Anytime you perform a sequencing experiment you will get _some_ microbial/fungal contamination. Every time. You can even check this yourself today. Analyse any publicly available (unprocessed) whole genome sequencing data. Usually the contamination is <1% but it’s there.

This study hasn’t ruled out contamination as the cause for the results. Given that, it’s very likely to be BS.

> You can even check this yourself today.

As much as I would love to be able to do this, I’m unsure where to start, and while I’m certain there would be a stackoverflow community for it, I wouldn’t even know what to ask.

I know this sounds like a joke comment, but I feel like we live in a time where someone could post some Jupyter notebooks on the matter, and for someone to create a step by step video on YouTube to guide people through the process.

Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available)

Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice): fasterq-dump SRR21812682

Download a microbial genome of interest, here is the link for common yeast: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF...

Install an alignment tool like bwa: https://github.com/lh3/bwa

Unzip the the genome file and create a bwa index: gunzip GCF_000146045.2_R64_genomic.fna.gz && bwa index GCF_000146045.2_R64_genomic.fna

Align: bwa GCF_000146045.2_R64_genomic.fna SRR21812682.fastq (or whatever the fastq files are named)

If you get any alignment results, you've "found" fungal DNA in a human sample. This is a highly simplified workflow, but covers the basic ideas. One of the papers is free and the method sections covers their workflow (it is much more complicated):

https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8

Useful resources: https://www.biostars.org/ https://rosalind.info/problems/list-view/?location=bioinform... https://www.cancer.gov/about-nci/organization/ccg/research/s... (source data for this paper, cancer specific sequencing data)