Third speaker i really need to start listening to introductions

What is quantitative metagenomics?

In contrast to the last speaker this is a culture free approach to see what bacts are present in microbial communities. An advantage is that relative abundance of bact can be compared between samples

This approach relies on having accurate sequence knowledge from BLAST.  Overcomable biases can come from the amount of dna present being related to gene length. By only looking at relevant domains of proteins, distinct portions and not common filler accuracy can be increased. Copy number can be a problem. Thresholds to determine phylum and genus are arbitrary. I didnt completely understand a lot of the statistics involved, pairwise comparisons and phylogenic trees. Some clades are relatively easy to quantify, some like the clostridiales are very difficult. They use 16s rRNA reference genomes.

They’ve done some work on human gut flora, this data is available online. They coined ‘enterotypes’ for the 3 distinct gut community clusters.

They think enterotypes are stable symbiotic host microbe interactions. Its only based on 33 people. Are there more? Are they stable over time? Are they affected by diet? Information from donors sbout diet showed some correlation to the clusters. Very interesting stuff.

I dont know what the state of quantitative metagenomics vs culture is. Clearly we arent masters of either yet. I wish them the best of luck, its a very difficult challenge

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