3 ms·

You can pick up a handful of dirt and there's microorganisms in there that are undiscovered. I was hoping this was more of a macro organism.

WalterGR 1y ago
Really? As a layperson, that surprises me. It seems like a perfect opportunity for citizen scientists and kids who can make discoveries right in their back yards! Where might I learn more?
- chasd00 1y ago
  > Where might I learn more? the backyard ;)
- rotexo 1y ago
  My knowledge is out of date (I was in a microbiology PhD program starting in the early 2010s), but at that time, it was known that there are a whole lot out of micro-organisms out there, but many of them were probably difficult to grow as isolates in pure culture for a whole host of reasons. What people ended up doing is sequencing a ton of DNA from environmental isolates, and trying to assemble whole genomes from the 100-200 base pair sequenced DNA fragments that you would get out of a sequencer (which is challenging for a whole host of other reasons). Then, if you believed in the genome assemblies you got out of that process, you could compare those inferred genomes to known genomes, see how similar they are, guess at the metabolic pathways those organisms might possess, etc. Not sure what the state of the field is now, and I don't really know too many specifics, because I never ended up studying too much in the way of microbial ecology. If you wanted to sequence a bunch of DNA out of environmental samples (pond water or something), you would probably search on google scholar for environmental DNA isolation to see what kind of kits people are using, and then you would probably get an Oxford Nanopore minION, make a sequencing library out of the extracted environmental DNA using their ligation sequencing kit, and then run that library on as many flow cells as you can afford (each flow cell costs ~$1000, and you sequence a library on each flow cell for 3 days to get as much sequencing data as you can). Oxford Nanopore presents a relatively low barrier to entry in comparison to the high-throughput sequencers used in academic, clinical, and Pharma settings, and it gives you sequencing reads potentially as long as the physical DNA fragments present in your sample, but it has a lower sequencing throughput in comparison to the big short-read sequencers. For this kind of metagenomic discovery work, you want as high a sequencing depth as possible, because an unknown organism might be at a low abundance in your sample compared to well-studied, common organisms, so you need more sequencing data to detect it. Then you would run some genome assembly software (https://www.metagenomics.wiki/tools/assembly https://www.metagenomics.wiki/tools/assembly), and then look into comparing your assembled genomes to known environmental isolates, and annotate those genomes to get a sense of which enzymes are encoded by genes in the genome. That all sounds straightforward, but there are probably tons of different possible computational tools to consider.
- chasil 1y ago
  Google turns up plenty of hits. https://www.sciencealert.com/life-deep-beneath-the-soil-dominated-by-mysterious-new-phylum-of-bacteria https://www.sciencealert.com/life-deep-beneath-the-soil-domi...
- chasil 1y ago
  Not fishing for an upvote, but you might like this Kurzgesagt video. https://m.youtube.com/watch?v=VD6xJq8NguY https://m.youtube.com/watch?v=VD6xJq8NguY
- hulitu 1y ago
  > Where might I learn more In the fridge in company's kitchen ?
deleted 1y ago
[deleted]
fakedang 1y ago
You don't need to look for dirt either. Your stomach has more than a million different microorganisms that have not been discovered, mapped and documented.

WalterGR 1y ago

Really? As a layperson, that surprises me. It seems like a perfect opportunity for citizen scientists and kids who can make discoveries right in their back yards! Where might I learn more?

chasd00 1y ago
> Where might I learn more? the backyard ;)
rotexo 1y ago
My knowledge is out of date (I was in a microbiology PhD program starting in the early 2010s), but at that time, it was known that there are a whole lot out of micro-organisms out there, but many of them were probably difficult to grow as isolates in pure culture for a whole host of reasons. What people ended up doing is sequencing a ton of DNA from environmental isolates, and trying to assemble whole genomes from the 100-200 base pair sequenced DNA fragments that you would get out of a sequencer (which is challenging for a whole host of other reasons). Then, if you believed in the genome assemblies you got out of that process, you could compare those inferred genomes to known genomes, see how similar they are, guess at the metabolic pathways those organisms might possess, etc. Not sure what the state of the field is now, and I don't really know too many specifics, because I never ended up studying too much in the way of microbial ecology. If you wanted to sequence a bunch of DNA out of environmental samples (pond water or something), you would probably search on google scholar for environmental DNA isolation to see what kind of kits people are using, and then you would probably get an Oxford Nanopore minION, make a sequencing library out of the extracted environmental DNA using their ligation sequencing kit, and then run that library on as many flow cells as you can afford (each flow cell costs ~$1000, and you sequence a library on each flow cell for 3 days to get as much sequencing data as you can). Oxford Nanopore presents a relatively low barrier to entry in comparison to the high-throughput sequencers used in academic, clinical, and Pharma settings, and it gives you sequencing reads potentially as long as the physical DNA fragments present in your sample, but it has a lower sequencing throughput in comparison to the big short-read sequencers. For this kind of metagenomic discovery work, you want as high a sequencing depth as possible, because an unknown organism might be at a low abundance in your sample compared to well-studied, common organisms, so you need more sequencing data to detect it. Then you would run some genome assembly software (https://www.metagenomics.wiki/tools/assembly https://www.metagenomics.wiki/tools/assembly), and then look into comparing your assembled genomes to known environmental isolates, and annotate those genomes to get a sense of which enzymes are encoded by genes in the genome. That all sounds straightforward, but there are probably tons of different possible computational tools to consider.
chasil 1y ago
Google turns up plenty of hits. https://www.sciencealert.com/life-deep-beneath-the-soil-dominated-by-mysterious-new-phylum-of-bacteria https://www.sciencealert.com/life-deep-beneath-the-soil-domi...
chasil 1y ago
Not fishing for an upvote, but you might like this Kurzgesagt video. https://m.youtube.com/watch?v=VD6xJq8NguY https://m.youtube.com/watch?v=VD6xJq8NguY
hulitu 1y ago
> Where might I learn more In the fridge in company's kitchen ?

deleted 1y ago

[deleted]

fakedang 1y ago

You don't need to look for dirt either. Your stomach has more than a million different microorganisms that have not been discovered, mapped and documented.