Over 140k virus species in the human gut, half of which are new to science(sanger.ac.uk)
sanger.ac.uk
Over 140k virus species in the human gut, half of which are new to science
https://www.sanger.ac.uk/news_item/scientists-identify-over-140000-virus-species-in-the-human-gut-half-of-which-are-new-to-science/
92 comments
An experience I had relating to medications and the stomach: I had salmonella food poisoning, week later I'm better and then I get a call from doctor who had got tests back saying I had salmonella and was insistent I take this medication ciproxin. I questioned it as was feeling better. Anyhow took the medication that turned out to be broad-spectrum and it killed all the bacteria et all in my stomach. Week of shitting like a baby (green) and was worst that second week and had gone back to work, yet ended up off ill again. Since then had issues with stomach, mood, even tendons and few other aspects and went from sporty type to not being able to do any sports.
I saw an emergency doctor for a bad upper-respiratory infection (coughing blood) and was prescribed Augmentin for 10 days. It abolished the lung issue but wiped out my gut bacteria and gave me severe IBS-D.
That was seven years ago. I was forced to quit my job. I couldn't travel at all, even across town. I became dreadfully sick with even light physical exertion. After five years of every test, diet, medication, and therapy available to me I was prescribed medication (eluxadoline) which is effective, but costs me $24,000/year and is not covered by insurance. I still have flare-ups once a month but at least I can ride my bicycle again.
I wish I could sue the doctor who stole my twenties from me. But I stand no chance in court.
That was seven years ago. I was forced to quit my job. I couldn't travel at all, even across town. I became dreadfully sick with even light physical exertion. After five years of every test, diet, medication, and therapy available to me I was prescribed medication (eluxadoline) which is effective, but costs me $24,000/year and is not covered by insurance. I still have flare-ups once a month but at least I can ride my bicycle again.
I wish I could sue the doctor who stole my twenties from me. But I stand no chance in court.
So sad to hear this.
I took a lot of anti biotics as a kid. I'm pretty sure it killed off whatever gut microbiome I had multiple times over.
Never really had an issue except for becoming fat. Except for headaches. Which I never really thought about for many many years. You know, just take a pill. Probably took 20 years for me to figure it out somewhat.
This may or may not work at all for you and even for myself I can't really scientifically say anything about it. But what helped me was probiotics. I had to try a lot of them. And it got worse first before it got better while the bacteria were fighting with each other and I'm not sure what would happen if I stopped them.
However the best explanation I have found so far is that these probiotics that have Bacillus Subtilis in them made the difference. I don't want to advertise a specific product but since I've been asked before, what I take is Garden of Life Primal Defense Ultra. I tried others before and the one difference is Bacillus Subtilis. YMMV but worth a try if you ask me. I did combine it with a Keto diet too but I'm no longer on it and still fine.
Also in case you drink beer for example, I get worse when I have beer. Hard liquor? Absolutely fine now with the probiotics but beer still screws me up if I have it for a longer period of time.
I took a lot of anti biotics as a kid. I'm pretty sure it killed off whatever gut microbiome I had multiple times over.
Never really had an issue except for becoming fat. Except for headaches. Which I never really thought about for many many years. You know, just take a pill. Probably took 20 years for me to figure it out somewhat.
This may or may not work at all for you and even for myself I can't really scientifically say anything about it. But what helped me was probiotics. I had to try a lot of them. And it got worse first before it got better while the bacteria were fighting with each other and I'm not sure what would happen if I stopped them.
However the best explanation I have found so far is that these probiotics that have Bacillus Subtilis in them made the difference. I don't want to advertise a specific product but since I've been asked before, what I take is Garden of Life Primal Defense Ultra. I tried others before and the one difference is Bacillus Subtilis. YMMV but worth a try if you ask me. I did combine it with a Keto diet too but I'm no longer on it and still fine.
Also in case you drink beer for example, I get worse when I have beer. Hard liquor? Absolutely fine now with the probiotics but beer still screws me up if I have it for a longer period of time.
This is really helpful info, thanks for writing the comment!
I don't know why precisely this story but it left a bit of an impact. I'm sorry for your lost twenties. I hope you can make the best of it.
If your hunch that the antibiotics' effects on your gut bacteria was the cause is correct, have you considered a fecal microbiota transplant to restore a healthier mix?
https://en.wikipedia.org/wiki/Fecal_microbiota_transplant
https://en.wikipedia.org/wiki/Fecal_microbiota_transplant
Yes! In 2019, the experimental medicine department at my local university hospital started scheduling FMT procedures. They're suspended now because of COVID-19 restrictions (much like dentists and optometrists). But I'm in the queue. Somewhat awkwardly, I am responsible to nominate a suitable donor.
