Hello,

I am carrying out a metagenomic study and I would like to know if there are studies listing microbial species associated with environmental contamination. If I find, for instance, crAssphage in stools, this virus is reported as a common presence in the intestinal locus. Is this virus present as a contaminant let's say on a bench as well? 

Are there species that signal contamination of samples?
Yes, metagenomics is full of contaminating sequences and there is a whole literature on this going back many years, just a few of which are represented here:

 - the worse the assembly, the greater the contamination problems
 - contaminants are technology-specific nanopore has different contaminants to illumina
 - many labs have contaminants too
 - clean environments and positive / negative controls are a must

https://www.biorxiv.org/content/10.1101/2020.01.26.920173v1.full.pdf Salzberg 2020 - RefSeq and Genbank contaminants

Infamous species (mostly with illumina adapters)
    Achromobacter
    Turkey
    various band worms
    Carp Cyprinus carpio

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0678-6

Reagent microbiome? https://www.nature.com/articles/s41564-018-0202-y

Quality and Contaminant free reference genomes?

FDA-ARGOS
https://www.nature.com/articles/s41467-019-11306-6

Practically removing contaminants: https://www.molecularecologist.com/2017/01/handling-microbial-contamination-in-ngs-data/
