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OT: The Evolution of Bacteria on a "Mega-Plate" Petri Dish (Kishony Lab)

Joe Gwinn

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Nov 22, 2009
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Boston, MA area
With all the wild talk about COVID and its ever-evolving variants (mutants, verily!) coming to get us all, with vaccines slowly declining in effectiveness, I thought it useful to see the process in action, in this case using commonplace bacteria, but it works the same across all living things. This is from Harvard Medical School, published in 2016.

The underlying peer-reviewed article is "Spatiotemporal microbial evolution on antibiotic landscapes", SCIENCE, 9 Sep 2016, Vol 353, Issue 6304, pp. 1147-1151, DOI: 10.1126/science.aag0822, which is behind a paywall. (You may see a PubPeer link banner; this may be followed or ignored.)

The best way to watch the following youtube video is full-screen in a darkened room.

The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab) - YouTube

Turning to COVID, what we are seeing is the same process in the wild, where it happens far slower than in the lab (optimized to be fast).

And this process is why all multicellular critters have immune systems. Actually, bacteria also have immune systems, to defend against bacteriophages (which are specialized viruses that infect only bacteria). COVID is in the process of evolving into an endemic disease, like the flu: spreads more easily, but less dangerous to those it infects.

Machine content: Viruses are little machines, with exceedingly small components, many of which physically move.
 

adammil1

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Mar 12, 2001
Location
New Haven, CT
COVID is in the process of evolving into an endemic disease, like the flu: spreads more easily, but less dangerous to those it infects.

Really neat video I wonder what they had to do to kill off the super bugs they created.

I have heard the claim spreads easier but less dangerous a lot lately but what makes them so sure about the latter part? Seems like the virus must mutate to survive against new vaccines and natural immunity but what incentives are there for it to become less dangerous? Why does the virus care how it mutates out to behave? I am genuinely curious as this is an area I have no knowledge in.


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Joe Gwinn

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Location
Boston, MA area
Really neat video I wonder what they had to do to kill off the super bugs they created.

They didn't say, but they probably autoclave all bio waste.


I have heard the claim spreads easier but less dangerous a lot lately but what makes them so sure about the latter part? Seems like the virus must mutate to survive against new vaccines and natural immunity but what incentives are there for it to become less dangerous? Why does the virus care how it mutates out to behave? I am genuinely curious as this is an area I have no knowledge in.

It basically comes from evolutionary genetics studies using the epidemic models one hears so much about these days. One sets up a cloud of epi models with a mutation process (or vice versa, depending on which community is doing the study), and let it rip for a few thousand generations, ultimately achieving stability. Whatever strategy dominates after 1000 generations wins. One also follows the process of getting there.

These kinds of studies predict that a pathogen that is too lethal kills its hosts off too fast to reliably infect the next wave, allowing the less-lethal mutants win. The other thing that helps is having a long period where the infected hosts are infectious but not yet sick, so the hosts go about their business blithely, spreading joy.

This is what the theory says. It turns out that over history, most diseases followed just such a course. Such as the flu.

 

boslab

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Jan 6, 2007
Location
wales.uk
Suppose the most successful viruses are massively contagious without harming (much) the host, least successful kill the host before jumping to a new one
Seems common sense, however goes wrong with a bit of gain of function tinkering by dr frankenfucky
Mark
 

adammil1

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Joined
Mar 12, 2001
Location
New Haven, CT


They didn't say, but they probably autoclave all bio waste.




It basically comes from evolutionary genetics studies using the epidemic models one hears so much about these days. One sets up a cloud of epi models with a mutation process (or vice versa, depending on which community is doing the study), and let it rip for a few thousand generations, ultimately achieving stability. Whatever strategy dominates after 1000 generations wins. One also follows the process of getting there.

These kinds of studies predict that a pathogen that is too lethal kills its hosts off too fast to reliably infect the next wave, allowing the less-lethal mutants win. The other thing that helps is having a long period where the infected hosts are infectious but not yet sick, so the hosts go about their business blithely, spreading joy.

This is what the theory says. It turns out that over history, most diseases followed just such a course. Such as the flu.


I hope you're right but it still feels like a lot of wishful thinking pushed by people who so often seem to enjoy hearing their voices on TV more than they enjoy being right.