You should get a family member from what research I did into IBS and fecal transplants as a possible cure.
I don't know where you are, but with so many medical workers now vaxxed in US, my impression is hospitals/etc are mostly eager to catch up on delayed non-pandemic procedures.
If your own nearest option is still slow or requires a personally-nominated donor, other providers offering the freeze-dried pills, perhaps even via telemedicine, might be an option. Good luck!
If your own nearest option is still slow or requires a personally-nominated donor, other providers offering the freeze-dried pills, perhaps even via telemedicine, might be an option. Good luck!
I wonder whether its possible to transplant the bacteria out before such a treatment and introduce them again later..
> I wonder whether its possible to transplant the bacteria out before such a treatment and introduce them again later..
In theory yes, but there is the challenge of avoiding re-infection with the one species you're being treated to eliminate.
In theory yes, but there is the challenge of avoiding re-infection with the one species you're being treated to eliminate.
Perhaps if a sample could be collected when healthy and frozen for long-term storage.
In my experience antibiotics were prescribed for acute symptoms that quickly worsened. I don't think they would have delayed my treatment for the hours or days needed to collect a pre-treatment sample.
In my experience antibiotics were prescribed for acute symptoms that quickly worsened. I don't think they would have delayed my treatment for the hours or days needed to collect a pre-treatment sample.
Or find a way to trigger creating the positive bacteria.
Kevin rose did a podcast with https://pendulumlife.com/ that made that seem like a great path
Kevin rose did a podcast with https://pendulumlife.com/ that made that seem like a great path
Consider a raw milk diet for a while. Maybe probiotics and prebiotics. CRON-o-meter. There's such a thing as stool transplant.
Have you researched fecal transplants? I've seen some evidence to suggest they can restore a microbiome after e.g. chemotherapy or broad-spec antibiotics.
There were some studies going on in the US for various IBD issues but they ended them after several people got life-threatening infections.
I became aware of them watching a documentary upon Hitler many years ago - he was a fan of them apparently. Though wasn't aware at the time and quick dig shows it's not something the health service in the UK offer even today. Alas I can't afford private health care and not had great experiences with doctors, indeed any dealing been disaster on some level that I won't go thru them as it will just depress the hell out of me though the one when the a doctor said the stitches I'd had done was the worst job he'd seen in his entire life and he was a field medic during WW2, kinda gives an idea.
But certainly as a treatment - it has merit and wished was explored more. Just wished known about it at the time.
But certainly as a treatment - it has merit and wished was explored more. Just wished known about it at the time.
Yeah cipro kills everything. I used to carry a script for it while traveling in case of emergencies.
>went from sporty type to not being able to do any sports
Can you elaborate on this? I'm curious as to the general details.
Can you elaborate on this? I'm curious as to the general details.
Sure, used to do kendo and professional swimming and was doing paint-ball tournament level. That all ended due to tendon issues, and also much lowered energy levels.
Ciprofloxacin? It has a black box warning from the FDA. Specifically for tendon issues.
“ Fluoroquinolones, including CIPRO®, are associated with an increased risk of tendinitis and tendon rupture in all ages. This risk is further increased in older patients usually over 60 years of age, in patients taking corticosteroid drugs, and in patients with kidney, heart or lung transplants (see WARNINGS). Fluoroquinolones, including CIPRO, may exacerbate muscle weakness in persons with myasthenia gravis. Avoid CIPRO in patients with known history of myasthenia gravis (see WARNINGS).”
https://www.accessdata.fda.gov/drugsatfda_docs/label/2013/01...
All the quinolones also associated with lots of internet reports of ill health in a variety of respects, but tendinitis is the official warning.
Actually I see there is an updated warning about central nervous system damage now too. FDA recommends they only be used as a last resort.
Sorry you had that experience. I had Cipro about ten years ago, wasn’t really necessary. Can’t say for sure it did anything but my reaction was intense while on it, and I had much worsened general digestion and overall health after that point.
https://www.fda.gov/news-events/press-announcements/fda-upda...
