Vampirococcus lugosii

Some months ago, in the lab, we had to validate whole genome sequencing method. We tested the method on ourselves, by sampling our own cheek swabs and sequencing it on an illumina novaseq 6000 machine. Basically I had my genome and my oral microbiome sequenced for free. While I still have not had the time to think of what to do with my genome, and understand how to do it, I had a quick look at my oral microbiome.

Quickly, I quality-filtered raw reads and aligned them to the human reference genome. Those that did not align were used as inputs to MetaPhlAn 4.

Here is what came out:

Metaphlan found 257 different species of Bacteria, belonging to 10 phyla.

A lot of bugs, such as the most abundant species Veillonella parvula, Scardovia wiggsiae ,Porphyromonas endodontalis and so on are associated to cavities, poor oral hygene and so on. I swear I brush twice a day and floss!I had a cavity in my wisdom tooth back then, which was then removed, and I also have got a professional cleaning inbetween. Hopefully these bugs are now gone.

What was cool is some weird phyla such as or Saccharibacteria and Candidatus Absconditabacteria. Looking up for what they are, I came across this paper which was pretty cool: "Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii".

Both phyla belong to the The Candidate Phyla Radiation (CPR), a large group of mainly uncultured bacteria, predominately symbionts of other organisms. They have small genomes (often < 1 Mb) and limited metabolic capacities. They are often very small in size too, and can go through 0.2 um filters. They miss ability for de novo biosynthesis of many essential compounds, such as all amino acids and vitamins. They are described as epibiotic parasites of other bacteria and could contribute to the control of bacterial populations in diverse ecosystems. A species "Vampirococcus lugosii", which was found in a salt lake in Spain is a predatory bacteria.

V. lugosii grows attached to cells of its specific host, the anoxygenic photosynthetic gammaproteobacterium Halochromatium sp., sucking up its cytoplasmic content like a vampire.

It is cool to know that in my mouth there are vampire bacteria too.

More info here too: "Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts". Code (at least the R part) here.

Composition of my mouth microbiome at phylum level.

Top 25 most abundant species detected

Species belonging to Candidatus_Absconditabacteria