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    Study Some scientists are using chatbots to write all or part of their papers. 454 words that have increased in studies since ChatGPT was released (Jul 2025) Delving into LLM-assisted writing in biomedical publications through excess vocabulary

    Can you provide a source on this? I've heard they are looking into other types of AI but my understanding was that the best and closest to AGI were all LLMs. I have not done much research in this area though. I've heard that the so-called "alignment problem" - AI being aligned to human...
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    Article FDA names former pharmaceutical company executive, Dr. George Tidmarsh, to oversee US drug program, CDER (2025)

    It seems like you're conflating a lot of different things with this statement or perhaps I am misunderstanding you. It seems like you are calling me naive and a MAGA supporter. Is that correct? I'm definitely not part of "MAGA." I am located in the U.S. but I've never voted for Trump. My...
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    Article FDA names former pharmaceutical company executive, Dr. George Tidmarsh, to oversee US drug program, CDER (2025)

    I've changed my opinion of Makary after hearing more of his interviews and reading more articles about what he's doing. He seems pro big-pharma when initally he was claiming to be skeptical.
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    Article Finch wins US jury trial against Ferring over fecal-transplant patents (Aug 2024, Rebyota)

    Would it be worth trying to contact Finch? About improving the quality of their donors and getting their product approved for other conditions (i.e. IBS) From their website it seems like they are trying to patent FMT for C. diff, autism, IBD, Parkinson's, etc, and they have 70 patents related...
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    FMT Faecal microbiota transplant in Parkinson’s disease: pilot study to establish safety & tolerability (Jul 2025, n=12, enema over 6 mo, Biomebank) No significant motor symptom changes. No sustained improvement in non-motor symptoms.

    It's interesting that there was a trend toward reduced daily off time during the "induction phase" of about 1 FMT per week that disappeared when they switched to the "maintenance phase" of 1 FMT per month.
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    Has anyone else tried Keto Diet or similar to modify their gut biome?

    I've been on a ketogenic diet for a little over a year. That's because carbs tend to give me extreme bloating and discomfort. Fiber makes things worse for me too (causes loose stool and urgency) especially soluble fiber. Keto hasn't magically cured me but I feel less bad eating that way...
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    Study Some scientists are using chatbots to write all or part of their papers. 454 words that have increased in studies since ChatGPT was released (Jul 2025) Delving into LLM-assisted writing in biomedical publications through excess vocabulary

    This is scary. AI sometimes hallucinates citations that don't exist, which apparently happened in the recent MAHA report. I wonder if that's happened in other recent peer-reviewed studies. We know AI lies often too, so I don't see why they think it would be safe to use in scientific studies -...
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    Other H. Pylori bacteria that causes stomach ulcers may protect the brain from Alzheimer’s and Parkinson’s (Jun 2025) Helicobacter pylori CagA protein is a potent and broad-spectrum amyloid inhibitor

    Is this actually true? At least for Alzheimer's I thought that the research demonstrating there is a causal relationship was falsified, and that the drugs they developed based on this theory, which target beta-amyloid plaques, do not help Alzheimer's patients...
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    FMT Fecal transplants: Study is a 'wake-up call' for the field as researchers identify unintended consequences. (Jun 2025, mice) Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects

    Too bad it's not open access. Results seem way overstated. They didn't use normal mice but antibiotic-treated mice. That likely dramatically affected their results and therefore makes them less translatable to situations where FMTs are given without antibiotic pre-treatment. Interesting they...
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    Early development In utero human intestine contains maternally derived bacterial metabolites (May 2025, n=21)

    The references mention analyzing fetal tissue samples so I assume the article followed the same methodology. They don't specify how they obtained the samples in most cases but I suspect it was through abortion procedures. https://www.cell.com/developmental-cell/fulltext/S1534-5807(19)30737-3...
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    I wonder if someone read the letter I gave to Senator Cassidy or if they were already aware of the connection. I never heard anything back of course though. He mentions it again around 12 minutes in. If they (HHS) come out and say there is a connection between autism and the microbiome I feel...
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    Diet Diet outperforms microbial transplant to drive microbiome recovery in mice (April 2025)