“ Fluoroquinolones, including CIPRO®, are associated with an increased risk of tendinitis and tendon rupture in all ages. This risk is further increased in older patients usually over 60 years of age, in patients taking corticosteroid drugs, and in patients with kidney, heart or lung transplants (see WARNINGS). Fluoroquinolones, including CIPRO, may exacerbate muscle weakness in persons with myasthenia gravis. Avoid CIPRO in patients with known history of myasthenia gravis (see WARNINGS).”
https://www.accessdata.fda.gov/drugsatfda_docs/label/2013/01...
All the quinolones also associated with lots of internet reports of ill health in a variety of respects, but tendinitis is the official warning.
Actually I see there is an updated warning about central nervous system damage now too. FDA recommends they only be used as a last resort.
Sorry you had that experience. I had Cipro about ten years ago, wasn’t really necessary. Can’t say for sure it did anything but my reaction was intense while on it, and I had much worsened general digestion and overall health after that point.
https://www.fda.gov/news-events/press-announcements/fda-upda...
I also had the pleasure of taking cipro about 10 years ago. Since, then I have met hundreds of people. Symptoms of adverse reaction include depression/anxiety, tendon/muscle pain, tendon ruptures, vision issues, such as visual snow and floaters. These issues are widely underreported as negative symptoms may show up even up to 12 months after medication was stopped.
I have seen 40+ physicians at Mayo, Rush and other popular hospital networks, only one doctor said it's a possibility. Others outright dismiss it and look for alternative diagnosis.
However, there are some recent discoveries and theories. There was a study which found DNA adducts from cipro, others are looking at mtDNA and collagen issues.
For anyone reading please research any flouroquinolone antibiotic before taking them. It is A SERIOUS medication and not like other antibiotics.
The worst part of FQAD (Flouroquinolone Associated Disability) as it is a thing now, there is ZERO tests to confirm it. If it happens to you, you will be dismissed and ignored by the medical community. I know doctors, pharmacists who had a negative reaction and were outright called crazy by their colleagues. An optometrist who was quite outspoken was dropped by some insurance companies as this view is "controversial". Many older flouroquinolone antibiotics have been taken off the market completely due to severe adverse reactions.
I have seen 40+ physicians at Mayo, Rush and other popular hospital networks, only one doctor said it's a possibility. Others outright dismiss it and look for alternative diagnosis.
However, there are some recent discoveries and theories. There was a study which found DNA adducts from cipro, others are looking at mtDNA and collagen issues.
For anyone reading please research any flouroquinolone antibiotic before taking them. It is A SERIOUS medication and not like other antibiotics.
The worst part of FQAD (Flouroquinolone Associated Disability) as it is a thing now, there is ZERO tests to confirm it. If it happens to you, you will be dismissed and ignored by the medical community. I know doctors, pharmacists who had a negative reaction and were outright called crazy by their colleagues. An optometrist who was quite outspoken was dropped by some insurance companies as this view is "controversial". Many older flouroquinolone antibiotics have been taken off the market completely due to severe adverse reactions.
> However, there are some recent discoveries and theories. There was a study which found DNA adducts from cipro, others are looking at mtDNA and collagen issues.
Have any links? And find anything that helped?
I’m doing much better than I was before. But not knowing whether the issues are due to Cipro I also can’t be sure that anything I tried addressed it.
Have any links? And find anything that helped?
I’m doing much better than I was before. But not knowing whether the issues are due to Cipro I also can’t be sure that anything I tried addressed it.
A decent place to get information is a subreddit r/floxies.
There isn't any treatments yet, however, magnesium seems to be a supplement that helps a lot of people. Check out the subreddit.
I was prescribed Ciprofloxacin for traveler's diarrhea when I was traveling internationally for an extended period of time. I knew it was some hardcore stuff, so I didn't use it until it was a last resort. A single dose, and within 40 minutes I was experiencing neurological effects. I called a nurse-on-call and was told to discontinue. No permanent effects I know of, but it basically gave me temporary dementia. Definitely a medication that should come with stronger warnings. I know it's the only valid treatment for anthrax infections, but for general use it should not be prescribed.
A coworker of mine had long term health issues from taking a powerful antibiotic. He changed his diet to only include "non gut fermenting food" (not sure what that includes) and his issues went away.
His issues were different than yours, but I think it was the same antibiotic. In any case, worth considering a dietary change.
His issues were different than yours, but I think it was the same antibiotic. In any case, worth considering a dietary change.
Your coworker was probably referring to the low-FODMAP diet. People say it works and some doctors recommend it, but the data isn't quite there yet. Either way, yeah it's worth a try for people with GI issues. For anyone considering it, the highest quality information will come from your health provider.