As far as I can tell evolutionary forces gives the virus 3 main objectives #1 evolve to evade immunities in the community #2 if at all possible try to become as infective as possible prior to being detected, and #3 make sure you don't kill the host off prior to replicating and infecting at least 3-7 others so as to hit an exponential reproduction cycle.

If you don't believe me look at the AIDS virus that thing never got less deadly with time and was perfectly happy killing off the host. Good thing that one didn't spread thru airborne transmission or I bet humanity would look quite different.

Seems like the whole level of severity and how the virus effects the host is just a luck of the draw type of thing. Assuming the virus doesn't kill the host too quickly how we feel after our infection is of little concern to the virus.


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lucky7

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Sep 6, 2008
Location
Canada
Bacteria =/= viruses.

Did smallpox become less virlent over time?

Nope. it was vaccinated out of existence.

You can add rabies and nipah to the list of viral nasties that aren’t getting less virulent.

Rabies can be prevented by vaccination, nipah not so much.

Back to speed of mutation (not my area of expertise). Was reading a few papers today suggesting that covid has a mutation every 2.5 days. Obviously the vast majority of mutations are dead ends for the virus, but gives an idea why people worry so much about unvaccinated people who have higher levels of virus in their system and spread it to more folks over many more days. Sooner or later, with so much virus running around uncontrolled, there will be a mutation with benefit to the virus. Enter omicron…. And the next….

L7
 

GregSY

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Jan 1, 2005
Location
Houston
I've always heard that a virus is much different than bacteria. So I'm not sure if watching bacteria evolve transfers to how viruseses evolve.



The COVID virus has been a shit-show.....the medical community at the ground level has done well, but the medical bureaucracy has done so poorly. Add in the appallingly poor performance of the Biden Administration. Add in the media's usual ineptitude. Add in how the Chinese have come out smelling like a rose - made a profit, even - for having created this fiasco.

I'm still amazed how no one in a position of leadership has done what's always worked for diseases....give people the best available information on how to treat it. Develop and provide access to medicines. Tell people what to expect when you get it and how to manage it. All I've seen is an abundance of 'how to avoid it'. The idea that you're going to prevent the spread of an airborne virus on a widespread basis is just flat stupid. People breathe.

Polio vaccines? Small pox vaccines? Developed by far smarter people with far purer motives, and neither of those diseases are airborne. And we didn't have a President who has continued to fail and alienate over half the country. Different ball game.
 

lucky7

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Sep 6, 2008
Location
Canada
I've always heard that a virus is much different than bacteria. So I'm not sure if watching bacteria evolve transfers to how viruseses evolve.



The COVID virus has been a shit-show.....the medical community at the ground level has done well, but the medical bureaucracy has done so poorly. Add in the appallingly poor performance of the Biden Administration. Add in the media's usual ineptitude. Add in how the Chinese have come out smelling like a rose - made a profit, even - for having created this fiasco.

I'm still amazed how no one in a position of leadership has done what's always worked for diseases....give people the best available information on how to treat it. Develop and provide access to medicines. Tell people what to expect when you get it and how to manage it. All I've seen is an abundance of 'how to avoid it'. The idea that you're going to prevent the spread of an airborne virus on a widespread basis is just flat stupid. People breathe.

Polio vaccines? Small pox vaccines? Developed by far smarter people with far purer motives, and neither of those diseases are airborne. And we didn't have a President who has continued to fail and alienate over half the country. Different ball game.

Correct, polio is fecal-oral not airborne, but smallpox, like chicken pox is airborne as well as direct contact. Latest covid, alas, is definitely not respiratory droplets but is even more infectious aerosol spread. Gah.

L7
 

Bill D

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Apr 1, 2004
Location
Modesto, CA USA
A virus does best when it does not kill it's host. The most successful virus is the common cold. If you catch a cold you get a little sick but are still well enough to go out and infect others. If it killed you you would be dead and buried and stop infecting living beings.
Did the Spanish flu(Fort Riley flue) mutate and become the common cold? It killed about 50 million people in total. I bet that many get the common cold each year. So the common cold is much more succesful.
Bill D
 

GregSY

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Location
Houston
I haven't studied smallpox in great detail, but what I have read says while it can be airborne, but you have to work pretty hard at it. You won't catch it by talking to the lady at the checkout lane....you might catch it by having extended, face-to-face oral intercourse (social, not sexual) with the slattern you have bedded for the night.
 

