There probably are an awful lot of them. Of all the bacteria that exist in the world (detectable by genomic methods) only a tiny fraction can be isolated and grown on their own. [1][2]
In many cases it might be that we just don't know how to provide the right environment, but part of it is that many bacteria only grow together with partner bacteria of other species [3] [4] For that matter, there are many bacteria that have lifestyles based around living on biofilms created by conspecifics. [5]
Just wanted to add some color to this good comment.
In the human context we are much closer to being able to culture anything we want. I would estimate that we are at 75% coverage now -- pick a species detected genomically in the human gut (or skin/vagina/nose, etc.) and we are likely to be able to culture it or a type strain of its species 75% of the time. For a long time we overestimated human microbial diversity because of bad genomic methods and error rates with the early 454 and then Illumina sequencers. This error rate, coupled with the fact that we can't easily replicate culture conditions for the vast majority of earth's bacterial biomass (i.e. the deep lithosphere or the oceans) led to this persistent if somewhat untrue description of the unculturability of human microbes.
[0] gives an estimate of 35-65% of human/mouse gut microbes having a culturable representative. This paper is from 2017, and there have been a lot of advancements since then.
[1] is a good non-review paper where they got 73% of the genomically defined species via just a single cultivation medium
There are others, but I finished my PhD in culturomics-related stuff in 2021, and haven't kept up as much as I should. Everything the OP cited about lithospheric, deep ocean, etc. still applies as far as I know. Those environments are just very hard to recreate with their pressure, temperature, and nutrient requirements.
They’re usually only observable in the rare case that they get randomly captured on an electron microscope slide. The genomic method is complicated because there’s so much data it’s hard to extract the signal and reassemble the snippets. There’s already more data than we know what to do with.
That said, recently a fellow HNer used the genomic method on old data and may have discovered a new class of life one step down from viruses: https://news.ycombinator.com/item?id=42547489
One of my long bets is that there are bacteria causing gastroenteritis that do not reproduce on growth media. I doubt very much that all of our problems are caused by chemicals.
There’s too many stories in modern medicine still that sound like, “if we can’t see it, you’re not sick.” There’s at least one more h pylori out there somewhere.
Occam’s razor doesn’t matter for shit when it comes to biology.
The vast majority of GIs would agree with the grandparent post, but it even goes deeper than that. Pathogenicity of common bacteria is heavily mediated through HGT and interspecies microbial signaling - meaning that there’s plenty we don’t know about even the most studied organisms when they’re in a dynamic environment with other neighbors.
In other words, we know there are multiple layers of activity taking place that we’ve barely scratched the surface on research-wise, so we have good reason to believe that simpler explanations are almost certainly reductive and wrong.
When results started coming out about the microbiome and health and there weren't any practical results (a poop pill that changes things) I thought it was one of those fads like gluten free or high-functioning autism.
The results have kept coming and it's hard not to believe the gut-health connection now but it's still frustrating that it doesn't translate to any therapy.
Yeah, I’ve definitely followed that same path as the field has progressed - but I’ve come to view gut health as something akin to soil health.
Compost does great things for plants, but you can’t sprinkle mycorrhizal fungi or banana peels on top of barren earth and call it a day. Similarly, you can’t throw probiotic bacteria or kimchi into a GI tract and call it a day.
Instead, in both cases, you have to holistically balance and change inputs over time to see results, taking into account the unique, pre-established state of the system. That makes for difficult research when so much of labwork is about controlling and isolating variables, and IMO, is the biggest factor in why we’re not seeing those pre-packaged applications yet.
I've been working on a monologue about reductivism vs reductionism and it reminds me of Doug Hofstader setting up a dialectic between reductionism and holism with the problem that you can't say holism has the same presence that reductionism has.
But soil health really is a place where holism reigns, thanks for reminding me!