IMO it's a workaround and doesn't address whatever core issue someone might have, but often with GI stuff we don't have a "cure" so workarounds are all people have.
IMO it's a workaround and doesn't address whatever core issue someone might have, but often with GI stuff we don't have a "cure" so workarounds are all people have.
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>For anyone considering it, the highest quality information will come from your health provider.
That seems like a dubious assertion in a thread about peoples intestinal flora being destroyed by recommendations from their "health provider"s.
That seems like a dubious assertion in a thread about peoples intestinal flora being destroyed by recommendations from their "health provider"s.
I personally got the low fodmap recommendation from my health provider.
What you're describing is called a low FODMAP diet. A family member has tried this diet for about a month to great success. They were fine for the last 1-2 years and then ate a coconut yogurt and the symptoms came back. They are back on the low FODMAP diet again and things have gotten better but they have like two to three more weeks before they are on their normal diet again.
You’re actually not supposed to do it permanently. The idea is eliminate, then work back in each of the six different sugars in small quantities to see what is tolerated.
If you’re zero fodmap for years you lose all the bacteria that digest them and are left even more susceptible.
If you’re zero fodmap for years you lose all the bacteria that digest them and are left even more susceptible.
This sounds like specific carbohydrate diet, IBD-AID diet, low-FODMAP, or similar. There are a bunch of options with different things prohibited - doing some sort of individual elimination and reintroduction seems like the only option to figure out one that works for you.
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1 point by zabzonk 1 minute ago | edit | delete [–]
You could probably sue him. Antibiotics should only be prescribed for salmonella food poisoning (and almost all similar gut problems) in severe cases - normally all you have to do is keep hydrated and you will get over it. Otherwise you run the risk of introducing antibiotic resistance, so such treatments may become ineffective in severe cases.
Not a medic. Used to be a microbiologist.
You could probably sue him. Antibiotics should only be prescribed for salmonella food poisoning (and almost all similar gut problems) in severe cases - normally all you have to do is keep hydrated and you will get over it. Otherwise you run the risk of introducing antibiotic resistance, so such treatments may become ineffective in severe cases.
Not a medic. Used to be a microbiologist.
Have a family member who has had to take antibiotics in various occasions, including cipro. She takes probiotics (pills and probiotic yogurt) after each antibiotic. Don’t know if it works but seems to keep diarrhea at bay, and help with ‘brain fog’
A bit more than a hypothesis. There are numerous scientific studies on nih.gov about this topic. I don't have their links handy, but I have run across them when researching gut health. I find it is easiest to search their site using google. e.g. "site:nih.gov some topic" in google works best with them.
Almost certainly the case, for the well known issue you mention of antibiotics. A more interesting question to me is when we'll be replenishing people's viral biome and bacterial one too. There are these recent studies trying to fix intestinal issues by taking one person's ... well crap and sharing it with others to replenish their biome https://en.wikipedia.org/wiki/Fecal_microbiota_transplant
Anti-virals aren't like anti-biotics, we don't have great general purpose antivirals. Adamantine, interferons, etc are used generally, but their efficacy is pretty poor.
That's why hepatitis C was so difficult to treat. It required a very specific molecule to inhibit an enzyme specific to hepatitis C.
That's why hepatitis C was so difficult to treat. It required a very specific molecule to inhibit an enzyme specific to hepatitis C.
The situation with general purpose antivirals appears to be about to change, though: https://blogs.sciencemag.org/pipeline/archives/2021/03/04/mo...
That's assuming that these species won't just be eventually reintroduced through food, air, human interaction etc.
I had this happen with a strong antibiotic and a longer than usual course.
My gut has seen a lot from various parts of the world. It's like starting over.
The more places I revisit, the better things have become.
But yeah, significant changes. Ahem... lots of irregularity, as if many foods were new. (and in a sense they were)
The reintroduction idea is valid IMHO, based on some of my own experiences.
My gut has seen a lot from various parts of the world. It's like starting over.
The more places I revisit, the better things have become.
But yeah, significant changes. Ahem... lots of irregularity, as if many foods were new. (and in a sense they were)
The reintroduction idea is valid IMHO, based on some of my own experiences.
I'm a fan of having some lacto fermented foods in my diet on the regular. seems to help with promoting a nice gut biome but that's just an anecdote. worst case kombucha and kimchi are tasty.
I do this too, though I do not find either of the k's particularly tasty.
