, 9 tweets, 5 min read Read on Twitter
The next speaker is @KnightsDan with "New methods for affordable and high-resolution shotgun sequencing"
#MBCongress2019
@KnightsDan Dan Knights: There is a big need for cheap tools (like 16S) that have a high level of information content (like WGS). We started to develop affordable methods of the whole workflow.
#MBCongress2019
@KnightsDan Dan Knights: How can we automate the lab work? How can we do shallower sequencing to save some money?
See our publication here: msystems.asm.org/content/3/6/e0…
#MBCongress2019
@KnightsDan Dan Knights: With moderate depth shotgun sequencing, you get much better information than 16S. Even with 5000 reads (shotgun) you can almost get the same signal (betadiv ordination plot) as with 50 million reads.
#MBCongress2019
@KnightsDan Dan Knights: 10K gives alpha/beta diversity, 500k gives strains, 2M ($99) gives strains at 0.01%, 20-50M ($500) reads allows assembly of new genomes. Big step between these last 2. You can start by 2M reads, then follow up by deep shotgun sequencing on subset.
#MBCongress2019
@KnightsDan Dan Knights: Using this approach we sequenced gut microbiome of 34 people over time, correlated that with diet. Most folks have stable gut communities, despite super variable dietary intake.
#MBCongress2019
@KnightsDan Dan Knights: In two people who followed a (super stable) soylent diet, there was as much variation in gut microbiome as in regular, variable diets.
#MBCongress2019
@KnightsDan Dan Knights: We found that microbiome pairs with food groups (e.g. vegetables, eggs), not with nutrients (kale vs spinach). But every person responds differently to each food group.
#MBCongress2019
@KnightsDan @threadreaderapp bring on the unroll
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