13 ms·

Everything You Ever Wanted to Know about E. Coli (2008)

42 points by angrygoat 2y ago

pazimzadeh 2y ago
The article touches on the versatility of E. coli, but doesn't explicitly mention the extreme diversity within what we call E. coli. Even just within the subset of E. coli which causes UTI's, 25-40% of the genome varied between strains. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/) This diversity wasn't really appreciated in 2008 when many E. coli genomes hadn't been sequenced yet.
- lysozyme 2y ago
  Good point! And a related topic, we call the organism that lives happily in our gut E. coli and we also call the organisms that cause disease the same name. What’s the difference? It turns out that the Escherichia coli (to spell out its Latin binomial) that cause disease are in some sense “diseased” themselves: the genes that enable them to be pathogenic, or make them pathogenic, I should say, are originally from a phage, a type of virus that infects bacteria [1]. In a manner that is not the same as, but conceptually similar to how HIV inserts its genes into the human’s genome, phages insert their genes (termed the “prophage”) into the bacterial genome. In addition, most strains of pathogenic Escherichia are also holding on to an entirely separate, small, circular “genome” called a plasmid, also of exogenous origin, that contains additional genes that make them pathogenic. So in addition to wide genome variation within the “species” (which is not really the same thing for bacteria as for mammals, mind you) of Escherichia coli, many subtypes have additional genetic material from endogenous sources that substantially changes their observed characteristics (phenotype). 1. https://en.m.wikipedia.org/wiki/Escherichia_coli_O157:H7 https://en.m.wikipedia.org/wiki/Escherichia_coli_O157:H7
  - thelaxiankey 2y ago
    Also happen to be in microbiology, but pretty far from the medical side of things. Do you have a citation on the fact that 'most' pathogenic strains have a plasmid making them so? Some guys in our lab have been playing around with plasmid copy number lately (in a largely 'basic science' kind of way) -- this could give some nice context for that work.
koeng 2y ago
I use E.coli on a pretty daily basis for cloning. It's alright, and there is so much work that has gone into it as a chassis organism, but overall there are definitely better organisms out there if we just took the time to figure them out (Vibrio natriegens and Bacillus subtilis are two examples). We absolutely do not have a clear idea of how E.coli works. Hell, we don't even know how almost 1/3 of the genes work on JCVI-Syn3a works, a minimal genome we synthetically created. Far fewer in E.coli.
- pazimzadeh 2y ago
  Better how? Cloning strains are particularly boring...what are you expecting to happen?
  - koeng 2y ago
    I'm expecting that it should grow 2x the speed, sporulate if needed, have natural competence systems for large modifications / genome engineering (lambda red aint there), have some environmental resistances that are uncommon in typical contaminants, have better protein secretion directly out of cloning strain, hell just an expression AND cloning strain, better stability in typical strains that dont require STBLE or whatever, better positive and negative selection markers, Vitamin B1 synthesis pathway for minimal medias, E115K fix in purB for DH5alpha so that they don't grow like crap on M9, the list just goes on.
    - pazimzadeh 2y ago
      What is the doubling time for the E. coli you are working with? E. coli will never form a spore (unless you engineer that somehow?), why would you want E. coli to sporulate? Some of the things you mention can be done by clinical strains. Couldn't you just make the E115K purB mutation if you want that? I agree that lambda red is limited.
      - koeng 2y ago
        Normal E.coli doubling time, which means about half the speed of Vibrio natriegens. I use NEB turbos sometimes, but they still don't bring down the liquid culture time down from overnight to within a day, mostly. I would want E.coli to sporulate because then shipping and distribution of strains is a lot easier. This was a problem back when I was shipping at FreeGenes and still is a problem. I used Bacillus subtilis to make the sporenet protocol which worked, but the vector backbone switching was pretty painful. Clinical strains == not necessarily GRAS. Also, they're clinical, so regulated by MTAs, which are a big no-no. I could make the E11K purB mutation, but why would I go through the effort in an inferior species of bacteria when I can invest my time into something like Vibrio natriegens? The payoff is better at the end.
mncharity 2y ago
Many numbers for E. coli: https://bionumbers.hms.harvard.edu/search.aspx?trm=coli https://bionumbers.hms.harvard.edu/search.aspx?trm=coli