I am a big fan of sour things so maybe that's why I like the taste. homemade kimchi is a lot tastier than the commercial stuff too.
Interesting. I will retry the k's when I have the opportunity.
Goodluck! The recipe that I use is basically this: https://www.maangchi.com/recipe/tongbaechu-kimchi
I tend to put more of the carrots, onions, and daikon in though as I like that crunch. I don't put in the harder to find ingredients and tend to ferment it a little over a week in a big vessel and then store it in smaller mason jars in the fridge. making carbon dioxide with vinegar and baking soda and then pouring it(just the invisible co2 though!!) over the ferment vessel has been flawless for my ferments. in any event controlled rot is fun... brewing your own kombucha is even easier too... basically making a sweet tea and pouring in a bottle of unflavored and still alive kombucha and it will make it on its own.
I tend to put more of the carrots, onions, and daikon in though as I like that crunch. I don't put in the harder to find ingredients and tend to ferment it a little over a week in a big vessel and then store it in smaller mason jars in the fridge. making carbon dioxide with vinegar and baking soda and then pouring it(just the invisible co2 though!!) over the ferment vessel has been flawless for my ferments. in any event controlled rot is fun... brewing your own kombucha is even easier too... basically making a sweet tea and pouring in a bottle of unflavored and still alive kombucha and it will make it on its own.
Do we have any general anti-virals? Seems like the few anti-virals we do have are pretty targetted towards certain types of viruses.
Up until this point, we have mostly just had broad-spectrum antibiotics, not antivirals. But, partly because of You Know What, they are getting a lot more attention lately: https://blogs.sciencemag.org/pipeline/archives/2021/03/04/mo...
Vitamin C seems to be what most animals on this planet use as general anti-viral. It also seems it works in humans in mega dozes and/or IV.
In any case "general antiviral" seems to be even worst thing then general antibiotic. Most of bacteria / viruses are commensal, you don't really want to disturb that. For example, bacteriophage viruses are now known to handle some of the 100% resistant bacteria in a matter of days.
IMO, the system is so complex that you should only support the crew that know how to handle that - i.e. your immune system - by providing resources they need (vitamins etc.) and avoid things detrimental for them (sugar, tonsillectomy etc.).
In any case "general antiviral" seems to be even worst thing then general antibiotic. Most of bacteria / viruses are commensal, you don't really want to disturb that. For example, bacteriophage viruses are now known to handle some of the 100% resistant bacteria in a matter of days.
IMO, the system is so complex that you should only support the crew that know how to handle that - i.e. your immune system - by providing resources they need (vitamins etc.) and avoid things detrimental for them (sugar, tonsillectomy etc.).
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Something like this already happen with c. Difficile taking over the gut and causing all sorts of troubles during antibiotic treatments.
This is absolutely true, which is why its usually recommended to take probiotics when you have to take antibiotics
> similar to the autoimmune and allergic issues resulting from overuse of antibiotics
Is this hypothesis too or a fact?
Is this hypothesis too or a fact?
Well that is also an hypothesis but with a lot more data to back it up than my idea: https://en.wikipedia.org/wiki/Hygiene_hypothesis
Bacteria can transfer sequences of DNA directly to each other in real time, through an amazing process called conjugation that looks like a sci-fi movie in outer space.
This is how gut bacteria can develop resistance so quickly. They don't have to go through a generational process of breeding and selection. They just share a piece of DNA code that confers immunity and they are good to go.
Let's take a look at this process in action, from the vantage point of the membrane wall of one bacterium:
Type 4 secretion system: ii- Pilus biogenesis
https://www.youtube.com/watch?v=ihlFqOK5cZM
This is how gut bacteria can develop resistance so quickly. They don't have to go through a generational process of breeding and selection. They just share a piece of DNA code that confers immunity and they are good to go.
Let's take a look at this process in action, from the vantage point of the membrane wall of one bacterium:
Type 4 secretion system: ii- Pilus biogenesis
https://www.youtube.com/watch?v=ihlFqOK5cZM
So the logic is to attack them with adaptable crew that look to them like sci-fi movie in outer space - viruses.
Those guys fight for millions of years. Its also in another dimension of reality we currently do not have much access to (only glimpses).
Those guys fight for millions of years. Its also in another dimension of reality we currently do not have much access to (only glimpses).
That video looks very interesting but how do I build some context on what any of these colored shapes are?
