What species are indicators of environmental contamination in metagenomic studies?

Question

[marongiu.luigi]

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?

Answer 1

[colindaven]

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/

[Carambakaracho]

IMHO, it's even worse in microbiomes, especially when you don't know what to expect. It's not trivial to discriminate between novel discovery, false assignment and contaminations.

Years back there's been the platypus conspiracy which I felt particularly amusing. The team I worked for detected platypus sequences with high abundance in samples from a customer who wanted to evaluate our performance only months earlier. Initially they didn't disclose the samples' origin and it was our first metagenomics project at that time.

The samples came from bird feces, you can imagine to what extend we "impressed" them...