1Thing #1

I started to write down in a little notebook some notes from podcasts that I listen to and decided to share them with you. Sometimes, it’s the main point of the episode, often it’s a side note that I found interesting. They will be tagged with 1thing.

#1/ A Chinese movie about Wu Zetian (the only female Empress of China, ruling 655-683 CE) featured historically-accurate costumes, but had to be edited as these were thought to be too revealing for modern standards. The History of China

New Paper: Microbial abundance, activity and population genomic profiling with mOTUs2

Fresh off the press in Nature Communications, an update on the mOTUs (marker gene-based operational taxonomic units) concept.

Basic summary of the motus concept

This concept was introduced in the first mOTUs paper, which itself built upon the specI concept:

  • Use single-copy marker genes to identify and quantify species in metagenomic samples. Single-copy marker genes are gene families such that (1) every1 organism has a gene in that family and (2) organisms only have one copy.
  • Use marker genes from both genomes and metagenomes to characterize species. Co-abundance can identify species in metagenomes even if there is no reference genome available for them.

What is new in motus2?

First of all, it updates the database with newer data, which is valuable for the tool, but this version includes a few conceptual improvements as well:

Fig 1b from the manuscript: Ref-mOTUs are mOTUs from which a reference genome is available, meta-mOTUs are those inferred only from metagenomics
  1. There is a better integration between the reference-derived and the metagenomic-identified mOTUs.
  2. The first version was only relevant for human gut samples, this version includes mOTUs for multiple environments (see Fig 1b above).
Fig 4a from the manuscript: how well do metatranscriptomic-derived species abundances correlate with metagenomics-ones? mOTUs does much better than kraken or metaphlan2 (which, to be fair, were never designed for this usage).
  1. We show that mOTUs work well with metatranscriptomics data to estimate species abundances. As these are housekeeping genes, their expression is constant enough that one can use mOTUs as a good proxy for species abundance (this was benchmarked by using samples from which both metagenomics and metatranscriptomics are available; see Fig 4a above).
  2. SNV profiles on the marker genes are a good proxy for SNV profiles on the whole genome, so that marker genes can be used for subspecies identification, whereas before we had used the whole genome.

You can get the tool from https://motu-tool.org/, through bioconda, and there is a module for running it through NGLess.

  1. Every is used in the biological, not logical sense; that is, it means >90% of the time that we know about it, but, there are exceptions; also we might not know anything of the 99% of organisms out there.