I've done a little skimming of comments here and I don't want to reply to any specific comment. But some general thoughts:
Some conditions cause severe malabsorption and then doctors medically prescribe digestive enzymes. These enzymes can be effectively used to combat viral infections if you take them on an empty stomach between meals instead of with meals like they are supposed to be used.
Random spontaneous thought: Maybe this is one of the things fasting does that has an impact on health. When you don't eat, digestive enzymes in the body attack microbes. (And the gut is home to 70 to 80 percent of the immune cells in the body. There's a lot happening there.)
Also: one of the things that makes gut issues complicated is you need to keep the stomach sufficiently acid to do its job while trying to address chemical imbalances and other stuff. If your stomach gets to be too alkaline, you can outright start throwing up from inability to digest food at all.
Keep in mind that viruses are made of RNA and DNA is just two strands of RNA bolted together, basically. (Those are laymen's terms, because I'm a layman. If anyone knows the fancier, more accurate explanation, feel free to have at it.)
So there is research suggesting that viruses are actually a source of genetic material for humans.
It helps me to think of all this like some messy, organic soup of code. Or nanomachines exchanging code. Something like that.
DNA is the code that writes physical reality* and it's quite small and gets swapped out and we are only just beginning to understand all that.
(Edit: not all physical reality. Just the biology bits.)
Some conditions cause severe malabsorption and then doctors medically prescribe digestive enzymes. These enzymes can be effectively used to combat viral infections if you take them on an empty stomach between meals instead of with meals like they are supposed to be used.
Random spontaneous thought: Maybe this is one of the things fasting does that has an impact on health. When you don't eat, digestive enzymes in the body attack microbes. (And the gut is home to 70 to 80 percent of the immune cells in the body. There's a lot happening there.)
Also: one of the things that makes gut issues complicated is you need to keep the stomach sufficiently acid to do its job while trying to address chemical imbalances and other stuff. If your stomach gets to be too alkaline, you can outright start throwing up from inability to digest food at all.
Keep in mind that viruses are made of RNA and DNA is just two strands of RNA bolted together, basically. (Those are laymen's terms, because I'm a layman. If anyone knows the fancier, more accurate explanation, feel free to have at it.)
So there is research suggesting that viruses are actually a source of genetic material for humans.
It helps me to think of all this like some messy, organic soup of code. Or nanomachines exchanging code. Something like that.
DNA is the code that writes physical reality* and it's quite small and gets swapped out and we are only just beginning to understand all that.
(Edit: not all physical reality. Just the biology bits.)
> viruses are made of RNA
Depending on the species, a virus can contain either DNA or RNA as its genetic material. Check out the Baltimore classification (https://en.wikipedia.org/wiki/Baltimore_classification) for more info.
> So there is research suggesting that viruses are actually a source of genetic material for humans.
They are! Endogenous retroviruses and the syncytin protein (involved in placental development) are some known examples.
Depending on the species, a virus can contain either DNA or RNA as its genetic material. Check out the Baltimore classification (https://en.wikipedia.org/wiki/Baltimore_classification) for more info.
> So there is research suggesting that viruses are actually a source of genetic material for humans.
They are! Endogenous retroviruses and the syncytin protein (involved in placental development) are some known examples.
Great comment.
I recommend Bromelain (from Annas stem) as one of those enzymes which is virtually side effect free.
I recommend Bromelain (from Annas stem) as one of those enzymes which is virtually side effect free.
For those interested in the topic of microbes living in/on our bodies, I highly recommend Ed Yong's book I Contain Multitudes:
https://www.goodreads.com/book/show/27213168-i-contain-multi...
He is a fantastic writer, and I really enjoyed the book. You might also be familiar with his COVID articles for The Atlantic, which were some of the best coverage of COVID issues throughout 2020.
https://www.goodreads.com/book/show/27213168-i-contain-multi...
He is a fantastic writer, and I really enjoyed the book. You might also be familiar with his COVID articles for The Atlantic, which were some of the best coverage of COVID issues throughout 2020.
Thanks for sharing. I'm intrigued by the topic but every time I've tried to find some good reading material, I've found myself going down some pseudo-science rabbit holes.
"10% Human: How Your Body's Microbes Hold the Key to Health and Happiness" by Alanna Collen (2016) is another good book on this topic.
I would add Carl Zimmer’s “A Planet of Viruses” as well.
I read the book "Never Home Alone" [1] a year or two ago, which is about all the different microbes and insects and such that are in the environment around us.
One of the things the author mentioned a few times is to never assume that something you find around your house has been cataloged or studied before. There are relatively few scientists who study such things.