The way in which prokaryotes like bacteria and eukaryotes like most multicellular organisms handle their genomes is part of this - prokaryotes are much more promiscuous in taking up and emitting genetic material, which is part of how you get so many different variants of the same "species" of bacteria, whereas eukaryotes are much more protective of their genomes and rely more on variable gene expression (in other words, which parts of the genome are going to be uncovered and available to read), rather than changes in the genome, to determine how they behave and what they "do".
One thing that I think is sharply underappreciated is how much cross-talk there is within bacterial communities as is - it's a normal state of affairs for a full metabolic pathway to span between multiple species (so, one bacterial species takes the starting molecule, performs a set of transformations, emits it into the environment, a second species takes up that derived material, modifies it further, re-emits it, and a third species, or even the first species again, takes it up and continues the chain). A bacteria has a cell wall, but that's a tool used as part of many of the bacteria's function, which means you really need to look at a bacteria's "zone of influence" inside and outside the cell wall to understand what it's doing.
So, given the flexibility of prokaryotic genomes, I think a bacterial colony containing multiple species or multiple variants of the same species might really be the prokaryotic equivalent of a multicellular organism, in which case they're absolutely everywhere, to a degree where focusing in on a single species of bacteria in any given context might be as reductive as focusing in on a single variant of human cell while evaluating how humans function.
Can someone explain why there arent more multicellular bacteria?
There probably are an awful lot of them. Of all the bacteria that exist in the world (detectable by genomic methods) only a tiny fraction can be isolated and grown on their own. [1][2]
In many cases it might be that we just don't know how to provide the right environment, but part of it is that many bacteria only grow together with partner bacteria of other species [3] [4] For that matter, there are many bacteria that have lifestyles based around living on biofilms created by conspecifics. [5]
[1] Like dark matter
[2] https://www.worldwidejournals.com/international-journal-of-s...
[3] https://ecampusontario.pressbooks.pub/microbio/chapter/10-2-...
[4] https://teamaquafix.com/sulfide-reducing-bacteria/?form=MG0A...
[5] https://en.wikipedia.org/wiki/Biofilm
Just wanted to add some color to this good comment.
In the human context we are much closer to being able to culture anything we want. I would estimate that we are at 75% coverage now -- pick a species detected genomically in the human gut (or skin/vagina/nose, etc.) and we are likely to be able to culture it or a type strain of its species 75% of the time. For a long time we overestimated human microbial diversity because of bad genomic methods and error rates with the early 454 and then Illumina sequencers. This error rate, coupled with the fact that we can't easily replicate culture conditions for the vast majority of earth's bacterial biomass (i.e. the deep lithosphere or the oceans) led to this persistent if somewhat untrue description of the unculturability of human microbes.
[0] gives an estimate of 35-65% of human/mouse gut microbes having a culturable representative. This paper is from 2017, and there have been a lot of advancements since then.
[1] is a good non-review paper where they got 73% of the genomically defined species via just a single cultivation medium
There are others, but I finished my PhD in culturomics-related stuff in 2021, and haven't kept up as much as I should. Everything the OP cited about lithospheric, deep ocean, etc. still applies as far as I know. Those environments are just very hard to recreate with their pressure, temperature, and nutrient requirements.
[0] https://doi.org/10.1038/s41564-023-01426-7 [1] https://www.nature.com/articles/nature17645
Edit: typos
> [1] Like dark matter
https://en.m.wikipedia.org/wiki/Microbial_dark_matter
They’re usually only observable in the rare case that they get randomly captured on an electron microscope slide. The genomic method is complicated because there’s so much data it’s hard to extract the signal and reassemble the snippets. There’s already more data than we know what to do with.
That said, recently a fellow HNer used the genomic method on old data and may have discovered a new class of life one step down from viruses: https://news.ycombinator.com/item?id=42547489
One of my long bets is that there are bacteria causing gastroenteritis that do not reproduce on growth media. I doubt very much that all of our problems are caused by chemicals.
There’s too many stories in modern medicine still that sound like, “if we can’t see it, you’re not sick.” There’s at least one more h pylori out there somewhere.
What would Occam says about this though?
Occam’s razor doesn’t matter for shit when it comes to biology.
