figure
Pre‐work Testing bead‐beating (BB) and Molzym	1. Testing Molzym +BB	4 big biopsies (~5 mm) of patient nr.3 of resected colon	Figure A1 in Appendix 2
	2. Testing Molzym +BB with PBS wash	2 big biopsies of patient nr.4 of resected colon	Figure A2 (Biopsy and PBS wash isolated separately) in Appendix 2
	3. Testing Molzym enrichment on bacterial composition	4 mock communities	Figure A3 in Appendix 2
Change to independent protocol with tweakable steps; change from DNA isolation strategy 1 to 2.
Protocol setup Detergent selection	4. Testing bacterial lysis under protocol conditions	Pure bacterial cultures	Figure 2a
	5. Testing which detergent causes the least difference to PBS	Total of 20 forceps (small) biopsies of patient nr. 1 + 2 of the resected colon (10 per patient) a	Figure 2b + Figure A4 + A5 in Appendix 2
	6. Test whether the selected detergent lyses human biopsies	6 big biopsies of patient nr. 7 of resected colon	Figure 2c
Protocol setup Confirm bacterial DNA enrichment	7. Test whether PBS wash should be included in DNAse treatment	12 big biopsies of patient nr. 5 + 6 of resected colons	Figure 3a+b
	8. Test which detergents result in the strongest bacterial DNA enrichment	Total of 20 forceps (small) biopsies of patient nr 1 + 2 of the resected colon (10 per patient) a	Figure 3c
Validation Sequencing results with our method	9. Evaluate whether the number of bacterial reads represents bacterial abundance by imaging	508 clinical in vivo acquired human biopsies of 224 patients	Figure 4a+b
	10. Observe which bacterial phyla are present		Figure 4c+d Figure A6 in Appendix 2
	11. Compare 16S with shotgun metagenomic sequencing of the same samples	15 follow‐up biopsies with high DNA yields	Figure 4e, f, and g Figure A7 in Appendix 2

^aSame material and experiment, but different aspects are shown in the figure.