December 20, 2019

Bioidentification of metagenomic samples

another case for alignment free methods

Context: Metagenomics

Let’s say you get a complex sample:

  • Environmental studies
  • Human microbiota
  • Archeology

You extract total DNA, you sequence all.

You got millions of reads

What is on these reads?

Problem: Identification

Now you ask:

  • What are the organisms on this sample?
  • How many of them?
  • What can they do?

Most of the reads do not align to any reference genome
(most of Prokaryotes have not been isolated)

Two approaches to identify a read

  • similarity based: i.e. alignment
    • highly specific
    • low sensitivity
  • composition based: \(k\)-mer frequency
    • low specificity
    • high sensitivity

Identification without alignment

Given a DNA read \(r\) we want to find which species \(S\) is the most probable origin of the read

We want to find an \(S\) that maximizes \(\Pr(\text{species is }S\vert \text{we saw }r)\)

Thus, the question is how to evaluate this probability. Some approaches:

  • Naïve Bayes Classification (Rosen 2008)
  • RaiPhy (Nalbantoglu 2011)

Nucleotide composition

Some properties of DNA composition tend to be conserved through evolution

For example, two phylogenetically close species usually have similar GC content

Generalizing the idea, we can consider the relative abundance of

  • di-nucleotides
  • tri-nucleotides
  • and longer oligomers of size \(k\)

An oligomer of size \(k\) is called \(k\)-mer


Given a sequence \(s\) of length \(L\), we characterize it by a vector counting all subwords of size \(k\)

Given a DNA “word” \(w\in {\cal A}^k\) of length \(k\), we define

  • Absolute frequency \(n_{(k)}(w;s)=\sum_j[s_j\ldots s_{j+k-1}=w]\)
  • Relative frequency \(f_{(k)}(w;s)=n_{(k)}(w;s)/\sum_{v\in\cal A} n_{(k)}(v;s)\)

Remember that \(\mathcal A = \{A,C,G,T\}\) and that \([Q]=1\) iff \(Q\) is true.

How many different k-mers?

The classification must be invariant to reverse complement

The representation should not change if we use either strand

  • \(D_k=4^{k/2} + 4[k\text{ even}]\) distinct values
  • \(D_k-1\) linearly independent values
  • So for \(k=1\) we have only one value: GC content

Prob. of a \(k\)-mer given a specie

Hypothesis to Test

We built a platform that allow us to test these hypothesis:

  • Phylogenetically close species have similar distribution of \(k\)-mer frequencies

  • Phylogenetically distant species have very different \(k\)-mer distributions

Reference Phylogenetic distance

For this analysis we need to know how long ago two species diverged

We used the values published in 2274 Studies, 50K Species

Hedges et al, Mol. Biol. and Evol. (2015)

Taxonomy or Phylogeny?

For this analysis we need to know how long ago two species diverged

Linnaean taxonomic ranks have some temporal inconsistencies

  • The class angiosperm has lower average age than the order of fungus < !– + an order of animal averages younger than genus of basidiomycete fungus ->
  • Ranks for prokaryotes are all older than the corresponding ranks of eukaryotes
Hedges et al, Mol. Biol. and Evol. (2015)

Reference Phylogenetic distance

We used the values published in

  • Hedges, S. Blair, Joel Dudley, and Sudhir Kumar. “TimeTree: A Public Knowledge-Base of Divergence Times among Organisms.” Bioinformatics 22, no. 23 (2006): 2971–72. doi:10.1093/bioinformatics/btl505.
  • Hedges, S. Blair, Julie Marin, Michael Suleski, Madeline Paymer, and Sudhir Kumar. “Tree of Life Reveals Clock-like Speciation and Diversification.” Molecular Biology and Evolution 32, no. 4 (2015): 835–45. doi:10.1093/molbev/msv037.
    • 2274 Studies, 50K Species

There is an recent update

  • Kumar, Sudhir, et al. “TimeTree: a resource for timelines, timetrees, and divergence times.” Molecular Biology and Evolution 34.7 (2017): 1812-1819.
    • 3163 Studies, 97K Species

Provides an estimation of divergence time ## The current presentation uses 2015 data

There are only 570 species in both TimeTree and RefSeq

Enough to make 163K comparisons

Phylogenetic distance for Reference species

Phylogenetic distance for Reference species

Comparing species using \(k\)-mer

Every species is represented by the frequency of each \(k\)-mer
(i.e. empirical probability distributions)

We can compare two probability distributions using the Total Variation distance: \[\mathrm{dist_{TV}}(p,q)=\frac{1}{2}\Vert p-q\Vert_1 = \frac{1}{2}\sum_i\vert p_i-q_i\vert\] (it happens to be half the Manhattan distance)

Since all probability distributions follow \(\sum_i\vert p_i\vert=\Vert p\Vert_1=1\), it is easy to see that the Manhattan distance is a good one.

Distribution of \(k\)-mer distances

Distribution of \(k\)-mer distances

Phylogenetic v/s k-mer distance

Phylogenetic v/s k-mer distance

Phylogenetic v/s k-mer distance

Phylogenetic v/s k-mer distance