    I suppose you haven't read this: Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT (2018) https://www.cell.com/cell/fulltext/S0092-8674(18)31108-5?
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    Relevant text of the article: It seems like the microbiome could fit into RFK's framework of ideas, if he is willing to make some modifications. He is right that too much focus was taken off fortifying the immune system, which the microbiome heavily influences, and instead on manufacturing...
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    I heard Martin Makary say in an interview that he believes microbiome disruption to be the most likely cause of autism, so hopefully he already relayed that information to RFK. I'm hoping for the same with respect to his influence.
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    Resarchers have looked at the deeper layers of mucosa and got good results? You said they didn't: I have been researching the mucosa layers and everything I've read indicates the microbiome exists within the lumen and the mucus layers on top of the mucosa's epithelial layer, and the deepest it...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    If you can't provide any studies that have looked at the layers of the mucosa you speak of in your theory then I don't understand why you are so convinced you are right, to be honest. It seems to me to be based on a hunch or speculation and not scientific underpinnings. I understand why you want...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    That's how I interpreted "clearing the microbiome," I'm glad that isn't your goal. If you had said partially clearing or suppressing the microbiome I would have gotten your meaning sooner. Apologies for the misunderstanding on my part. I get that this is what you think is happening but I do not...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    Yeah I don't think you can draw many conclusions about what it would take to clear the microbiome in the colon, and what the result would be, from the mucosa-destroying study in the duodenum. That's my opinion. The colon and duodenum are very different, especially with respect to the...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    Not sure if this is the right thread to post this in, but I have a few questions about the details of the "clearing existing microbiome" clinical trials we are asking the NIH to do. If all these questions have been answered elsewhere feel free to delete. Are these human trials, animal trials...
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    Antibiotics Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine (Apr 2025, n=18)

    Interesting this probably helps explain the mechanism by which vaccines can lead to autoimmune disease in some individuals. Not surprised at all that they gave antibiotics to healthy people. I was prescribed amoxicillin for a bacterial sinus infection that I was told would clear up on its own...
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    FMT Patient–donor similarity and donor-derived species contribute to the outcome of faecal microbiota transplantation for ulcerative colitis (Apr 2025, n=97)

    This is super interesting.
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    FMT Effects of clinical donor characteristics on the success of faecal microbiota transplantation for patients in Denmark with Clostridioides difficile infection: a single-centre, prospective cohort study (Feb 2025) sex, age, BMI, bristol stool type, antibiotic use, H pylori, birth mode, alpha diversity

    That's super interesting that they studied this. Maybe looser stool tend to contain a larger percentage of bacteria that are competitive with C. diff, or fill a similar niche, as opposed to firmer stools. Just speculating.
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    Just watched the clip, wow that's great they understand about antibiotic overuse and the microbiome, even better than I thought from the interview I heard. He said the risk of suicide is 3x greater in the year after taking antibiotics. I don't know if that's true but the fact of him saying that...
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    I can take another day this month to go there. Do you know when he is most likely to be there so I can increase the chances of seeing him? I'll draft up a letter too based on your other post on it. I think I'll emphasize the microbiome-autism connection though and possibly use the Alzheimer's...
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    This seems like the best we could have hoped for since Cassidy seems a lot more accessible than Kennedy. You literally talked to him and he took some time to listen. I don't know if Senator Cassidy knows that there is a microbiome connection to autism, possibly even in a majority of cases, but...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    Well it's at least partially correct i.e. lower route which obviously bypasses those things. We certainly should not be assuming mouse FMT is directly comparable to lower route human FMT, especially considering the differences sometimes seen between human upper and lower route FMT. Or do you...
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    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    There are several factors to consider when translating the conclusions of this and other FMT mouse studies to humans that I did not elucidate in my previous post. Mouse FMTs do not bypass any of their GI tract while human FMTs seek to bypass the acid-producing stomach and antimicrobial-compound...
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    Impact of gut health on food poisoning or sensitivities

    I have not read the studies on fermented foods in healthy people so I'll take your word for it since I don't plan on reading them anytime soon. (I would if I had more time/energy and was considering trying them though.) I have seen fermented foods widely promoted and I suppose I bought into the...
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    Impact of gut health on food poisoning or sensitivities