dgfoster

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Jun 14, 2008
Location
Bellingham, WA
Not all pathological microbes mutate to cause worse disease. The mutations are simple genetic accidents the huge majority of which are not helpful to spread of the microbe. But, the occasional (1 in billions) mutation may favor propagation of the virus or bacterium or may not favor propagation but just change behavior. A good case in point is Streptococcal infections. Strep used to cause a fair incidence of Rheumatic Fever and rheumatic heart disease as a consequence. However, once-common rheumatic heart disease is now a rarity. And the decrease in incidence is not fully explained by penicillin or improved health care. Strep simply has less tendency to cause rheumatic fever and rheumatic heart disease. No one knows why. The bug simply changed. I assume the same is true with Omicron---the mutation improves transmission but does not worsen the resulting disease. However, a disease that may be generally less severe per case may cause more net deaths and long term illness if it strikes much larger populations.

Denis
 

FredC

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Dewees Texas
To prevent this thread from going off the rails like almost every other covid thread, we might want to direct it at the coolant sump and all the nasties growing in there. If they nasties in there keep mutating maybe a ball bat will be needed to kill them as they crawl out. Or not.
 

GregSY

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Jan 1, 2005
Location
Houston
There are bad bacteria, and good bacteria. That's why it's paradoxical when a really hot girl lets her dog lick all over her mouth right after he gone done licking all over his ass....then she calls you a creep for offering to lick all over her ass.
 

adammil1

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Joined
Mar 12, 2001
Location
New Haven, CT
Was reading a few papers today suggesting that covid has a mutation every 2.5 days. Obviously the vast majority of mutations are dead ends for the virus, but gives an idea why people worry so much about unvaccinated people who have higher levels of virus in their system and spread it to more folks over many more days. Sooner or later, with so much virus running around uncontrolled, there will be a mutation with benefit to the virus. Enter omicron…. And the next….

L7

Thinking about it critically I would think it is actually quite the opposite.

Back when I read the Pfizer approval study they approved the vaccine when 100people in the control group got Covid and only 5 in the vaccinate population got it. So the vaccine was 95% effective on transmission. Then came Delta and we were reading stories of fully vaccinated car loads of people all getting Covid back in July, but at least they weren't in the hospital and all getting mild cases. Now we get to Omicron and I believe the hospitals are seeing far more fully vaccinated and boostered people. Inevitably without any update to the recipe I suspect sooner or later this vaccine will become rendered completely useless against the virus and not even worth taking.

At the end of the day the vaccine essentially serves as a layer of the 1X strength bacteria and forces the virus to mutate around it to make the vaccine less and less relevant. The unvaccinated I would think are doing us all a favor by not forcing the vaccine to mutate and develop resistance to the vaccine at their spot on the board.

Probably the better course of action would have been to limit use of the vaccine to people over the age of say 50 who didn't have Covid to keep the vaccine more relevant longer and then in parallel develop antiviral treatments that actually work so if you get sick you don't die from it.

Of course this administration was too stupid to learn from their predecessors, we now have the monoclonal antibodies, and now 2 pills approved from Merk and Pfizer that when given early all 3 offer remarkable results on early recovery and getting people back on their feet. The only thing that we don't have was a "warp speed" operation to have produced 100's of millions of doses of these treatments prior to them being approved so everyone today could enjoy getting Covid without the fear of death regardless of vaccination status.

Add to that I don't know what it is like in your area of the country but we have virtually no testing available here in CT. I have to book my Covid test 15days in advance to get a slot. So if I have a sore throat this morning rather than being able to find out if I have Covid I need to wait 15days to get a test and then 3 days for them to process the results. If you think I will quarantine for every sore throat and runny nose I get each winter until after I get a negative Covid test just incase I have Covid you are kidding yourself. However now you have the very real problem of people who should get tested aren't. Pretty amazing here we are January of 2022and it feels like we are in worse shape than we were Jan of 2021!

I think at this point the end of the pandemic will only really come when we get good rapid testing and availability of treatments that when taken right after a positive test have you back on your feet within 2-3days.
 

GregSY

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Location
Houston
The problem is you're applying logic and reason to a topic that is best handled by wild emotion, politics, and payoffs.
 








 
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