Gut Microbiome

The gut microbiome is getting a lot of attention lately. There’s even a show about it on Netflix. Scientists are linking the health of your gut microbiome to body weight (having a low diversity leading to obesity, as some are claiming), and also to mental health (depression and anxiety in particular). I’m hearing that you should eat 20-30 different fruits and vegetables to maintain healthy gut bacteria.

Anyway, I thought it would be good to create a new topic.

The obesity epidemic has become a global public health crisis in recent years and is continuing to worsen at an alarming rate. However, the pathophysiological mechanisms involved in the development of obesity and obesity-related diseases are still being unraveled. In the past ten years, the gut microbiota has been identified as a crucial player affecting the onset and progression of obesity and obesity-related diseases, especially with respect to changes in its composition and metabolites during obesity progression. Herein, we summarize the roles and mechanisms of gut microbiota’s composition and metabolite changes in the gut play in obesity and obesity related diseases. Furthermore, we discuss potential therapeutic treatments that can be used to modulate the gut microbiome composition and target the relevant metabolic pathways of obesity and obesity-related metabolic diseases.


An early hint that gut microbes might play a role in obesity came from studies comparing intestinal bacteria in obese and lean individuals. In studies of twins who were both lean or both obese, researchers found that the gut community in lean people was like a rain forest brimming with many species but that the community in obese people was less diverse—more like a nutrient-overloaded pond where relatively few species dominate. Lean individuals, for example, tended to have a wider variety of Bacteroidetes, a large tribe of microbes that specialize in breaking down bulky plant starches and fibers into shorter molecules that the body can use as a source of energy.

A new appreciation for the impact of gut microbes on body weight has intensified concerns about the profligate use of antibiotics in children. Blaser has shown that when young mice are given low doses of antibiotics, similar to what farmers give livestock, they develop about 15 percent more body fat than mice that are not given such drugs. Antibiotics may annihilate some of the bacteria that help us maintain a healthy body weight. “Antibiotics are like a fire in the forest,” Dominguez-Bello says. “The baby is forming a forest. If you have a fire in a forest that is new, you get extinction.” When Laurie Cox, a graduate student in Blaser’s laboratory, combined a high-fat diet with the antibiotics, the mice became obese. “There’s a synergy,” Blaser explains. He notes that antibiotic use varies greatly from state to state in the U.S., as does the prevalence of obesity, and intriguingly, the two maps line up—with both rates highest in parts of the South.

Yeah, I think for the last several years at least. I edited a book about it last month actually.

This book was pretty interesting:

(Well, the part I read. Still need to finish it, but that’s more about my limited ability to read for fun these days than the book itself.)

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[Ed Yong] makes terrible puns and regrets none of them.

Must be the editor.

supposedly there’s a way to transplant gut microbiome or something from a healthier person and you’d get his health too. Wonder how this is done?


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I’d say it’s more like seeding than transplantation. As to the method, if your imagination won’t get you there, Google should. :face_with_peeking_eye:


In the Netflix show, they featured a lady who was doing this on her own, first with her brother’s poop and then with her husband’s poop. She used a blender and made capsules that contained the poop and some other substance, which she would then take as pills. I can’t remember what her problem was (why she wanted to improve her gut bacteria).

But the problem with seeding is that you get the bad along with the good. Her brother had problems with depression, and she noticed that she was developing increased depression symptoms when seeding with her brother’s bacteria. So she switched to her husband’s bacteria and the depression symptoms disappeared.

I think this is some good confirmation that your gut microbiome plays a role in mental health.

It’s also good confirmation that people are crazy.


Procter and Gamble are cleaning up with Align (I’m here all week). It’s been around for decades. In trips to Mexico it’s worked very well for me, but the bacteria are engineered to die out (so you need to keep buying). Does do the job, though.

Pretty interesting topic, but I’d hate to accidentally chew open a poop capsule.

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They sell probiotic pills in the convenience stores here (or at least they used to). I’ll see if they are still on sale. I’m not sure I want to start taking such pills, though. Need to be convinced it’s better than just a good diet.



And to add to that:

Most of the best cheese-based sources of probiotics are those that have gone through aging but not heating, as the heat can kill off the bugs.

These include:

  • Swiss
  • provolone
  • aged cheddar
  • Gouda
  • Edam
  • Gruyère
  • Parmesan

Cottage cheese can contain live cultures, but make sure it says “live cultures” on the label. Blue cheeses, like Stilton, can also provide a wide range of bacteria.

The provolone cheese at Costco stinks pretty bad. I still like it but it drives my wife and daughter crazy. My little payback for all the stinky tofu they have eaten over the years.


I do this sometimes

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Good topic!
I’m onto a few spoons of natto each day. I guess has probiotics and is apparently the richest source of vitamin k2 one can find which may have many benefits.
Trying to get good at miso soup but find it a pain to get tasting how I would like.
Just came from px mart to pick up a few things to give kimchi a try…so Korean chili flakes, anchovy sauce, and non iodized salt which seems needed for better fermentation.
I’m actually trying it first using watermelon rind which itself has benefits.
If I can get the fermentation procedure down then I’ll try other kimchis. Looks like sauerkraut is a very similar process of vegetable fermentation…and no cultures are needed like with yogurt.
Anyway …watching this post.


You need hondashi flakes if you want miso soup to taste right. Nothing else will quite do it.


I can’t stand kimchi or cabbage in general, but I’ve made it a couple of times before using a combination of the three recipes below and it apparently turned out pretty well according to the person who ate it.

How To Brine Napa Cabbage for Kimchi

My Favorite Kimchi Recipe - A Small Batch DIY

Traditional kimchi recipe

The most painful part was having to keep tasting the brined cabbage during washing to check whether enough salt had been removed. :face_vomiting:

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I believe it.

I took a full spectrum antibiotic a few years ago and was left in a deep depression. I suspect it was caused from the antibiotics even though the doctors said it’s not a side effect of antibiotics.

I looked online and many people experienced the same and recommended to heal the gut. I ate kimchi and i did start to improve from that.

This is my experience


Is that the bonita flakes? Guess that would be my next addition. I’ve got the dried mushrooms and small fish but guess I need bonita and seaweed.
It really seems to be …simply complex.

Thanks. Those look like useful links. Think I read the Napa one earlier.
Ha…yeah , trickiest part seems to be the brining process to get good and safe fermentation but I also want to keep the sodium as low as possible.

Yes, you need both. You add them to taste but they really greatly enhance the flavor of miso soup. Just miso alone isn’t enough. Some diced salmon helps if you got them. Like those pieces of leftover salmon would be great for miso soup actually.

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