3 ms·

So I can't speak to the specifics of the startups you're referring to (I don't know who they are), but I will say I'm very surprised to have read this. The res

by dlss 12y ago

So I can't speak to the specifics of the startups you're referring to (I don't know who they are), but I will say I'm very surprised to have read this. The responsible development of new therapies is almost always a good thing. I'm confused to hear you say they're not FDA regulated, since the FDA is very clear: if it's intended to treat a disease, it's regulated. Perhaps you could explain what I'm missing? Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned.

aroch 12y ago
They're not marketed to cure a disease, they are "probiotics". They are using the yogurt rule >Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned. Yes the are, we have metagenomics on them (v4 rDNA sequence reads) not full seq data. We can't ID which bug and then grow it. We just know some of its rDNA is in the mix. Being able to phylotype =/= known microbe.
- dlss 12y ago
  > They are using the yogurt rule Ahh, you mentioned Autism spectrum, so I assumed that couldn't be the case. > we have metagenomics on them (v4 rDNA sequence reads) not full seq data There is plenty of genomic data beyond 16S. For the HMP, full sequencing of selected strains as well as hundreds of WGS metagenomes were done. And that's almost old news now, I'm sure there is even more being done currently. The result is basically either a full genome, or a set of giant chunks of the genome of the abundant microbes there. We don’t have all the genomes closed (although some are in the process!) but closing a genome is a very high bar and probably not worth it when you can get a lot of data from a fairly good set of large contigs. Can the assemblies be chimeric/wrong/whatever? sure, some of them will be, but at this point most assemblies are fairly good :)

by dlss 12y ago

aroch 12y ago

They're not marketed to cure a disease, they are "probiotics". They are using the yogurt rule >Also technical note: these microbes are not unknown/uncultured/unsequenced. See MetaHIT, the Human Microbiome Project and the American Gut Project you mentioned. Yes the are, we have metagenomics on them (v4 rDNA sequence reads) not full seq data. We can't ID which bug and then grow it. We just know some of its rDNA is in the mix. Being able to phylotype =/= known microbe.

dlss 12y ago
> They are using the yogurt rule Ahh, you mentioned Autism spectrum, so I assumed that couldn't be the case. > we have metagenomics on them (v4 rDNA sequence reads) not full seq data There is plenty of genomic data beyond 16S. For the HMP, full sequencing of selected strains as well as hundreds of WGS metagenomes were done. And that's almost old news now, I'm sure there is even more being done currently. The result is basically either a full genome, or a set of giant chunks of the genome of the abundant microbes there. We don’t have all the genomes closed (although some are in the process!) but closing a genome is a very high bar and probably not worth it when you can get a lot of data from a fairly good set of large contigs. Can the assemblies be chimeric/wrong/whatever? sure, some of them will be, but at this point most assemblies are fairly good :)