A workflow for investigating Bacteriome-Mycobiome interactions and networks within the Human gut microbiome. The analysis is based on illumina 16S bacteriome and ITS2 mycobiome samples.

Copyright Simon Wetzel and Mohamed Tarek Badr, Date: 20 April 2023, University of Freiburg, Germany

This code was used for the analysis of 16S/ITS2 sequencing samples for clinical studies carried out in institute of medical microbiology UMC Freiburg.

The sample analysis workflow uses illumina short read fastq files as an input. Bacteriome sequencing experiments are usually carried out using the following primers:

• 16S region V3-4 Klindworth et al. 341F 5′- CCT ACG GGN GGC WGC AG -3′, 805R 5′- GAC TAC HVG GGT ATC TAA TCC -3′ or V1-2 Donia et al. 27F 5'- AGAGTTTGATCCTGGCTCAG -3', 338R 5'- GCTGCCTCCCGTAGGAGT -3'

Mycobiome sequencing experiments are usually carried out using the following primers:

• ITS region 2 (ITS2) gene Ihrmark-gITS7-F 5'-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGARTCATCGARTCTTTG -3' Tedersoo-ITS4ngs-R 5'- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTTCCTSCGCTTATTGATATGC- 3'

The DNA extraction and library preparation is usually done as described here: https://www.mdpi.com/2073-4409/10/11/3226