42 points by angrygoat 2y ago

The article touches on the versatility of E. coli, but doesn't explicitly mention the extreme diversity within what we call E. coli. Even just within the subset of E. coli which causes UTI's, 25-40% of the genome varied between strains. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/) This diversity wasn't really appreciated in 2008 when many E. coli genomes hadn't been sequenced yet.

lysozyme 2y ago
Good point! And a related topic, we call the organism that lives happily in our gut E. coli and we also call the organisms that cause disease the same name. What’s the difference? It turns out that the Escherichia coli (to spell out its Latin binomial) that cause disease are in some sense “diseased” themselves: the genes that enable them to be pathogenic, or make them pathogenic, I should say, are originally from a phage, a type of virus that infects bacteria [1]. In a manner that is not the same as, but conceptually similar to how HIV inserts its genes into the human’s genome, phages insert their genes (termed the “prophage”) into the bacterial genome. In addition, most strains of pathogenic Escherichia are also holding on to an entirely separate, small, circular “genome” called a plasmid, also of exogenous origin, that contains additional genes that make them pathogenic. So in addition to wide genome variation within the “species” (which is not really the same thing for bacteria as for mammals, mind you) of Escherichia coli, many subtypes have additional genetic material from endogenous sources that substantially changes their observed characteristics (phenotype). 1. https://en.m.wikipedia.org/wiki/Escherichia_coli_O157:H7 https://en.m.wikipedia.org/wiki/Escherichia_coli_O157:H7
- thelaxiankey 2y ago
  Also happen to be in microbiology, but pretty far from the medical side of things. Do you have a citation on the fact that 'most' pathogenic strains have a plasmid making them so? Some guys in our lab have been playing around with plasmid copy number lately (in a largely 'basic science' kind of way) -- this could give some nice context for that work.

koeng 2y ago

I use E.coli on a pretty daily basis for cloning. It's alright, and there is so much work that has gone into it as a chassis organism, but overall there are definitely better organisms out there if we just took the time to figure them out (Vibrio natriegens and Bacillus subtilis are two examples). We absolutely do not have a clear idea of how E.coli works. Hell, we don't even know how almost 1/3 of the genes work on JCVI-Syn3a works, a minimal genome we synthetically created. Far fewer in E.coli.

pazimzadeh 2y ago
Better how? Cloning strains are particularly boring...what are you expecting to happen?
- koeng 2y ago
  I'm expecting that it should grow 2x the speed, sporulate if needed, have natural competence systems for large modifications / genome engineering (lambda red aint there), have some environmental resistances that are uncommon in typical contaminants, have better protein secretion directly out of cloning strain, hell just an expression AND cloning strain, better stability in typical strains that dont require STBLE or whatever, better positive and negative selection markers, Vitamin B1 synthesis pathway for minimal medias, E115K fix in purB for DH5alpha so that they don't grow like crap on M9, the list just goes on.
  - pazimzadeh 2y ago
    What is the doubling time for the E. coli you are working with? E. coli will never form a spore (unless you engineer that somehow?), why would you want E. coli to sporulate? Some of the things you mention can be done by clinical strains. Couldn't you just make the E115K purB mutation if you want that? I agree that lambda red is limited.
    - koeng 2y ago
      Normal E.coli doubling time, which means about half the speed of Vibrio natriegens. I use NEB turbos sometimes, but they still don't bring down the liquid culture time down from overnight to within a day, mostly. I would want E.coli to sporulate because then shipping and distribution of strains is a lot easier. This was a problem back when I was shipping at FreeGenes and still is a problem. I used Bacillus subtilis to make the sporenet protocol which worked, but the vector backbone switching was pretty painful. Clinical strains == not necessarily GRAS. Also, they're clinical, so regulated by MTAs, which are a big no-no. I could make the E11K purB mutation, but why would I go through the effort in an inferior species of bacteria when I can invest my time into something like Vibrio natriegens? The payoff is better at the end.

mncharity 2y ago

Many numbers for E. coli: https://bionumbers.hms.harvard.edu/search.aspx?trm=coli https://bionumbers.hms.harvard.edu/search.aspx?trm=coli