One of the anecdotes was that someone the author knew discovered two or three new species of insect just by going out into his backyard and looking around.
[1] https://www.goodreads.com/book/show/39088985-never-home-alon...
One of the things the author mentioned a few times is to never assume that something you find around your house has been cataloged or studied before. There are relatively few scientists who study such things.
One of the anecdotes was that someone the author knew discovered two or three new species of insect just by going out into his backyard and looking around.
[1] https://www.goodreads.com/book/show/39088985-never-home-alon...
I've always wondered this myself, how many bugs in my own backyard have never been studied or classified? When you include microscopic organisms, it is definitely in the many thousands.
I notice many here are talking about FMT. As I've suffered years with debilitating IBS (likely due to a terrible diet in my 20's) I have wanted to try FMT for years.
I am currently undergoing a 2 week FMT course at the Taymount Clinic in the UK. I must say I'm impressed with their professionalism and along with the transplants themselves they also offer advice on lifestyle changes to prevent a reoccurrence of dysbiosis.
It's too early to tell but feel like it is helping. If I have so called "leaky gut" then it will be a few more months before my gut fully heals. The hope is that I'll be able to eat gluten/dairy/sugars again without agonising symptoms of bloating, gas and diarrhoea.
I am currently undergoing a 2 week FMT course at the Taymount Clinic in the UK. I must say I'm impressed with their professionalism and along with the transplants themselves they also offer advice on lifestyle changes to prevent a reoccurrence of dysbiosis.
It's too early to tell but feel like it is helping. If I have so called "leaky gut" then it will be a few more months before my gut fully heals. The hope is that I'll be able to eat gluten/dairy/sugars again without agonising symptoms of bloating, gas and diarrhoea.
Super interesting! May I ping you about the results in a few months? Best of luck!
This is why the body is so hard to understand because all these viruses like have multiple feedback loops with each other or with groups.
Biology is enormously complicated. Imagine coming to a code base written in an entirely undocumented language, with 1.5 gigabytes of this incomprehensible source code (for human genome), and figuring out how this script works with the millions of other scripts of varying length in your gut or in the environment, given you have a very small working knowledge of the overall machine that runs this code and can't easily take it apart and try and figure out what is happening (short of experiments where you essentially try unplugging a single thing at a time and see what happens to the machine [mutant screen]).
Perhaps I'm being pedantic, but there is a crucial way in which the "DNA as source code" analogy breaks down: Even with an unknown language, you still knows basically how the computer itself works.
A better analogy is an unknown, minimized language, running on unknown hardware, whose chips run unknown and self-modifying microcode such that the same source code may not even produce the same results.
A better analogy is an unknown, minimized language, running on unknown hardware, whose chips run unknown and self-modifying microcode such that the same source code may not even produce the same results.
Yes and add that all in spaghetti code
With so many unknown species, how do we know that the gene sequences used to detect covid in PCR tests are actually only found in covid ? How do we know the specificity of the test ?
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I don't think we will ever get to understanding even 10%. I think the cause and effect of what happens in our mouth/throat/stomach/small/large intestines connection will ever ben understood. Unlike the advancements we've made in trying understand the brain which we've only begun.
From all that gather, the cause and effect like one bacteria's waste is another's feed to yet another etc.. I do know yes, we found certain vitamins are made in the gut including many hormones like why is 90% of Serotonin made in colon but bulk of it is used in the brain? It has been found that there are neurons in our gut thus the "2nd brain" Hypothesis.
Not going into specifics, I can tell you without a doubt my fasting has made a huge impact to my health although I'm not doing it long enough >5 days nor often enough. Further that by eating garbage high carb/sugar when back to "normal."
It's been speculated and I believe it's for real that if everyone fasts at least one full day a week and do IM 16:8 the rest. Most of the aliments people are currently dealing with will be almost gone.
I clearly feel going into ketosis after a full day of fasting.
I fast 3-5 days once a qtr and every week I fast Mondays.
If I had the money and motivation. I would start a startup that does the following: At your puberty, you bank/cryofreeze your blood and when you are the pinnacle of your gut/body health in your 20's cryofreeze your stool. Then in your 50-60's, reimplant your stool and your blood. We lose so much along the way, by the time we're in our later age, we need to reconstitute it to reinvigorate your gut and possibly reverse aliments. I truly believe this business model could work.