    I was responding to this person's individual situation and not everyone as general advice. This person mentioned being healthy and having no gut problems.
  30. I

    Enhancing Mucosal microbiota transplant, clearing the gut mucosa prior to FMT

    This is a literature review I did evaluating the above-cited evidence that there is a significant difference between the mucosal and fecal microbiomes in humans. My conclusion is that there is insufficent evidence due to two issues with the research: 1) the use of mouse studies and 2) the use of...
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    Impact of gut health on food poisoning or sensitivities

    https://pmc.ncbi.nlm.nih.gov/articles/PMC8733563/ Read the sections "Pathogen Resistance by Commensal Gut Microbiota" and "Gut Microbiota and Pathogen Colonization Resistance Mechanisms" Your microbiome has what's called "colonization resistance" to gut pathogens that cause food poisoning like...
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    Blog The FDA and FMT regulation, part 2. (Jul 2024, HumanMicrobes.org) I met with the FDA. Here's what I shared with them, and their response.

    That's called Southern hospitality. One of the nice things about living in Virginia :) It has been two weeks and I haven't gotten a response. I can try calling their office next week to follow up. I'll email you the comment I submitted on their website. There wasn't an option for a meeting...
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    Advocacy Continued letters and complaints to the FDA, NIH, and HHS (Jan 2025, FMT)

    Could you try complaining focusing on one specific study where harm was done (for example, the FMT study for C. diff that had to be stopped is a very clear example of patient harm being done, i.e. death) and cite the specific conditions in the donors (if you have info on the donors) that are...
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    Healthcare system Incoming trump admin with RFK signals new start for FDA

    That sucks you weren't able to get in. Sorry you woke up early and everything. Same with Fox News but I'm not surprised. Almost no one seems interested in this issue which is so bizarre. I don't fully understand it myself. I tried opening the article but it cost $. I did read that Bill Cassidy...
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    Outcomes Please help - anxiety/panic after FMT+yellow stool

    @Veronikakrov have you heard of histamine intolerance? When my histamines were really out of whack after antimicrobials I had severe anxiety, panic and insomnia. I still have the condition but to a lesser extent than before. Switching to a low-carb, low-histamine diet helped along with taking...
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    Advocacy Continued letters and complaints to the FDA, NIH, and HHS (Jan 2025, FMT)

    That sounds like a good idea. I'm happy to try to help with that. I don't have any relevant experience though just my own research on the microbiome and FMT. I know one person in academia who has some experience writing grants that I can ask for some advice on the process though.
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    Blog The FDA and FMT regulation, part 2. (Jul 2024, HumanMicrobes.org) I met with the FDA. Here's what I shared with them, and their response.

    @SFBayFMT5 Michael actually looked normal in person, not really like the picture. Except he is really tall. I saw him without the beard though. @Michael Harrop that's too bad about the NIH. How does someone get an appointment? With respect to protesting at RFK, Jr's hearing I think saying any...
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    Sharing My Autoimmune Recovery Journey + Solutions for your Gut Health (GAIP diet)

    Not really a great advertisement for GAIP for my situation for several reasons: I'm 5'5" and weigh 112 lbs, I can't afford to lose weight, let alone 25+ lbs I have carbohydrate intolerance There is insufficient protein on this diet One of my primary and most bothersome symptoms is fatigue which...
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    Sharing My Autoimmune Recovery Journey + Solutions for your Gut Health (GAIP diet)

    Same on fiber. I've read insoluble fiber can aggravate Crohn's (I have small bowel inflammation but unconfirmed if it's actually Crohn's) likely due to the physical irritation of an already inflamed intestinal lining. I'm also considering trying the diet though by slowly increasing the amount of...
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    Sharing My Autoimmune Recovery Journey + Solutions for your Gut Health (GAIP diet)

    https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2024.1208074/full Seems like GAIP (Goodbye Autoimmune Paleo) is a very strict diet comprised of essentially: 8-10 cups of raw vegetables and fruit 75% raw vegetables (leafy greens, crucifers) 25% raw fruit 1 cup...
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