, 12 tweets, 7 min read Read on Twitter
Christopher Mason @WeillCornell with "Modern methods for deliniating metagenomic complexity: defining clinical quality genome measurements and editing for the microbiome space"
#MBCongress2019
@WeillCornell Christopher Mason: We work on standardization of 16S and metagenomic analysis: Genome in a bottle (GIAB): extensive, public and un-embargoed data.
Ratios of 16S derived taxa vary a lot with primer choice.
Zymo has a good set of standards to monitor extraction.
#MBCongress2019
@WeillCornell Christopher Mason: MicrobialStandards.org lists many approaches, and our 2017 paper has suggestions for methods to use:
genomebiology.biomedcentral.com/articles/10.11…
#MBCongress2019
@WeillCornell Christopher Mason: How many species do I have? Each metagenomic tool gives a completely different number.
#MBCongress2019
@WeillCornell Christopher Mason: We have an ongoing project in our lab to sample the public environment, e.g. the subways of major cities #MetaSUB metasub.org
#MBCongress2019
@WeillCornell Christopher Mason: This way we are building genetic maps of public transportation systems and expanding the number of microbial taxa that are known. Which city has the most mystery taxa? Tokyo has the most novel peptides, Santiago has many novelty as well.
#MBCongress2019
@WeillCornell Christopher Mason: We are also mapping the antibiotic resistance gene abundance per city. Highly correlated with use of over-the-counter antibiotic use.
#MBCongress2019
@WeillCornell Christopher Mason: What can be learned from a surface? Skin bacterial communities ("microbial fingerprints") were some of the earliest application. Small molecules on your phones and shoes reveal differences between people.
#MBCongress2019
@WeillCornell Christopher Mason: We swabbed phones at JPMorgan, metagenomics sequencing, and used MetaGenScope, a basic pipeline for taxonomy and functional profiles.
#MBCongress2019
@WeillCornell Christopher Mason: We mapped DNA from phones to corn, apple, salads, orange, leather purse, often what people ate just before swabbing. But also skin microbes. Engineers had urogenital bacteria on their phones. We can predict who has cats or dogs.
#MBCongress2019
@WeillCornell Christopher Mason: Twin astronauts study - Firmicutes/Bacteroidetes ratio switched while in space. Can we sequence in space? Nanopore was tested by Kate Rubins and it worked well.
#MBCongress2019
@WeillCornell @threadreaderapp unroll this for me please
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