Dr. Emily, your information is so useful and so relevant! I look forward to reading these since I seem to now have IBS - source unknown. Although in my 70’s, I still find enjoyment in learning. Merci ☺️
Thank you so much, Catherine, that means a lot. I’m so glad the posts are helpful, and I love your curiosity. Wishing you some answers and relief with the IBS soon.
My old pup had inflammatory bowel disease and my internal medicine vet spent more time on replacing her microbiome than any of my physicians have and despite my gut issues of 20 years.
Hi Jan, I’m so sorry you’ve had to deal with gut issues for so long, sounds incredibly frustrating. Veterinary science and human medicine don’t always move at the same pace - it’s still such a new science, and we’re only just beginning to understand how best to work with it.
The repopulation can occur on carnivore as well. Seen it done. So how much of the gut reuteri was given to decide they don't return. One study? Doesn't seem rigorous science
Thanks for your comment, Irene. The study I mentioned is one of the most rigorous to date in terms of design, that looks at this research question. While the microbiome can adapt to different diets, the lack of fibre in a carnivore diet is concerning, since fibre is essential for supporting many "good" microbes.
I want to add and this can be confirmed meat protein supports an unfriendly bacteria which attacks the very thin small intestine wall. There is a reason so many Americans are experiencing colon cancers and gastric problems. Lots of excellent articles in New Scientist, available as an app. I don't recall sample size but there is form of statistics that can show significant trend and replicate studies are important. Still it is interesting that modern intestines may not support ancient microbes.
Thanks for your comment! There have been a lot of claims in this space, and it’s definitely sparked interest in certain types of microbes. That said, the study I shared is one of the best-quality trials we have to date in this area. The field’s still evolving, and I’m keeping a close eye on where the evidence goes next.
Thank you Matt! They explored an interesting research question that's for sure. I'll be curious to see if other studies in the future will see if other types of microbes find it easier to take hold. Let's see.
On a positive side, we were all born without any microbiome so clearly we can grow one. But, how robust? I imagine that decades of pesticide, antibiotics, chemical use has poisoned beneficial environmental microbes and created a toxic environment in our bodies making it difficult for probiotics to repopulate and thrive
Thanks for your comment Harry, it's an interesting one. I think we need to think of the gut microbiome as a competitive ecosystem. The microbes already living there are well-established and don’t want new competition for their food sources. So when we take probiotics, it’s not that they can’t help, but they often struggle to stick around.
So glad to hear this Tatty! And so sorry that you've been feeling overwhelmed, sometimes there's too many plates spinning - which is why I'm a big believer in keeping things simple and focussing on what matters when it comes to gut health.
Do you know if anyone is looking at the differences between the gut microbiome of breastfed infants and formula fed infants and how any differences impact health later in life?
Hi Jennifer, yes, there’s been quite a bit of research into differences in the microbiome between breastfed and formula-fed infants. The Quadram Institute, led by Professor Lindsay Hall https://quadram.ac.uk/people/lindsay-hall/ is looking into this if you're interested further. That said, I’m always mindful of how much pressure mums already face. Not everyone is able to breastfeed, and thankfully, there are many ways to support a healthy gut - through formula improvements, solid foods, and other exposures over time. The microbiome is flexible, and there’s no one perfect path.
Thanks, Jeff, really glad you enjoyed it. And totally agree that fibre beats fancy probiotics most of the time. I actually wasn’t too surprised by the limited effect in that study. Our gut microbiomes are incredibly complex and competitive, so it’s not always easy for new microbes to take hold. That said, a different strain or context might show different results, there’s still so much to learn and I think we'll see more studies like this in the coming years.
I farm and I pickle and I don't eat meat. We are switching our farm to using regen ag, so I'm on the same journey as our cocoa and vanilla. They seem to like it as well. Any thoughts on all this fizzy probiotic soda? Thanks again.
Love this, Ruth! Pickling and farming sounds like you're living most people's dream (and a powerful combo for gut and soil health). Fizzy fermented drinks like water kefir and kombucha can be a fun way to get some live microbes in, but I’d see them more as an occasional bonus than a foundation. Some are more about marketing than impact, and can contain a lot of added sugars - fine to enjoy occasionally but if you're wanting to look after your gut microbiome, then I'd look to regular kefir (a fermented milk drink) instead.
Agreed. I see the probiotic soda market going a bit crazy in the US at the moment, lots of new products. It’s giving me fake meat vibes, sucking up all the VC money.
When I had a stem cell transplant in 2022, the medical folks preparing me for the experience told me that the two doses of chemo I would receive were going to "ruin your GI tract." So when they had me meet with a nutritionist as part of the procedure to prepare me for going home, I asked what I could do to help rebuild my gut microbiome.
I got the broadest possible answer. Do your best to eat healthy. Lots of veggies, have some yogurt now and then. It was disappointing.