From all that gather, the cause and effect like one bacteria's waste is another's feed to yet another etc.. I do know yes, we found certain vitamins are made in the gut including many hormones like why is 90% of Serotonin made in colon but bulk of it is used in the brain? It has been found that there are neurons in our gut thus the "2nd brain" Hypothesis.
Not going into specifics, I can tell you without a doubt my fasting has made a huge impact to my health although I'm not doing it long enough >5 days nor often enough. Further that by eating garbage high carb/sugar when back to "normal."
It's been speculated and I believe it's for real that if everyone fasts at least one full day a week and do IM 16:8 the rest. Most of the aliments people are currently dealing with will be almost gone.
I clearly feel going into ketosis after a full day of fasting.
I fast 3-5 days once a qtr and every week I fast Mondays.
If I had the money and motivation. I would start a startup that does the following: At your puberty, you bank/cryofreeze your blood and when you are the pinnacle of your gut/body health in your 20's cryofreeze your stool. Then in your 50-60's, reimplant your stool and your blood. We lose so much along the way, by the time we're in our later age, we need to reconstitute it to reinvigorate your gut and possibly reverse aliments. I truly believe this business model could work.
There is clearly a marketplace opportunity here. For Elon’s samples, obviously.
I currently decided to give this startup https://www.thryveinside.com/ a try since they claim to help improve your gut microbiome. Anyone tried them before? Hard to asses how scientifically sound their offering is.
I personally don't think we have a clue as this article clearly states we've just begun to understand by not understanding.
I would be cautious since they are doing nothing but feeding you what they feel are "essential" gut bacterias.
the danger is, there has to be a balance. You can have an overgrowth that you may not be able to reverse.
Again, I think this article exemplifies what we don't yet know so, a company providing a ready made solution seems a little much?
The best thing you can do for your gut isn't yet practical which is to find a bio/genetic/ethnic compatible person and do an FMT and do the rebalancing this company is promising for real. yeah. a bit futuristic but have been done and proven to work if you need helping an aliment such as Crohn's.
I would be cautious since they are doing nothing but feeding you what they feel are "essential" gut bacterias.
the danger is, there has to be a balance. You can have an overgrowth that you may not be able to reverse.
Again, I think this article exemplifies what we don't yet know so, a company providing a ready made solution seems a little much?
The best thing you can do for your gut isn't yet practical which is to find a bio/genetic/ethnic compatible person and do an FMT and do the rebalancing this company is promising for real. yeah. a bit futuristic but have been done and proven to work if you need helping an aliment such as Crohn's.
bacteria species living in the human gut makes sense to me.
But what does it mean for a virus species to be located in the human gut? constantly reinfecting new stomach cells as they are generated? infecting the bacteria in the gut?
edit: I saw another comment recommending "I Contain Multitudes" so I figured I search it for "virus" (thanks libgen) and found this:
"There are viruses too, in unfathomable numbers – a “virome” that infects all the other microbes and occasionally the host’s cells."
But what does it mean for a virus species to be located in the human gut? constantly reinfecting new stomach cells as they are generated? infecting the bacteria in the gut?
edit: I saw another comment recommending "I Contain Multitudes" so I figured I search it for "virus" (thanks libgen) and found this:
"There are viruses too, in unfathomable numbers – a “virome” that infects all the other microbes and occasionally the host’s cells."
As the article says, they're bacteriophages, viruses which primarily infect the bacteria.
crAssphage? Did someone have a bit of fun with vocabulary?
It's short for cross-assembly phage. It keeps showing up in metagenomic studies (especially when doing cross-assembly of the metagenome), but it's mostly uncharacterized (or at least was, a handful of years back. Not sure about now). So the name implies that we can detect its presence and gets its genome with genetic analysis, but have very little idea of what it actually is or does.
Yes, mankind got advance enough to study it, but ended up spending all its money on celebrities and building stuff that nobody really need.
I wonder how anyone is able to study them while making skin care products that never work are more profitable than vaccine research.
You read history and wonder why many emperors wasted their resources on building palaces with gold, but we're even more inefficient today if you compare our resources and population. It's more attractive for kids to become an influencer than a scientist today and probably it always has been just like this.
I wonder how anyone is able to study them while making skin care products that never work are more profitable than vaccine research.
You read history and wonder why many emperors wasted their resources on building palaces with gold, but we're even more inefficient today if you compare our resources and population. It's more attractive for kids to become an influencer than a scientist today and probably it always has been just like this.
Just a hypothesis. But the number of viruses in the gut, the vast majority of which we know nothing about, does reveal an awful lot of room for unintended consequences.