The vast majority of GIs would agree with the grandparent post, but it even goes deeper than that. Pathogenicity of common bacteria is heavily mediated through HGT and interspecies microbial signaling - meaning that there’s plenty we don’t know about even the most studied organisms when they’re in a dynamic environment with other neighbors.
In other words, we know there are multiple layers of activity taking place that we’ve barely scratched the surface on research-wise, so we have good reason to believe that simpler explanations are almost certainly reductive and wrong.
When results started coming out about the microbiome and health and there weren't any practical results (a poop pill that changes things) I thought it was one of those fads like gluten free or high-functioning autism.
The results have kept coming and it's hard not to believe the gut-health connection now but it's still frustrating that it doesn't translate to any therapy.
Yeah, I’ve definitely followed that same path as the field has progressed - but I’ve come to view gut health as something akin to soil health.
Compost does great things for plants, but you can’t sprinkle mycorrhizal fungi or banana peels on top of barren earth and call it a day. Similarly, you can’t throw probiotic bacteria or kimchi into a GI tract and call it a day.
Instead, in both cases, you have to holistically balance and change inputs over time to see results, taking into account the unique, pre-established state of the system. That makes for difficult research when so much of labwork is about controlling and isolating variables, and IMO, is the biggest factor in why we’re not seeing those pre-packaged applications yet.
Soil health is a great example!
I've been working on a monologue about reductivism vs reductionism and it reminds me of Doug Hofstader setting up a dialectic between reductionism and holism with the problem that you can't say holism has the same presence that reductionism has.
But soil health really is a place where holism reigns, thanks for reminding me!
The way in which prokaryotes like bacteria and eukaryotes like most multicellular organisms handle their genomes is part of this - prokaryotes are much more promiscuous in taking up and emitting genetic material, which is part of how you get so many different variants of the same "species" of bacteria, whereas eukaryotes are much more protective of their genomes and rely more on variable gene expression (in other words, which parts of the genome are going to be uncovered and available to read), rather than changes in the genome, to determine how they behave and what they "do".
One thing that I think is sharply underappreciated is how much cross-talk there is within bacterial communities as is - it's a normal state of affairs for a full metabolic pathway to span between multiple species (so, one bacterial species takes the starting molecule, performs a set of transformations, emits it into the environment, a second species takes up that derived material, modifies it further, re-emits it, and a third species, or even the first species again, takes it up and continues the chain). A bacteria has a cell wall, but that's a tool used as part of many of the bacteria's function, which means you really need to look at a bacteria's "zone of influence" inside and outside the cell wall to understand what it's doing.
So, given the flexibility of prokaryotic genomes, I think a bacterial colony containing multiple species or multiple variants of the same species might really be the prokaryotic equivalent of a multicellular organism, in which case they're absolutely everywhere, to a degree where focusing in on a single species of bacteria in any given context might be as reductive as focusing in on a single variant of human cell while evaluating how humans function.
Not yet, it seems to be an open question.
See: "The Mystery of the Missing Multicellular Prokaryotes"
https://www.quantamagazine.org/the-mystery-of-the-missing-mu...
> biologists snapping images of the cyanobacteria under a microscope saw a cell that had grown a long, thin tube and grabbed hold of its neighbor.
Is there or has anyone explored a connection between this process and the endosymbiolsis that first created chlorplasts?
Those involved captured cynanobacteria. In the OP, if I understand correctly, at least sometimes the cyanobacteria is doing the capturing.
Relatedly, here is an account of someone working on global ocean surveys of microbes.
https://x.com/science_doodles/status/1879600503157592386
The Pattern Jugglers are real!!!
Related Anton video: https://youtu.be/kSGW8DmrWlU
Reminds me of Greg Bear's Blood Music and even Vitals.
Isn't this one of the main technological plot lines of Star Trek: Discovery?
Oh wait, my mistake. That's a universe teeming with networks of interconnected fungi.
You can see how easy it would be to make the mistake though, right?
Eywa