Thanks for sharing this, Paul. That does sound frustrating, especially when you were looking for real, actionable guidance. I’ve shared an 8 week series called Thriving Gut that digs into how to support your gut microbiome, which you may find useful. That said, there’s also a lot of overselling in this space. It’s really the foundational stuff that makes the biggest difference - fibre, variety, and a few fermented foods when you can. Wishing you all the best. https://dremilyleeming.substack.com/p/your-microbial-world-a-beginners
It's relatively new research. It appears that biomes are very important. A study at McGill institute found they could reduce chronic fatigue and brain fog by removing a bad bacteria via purging the GI tract and reinoculating with biomes from healthy folks. The gut absorbs tryptophan, the amino acid that makes us sleepy after ingesting tryptophan rich turkey. Tryptophan is a precursor to crucial serotonin-> minus yields brain fog. Probably not that simple, possibly other biochems from this amino acid.Apparently the bad bacteria blocks this absorption. Again New Scientist has had great articles from research on this and you can read through their app.
One final note: our brain and gut developed out of similar embryonic cells which may explain brain/gut headaches!
Thanks for your comment, Greg - love that you’re digging into this area, and you’re absolutely right that it’s a fast-moving field with lots of exciting findings. There has been some fascinating research, but it tends to still be early days, and we don’t yet always have consistent evidence on mechanisms. As you say - it's complicated, but exciting.
I studied neurobiology in school and found article about connection between gut and brain many years ago. However, I have a close relation with long covid and am trying to find relief for her. Apparently covid can live in the gut. With the report of fibromyalgia partly caused by bad microbe in biome and the symptoms of brain fog, achy joints and no energy plus odd facial itching possibly caused by lack of serotonin associated chemicals as the bad microbe blocks tryptophan the precursor to serotonin it seems like the culprit. As I said previously fibromyalgia study showed purging the gut and reintroducing healthy biome from another removed symptoms. Frankly I think in the future we may have stored personal biome to use post antibiotic or gut clearing procedures (colonoscopy.)
This is helpful, thanks. I'm also fascinated by the impact of stress on our gut microbiome, as there seems to be such an obvious link between stress and gut issues .
Dr. Emily, your information is so useful and so relevant! I look forward to reading these since I seem to now have IBS - source unknown. Although in my 70’s, I still find enjoyment in learning. Merci ☺️
Thank you so much, Catherine, that means a lot. I’m so glad the posts are helpful, and I love your curiosity. Wishing you some answers and relief with the IBS soon.
My old pup had inflammatory bowel disease and my internal medicine vet spent more time on replacing her microbiome than any of my physicians have and despite my gut issues of 20 years.
Hi Jan, I’m so sorry you’ve had to deal with gut issues for so long, sounds incredibly frustrating. Veterinary science and human medicine don’t always move at the same pace - it’s still such a new science, and we’re only just beginning to understand how best to work with it.
The repopulation can occur on carnivore as well. Seen it done. So how much of the gut reuteri was given to decide they don't return. One study? Doesn't seem rigorous science
Thanks for your comment, Irene. The study I mentioned is one of the most rigorous to date in terms of design, that looks at this research question. While the microbiome can adapt to different diets, the lack of fibre in a carnivore diet is concerning, since fibre is essential for supporting many "good" microbes.
I want to add and this can be confirmed meat protein supports an unfriendly bacteria which attacks the very thin small intestine wall. There is a reason so many Americans are experiencing colon cancers and gastric problems. Lots of excellent articles in New Scientist, available as an app. I don't recall sample size but there is form of statistics that can show significant trend and replicate studies are important. Still it is interesting that modern intestines may not support ancient microbes.
We'll see!
you sound a little behind the trend with what Dr William Davis has done with culturing your own R Reuteri and assoc studies. Good info though
Thanks for your comment! There have been a lot of claims in this space, and it’s definitely sparked interest in certain types of microbes. That said, the study I shared is one of the best-quality trials we have to date in this area. The field’s still evolving, and I’m keeping a close eye on where the evidence goes next.
Thanks Dr Emily, A good study and important info for today. Restacked.
Thank you Matt! They explored an interesting research question that's for sure. I'll be curious to see if other studies in the future will see if other types of microbes find it easier to take hold. Let's see.
On a positive side, we were all born without any microbiome so clearly we can grow one. But, how robust? I imagine that decades of pesticide, antibiotics, chemical use has poisoned beneficial environmental microbes and created a toxic environment in our bodies making it difficult for probiotics to repopulate and thrive
Thanks for your comment Harry, it's an interesting one. I think we need to think of the gut microbiome as a competitive ecosystem. The microbes already living there are well-established and don’t want new competition for their food sources. So when we take probiotics, it’s not that they can’t help, but they often struggle to stick around.
