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Posted 1/1/2022 3:02 PM (GMT 0)
Pretty amazing. I wish they’d start using this stuff for autoimmine, chronic lyme, ME/CFS. There’s always a trigger. Proves we’re each harboring hundreds - thousands of unknown bacteria and viruses

https://www.nytimes.com/2021/06/03/magazine/metagenomic-sequencing.html
Posted 1/1/2022 4:00 PM (GMT 0)
I read the article. What grabbed my attention the most was this: “co-president of the Chan Zuckerberg Biohub.” That name definitely sounded familiar, so I looked it up. So the wife of Fakebook has a BIOTECH company. Hmmm. According to Wiki, Fakebook company changed its name, too.

The other computer guru, BG, also has a foundation involved in healthcare.
Posted 1/1/2022 4:11 PM (GMT 0)
the nyt article is behind a paywall dcd - i cant see the story / narrative - but the published paper that seems to be referenced is this one
https://academic.oup.com/gigascience/article/9/10/giaa111/5918865

basically a paper reporting on the creation of cloud based open source analysis tool for processing the raw output of PCR machines - used to detect pathogens in human and animal samples - on a pay per use basis i assume - so researchers do not need to have large expensive computers in their own lab.

there have been companies out there offering this kind of mNGS type service to the public - for a few years now
Aperiomics is the one that comes to mind.

i believe Aperiomics use proprietary databases - so this approach using open source databases is a step in the right direction - as for me transparency is critical.

there are issues though -

as the paper above illustrates - depending on what database you use to do the analysis and the statistical techniques used to infer species - as well as any filtering / quality assurance steps used to pre-process the data - you can get different answers. its pretty a math intensive process with many variables.

there are also the sampling issues with pathogens that are at low abundance in human samples - eg lyme and bart - (maybe babesia too in chronic cases) - are known to be detected less than 50% of the time in human blood via PCR methods - that would apply to this approach also.
Posted 1/1/2022 4:25 PM (GMT 0)
Yup, hugely computationally intensive. The other issue is not only pathogen recognition, which I’m sure will only get better over time the more these databases grow, but more importantly figuring out what pathogens are causative agents. If we’ve each got several thousand in us, you need huge databases for each patient population to start to connect the dots. But similarly that too will improve over time. Seems like a step in the right direction to me.

Also makes me wonder to what extent we are really all carrying a viral load that we have no idea is there, feels like we’re all sick about 10-15y too early

Post Edited (dcd2103) : 1/1/2022 9:34:41 AM (GMT-7)

Posted 1/1/2022 4:37 PM (GMT 0)
yeap - the area of viruses inside the human body is huge - in both the numbers of different types and the sheer overall numbers of them

the vast majority are phages - living inside bacteria in our microbiomes - but no one knows what 90% of these are doing and how they might impact health ....
Posted 1/1/2022 6:44 PM (GMT 0)
Garzie I took a full page screenshot behind the paywall so you can read it:

https://ibb.co/f52jz28
Posted 1/1/2022 7:24 PM (GMT 0)
that's very kind of you Rainy - thank you

i found the article worth a read

as dcd mentions it hints at lots of as yet undocumented viruses and other organism in humans

the tool they have created is free to use - which is pretty cool
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