Loving the advice. So easy to actually DO… I feel inspired instead of endlessly overwhelmed !
So glad to hear this Tatty! And so sorry that you've been feeling overwhelmed, sometimes there's too many plates spinning - which is why I'm a big believer in keeping things simple and focussing on what matters when it comes to gut health.
Do you know if anyone is looking at the differences between the gut microbiome of breastfed infants and formula fed infants and how any differences impact health later in life?
Hi Jennifer, yes, there’s been quite a bit of research into differences in the microbiome between breastfed and formula-fed infants. The Quadram Institute, led by Professor Lindsay Hall https://quadram.ac.uk/people/lindsay-hall/ is looking into this if you're interested further. That said, I’m always mindful of how much pressure mums already face. Not everyone is able to breastfeed, and thankfully, there are many ways to support a healthy gut - through formula improvements, solid foods, and other exposures over time. The microbiome is flexible, and there’s no one perfect path.
Great write-up. As you said, the fuber is more important than the fancy probiotics.
I found the lkmited success in the study to be very surprising.
Thanks, Jeff, really glad you enjoyed it. And totally agree that fibre beats fancy probiotics most of the time. I actually wasn’t too surprised by the limited effect in that study. Our gut microbiomes are incredibly complex and competitive, so it’s not always easy for new microbes to take hold. That said, a different strain or context might show different results, there’s still so much to learn and I think we'll see more studies like this in the coming years.
I farm and I pickle and I don't eat meat. We are switching our farm to using regen ag, so I'm on the same journey as our cocoa and vanilla. They seem to like it as well. Any thoughts on all this fizzy probiotic soda? Thanks again.
Love this, Ruth! Pickling and farming sounds like you're living most people's dream (and a powerful combo for gut and soil health). Fizzy fermented drinks like water kefir and kombucha can be a fun way to get some live microbes in, but I’d see them more as an occasional bonus than a foundation. Some are more about marketing than impact, and can contain a lot of added sugars - fine to enjoy occasionally but if you're wanting to look after your gut microbiome, then I'd look to regular kefir (a fermented milk drink) instead.
Agreed. I see the probiotic soda market going a bit crazy in the US at the moment, lots of new products. It’s giving me fake meat vibes, sucking up all the VC money.
Are you talking about kombucha? I think it is naturally fizzy.
When I had a stem cell transplant in 2022, the medical folks preparing me for the experience told me that the two doses of chemo I would receive were going to "ruin your GI tract." So when they had me meet with a nutritionist as part of the procedure to prepare me for going home, I asked what I could do to help rebuild my gut microbiome.
I got the broadest possible answer. Do your best to eat healthy. Lots of veggies, have some yogurt now and then. It was disappointing.
Thanks for sharing this, Paul. That does sound frustrating, especially when you were looking for real, actionable guidance. I’ve shared an 8 week series called Thriving Gut that digs into how to support your gut microbiome, which you may find useful. That said, there’s also a lot of overselling in this space. It’s really the foundational stuff that makes the biggest difference - fibre, variety, and a few fermented foods when you can. Wishing you all the best. https://dremilyleeming.substack.com/p/your-microbial-world-a-beginners
It's relatively new research. It appears that biomes are very important. A study at McGill institute found they could reduce chronic fatigue and brain fog by removing a bad bacteria via purging the GI tract and reinoculating with biomes from healthy folks. The gut absorbs tryptophan, the amino acid that makes us sleepy after ingesting tryptophan rich turkey. Tryptophan is a precursor to crucial serotonin-> minus yields brain fog. Probably not that simple, possibly other biochems from this amino acid.Apparently the bad bacteria blocks this absorption. Again New Scientist has had great articles from research on this and you can read through their app.
One final note: our brain and gut developed out of similar embryonic cells which may explain brain/gut headaches!
Thanks for your comment, Greg - love that you’re digging into this area, and you’re absolutely right that it’s a fast-moving field with lots of exciting findings. There has been some fascinating research, but it tends to still be early days, and we don’t yet always have consistent evidence on mechanisms. As you say - it's complicated, but exciting.
I studied neurobiology in school and found article about connection between gut and brain many years ago. However, I have a close relation with long covid and am trying to find relief for her. Apparently covid can live in the gut. With the report of fibromyalgia partly caused by bad microbe in biome and the symptoms of brain fog, achy joints and no energy plus odd facial itching possibly caused by lack of serotonin associated chemicals as the bad microbe blocks tryptophan the precursor to serotonin it seems like the culprit. As I said previously fibromyalgia study showed purging the gut and reintroducing healthy biome from another removed symptoms. Frankly I think in the future we may have stored personal biome to use post antibiotic or gut clearing procedures (colonoscopy.)
This is helpful, thanks. I'm also fascinated by the impact of stress on our gut microbiome, as there seems to be such an obvious link between stress and gut issues .