This is not an easy one to answer. It is a balance. Perhaps alternating may help.
Yes. Doxycycline does affect the intestinal microbiome, but generally less profoundly than many broad-spectrum antibiotics, particularly β-lactams, clindamycin, and fluoroquinolones. Its effects are complex and depend on dose, duration, route of administration, diet, and the individual's baseline microbiome.
Your question about Bifidobacterium is particularly important because this genus has been associated with immune homeostasis and, in several studies, with improved responses to immune checkpoint inhibitors.
Does doxycycline reduce Bifidobacterium? The answer is yes, it can, but the effect is variable.
Several human and animal studies have shown that doxycycline or other tetracyclines can:
Reduce the abundance of Bifidobacterium
Reduce Lactobacillus
Decrease overall bacterial diversity during treatment
Increase the relative abundance of some opportunistic organisms
However, these changes are often less dramatic than those produced by antibiotics such as clindamycin or ciprofloxacin. Importantly, recovery of the microbiome frequently begins after the antibiotic is discontinued, although recovery may be incomplete after prolonged or repeated courses.
Practical implications for your metabolic oncology protocol
This is an important consideration because doxycycline is one of the cornerstone agents for targeting mitochondrial function and cancer stem cells in your protocol. Rather than abandoning doxycycline because of microbiome concerns, a reasonable approach would be to actively support the microbiome during treatment.
For patients receiving prolonged doxycycline, I would consider:
A diet rich in diverse plant fibers (as tolerated)
Daily fermented foods or a thoughtfully selected probiotic
Consideration of periodic microbiome recovery phases if clinically appropriate
Avoidance of additional unnecessary antibiotics
Monitoring for gastrointestinal symptoms that may suggest significant dysbiosis
From a biological perspective, this represents a trade-off: doxycycline may transiently reduce beneficial organisms such as Bifidobacterium, yet it also targets mitochondrial metabolism in cancer cells and cancer stem cells. Optimizing both anti-tumor efficacy and microbiome health may therefore offer the greatest overall benefit.
Increasing levels of the bacteria Akkermansia muciniphila is one of the most interesting strategies in current digestive health, as this bacterium is responsible for strengthening the colon's mucus barrier, leading to better immune balance and reduced systemic inflammation.
Akkermansia lives in the mucous layer of the intestine, right in the intestinal wall. Unlike many other microbes that feed on food, Akkermansia helps regenerate the intestinal mucosa, keeping it strong, resilient, and able to protect against inflammation and imbalance. This is why Akkermansia is so vital for overall health: it literally strengthens the intestinal barrier, which is essential for absorbing nutrients, maintaining a healthy metabolism, and keeping toxins at bay.
Studies have shown that people with higher levels of Akkermansia tend to have less body fat, better insulin sensitivity, and better weight regulation; it has earned the nickname "the slimming bug." Here are the fundamental pillars to nourish and stimulate its growth:
1. Foods Rich in Polyphenols: Unlike other bacteria, Akkermansia loves antioxidant compounds that the body doesn't easily absorb in the small intestine.
--- Red and dark fruits: Blueberries, raspberries, blackberries, and especially pomegranate (rich in ellagitannins).
--- Beverages: Green tea and coffee are excellent allies.
--- Nuts: Walnuts and pistachios provide polyphenols that promote its proliferation.
--- Apple peel, naturally rich in pectin and polyphenols, is a favorite energy source for Akkermansia.
--- Broccoli is useful for reducing weight, blood glucose levels, fat accumulation, and insulin resistance associated with AHGSD, relieving inflammation and liver and ileal damage, and improving the body's antioxidant capacity. Furthermore, broccoli can optimize the structure of the gut flora, promote the growth of Allobaculum, Muribaculaceae, Akkermansia, Eubacterium, and Bacteroides, and reduce bile acid deposition.
2. Specific Prebiotics. Certain fibers act as direct "fuel" for these bacteria:
---Resistant starch: Found in legumes, raw oats, or potatoes that have been cooked and then cooled (retrogradation process).
---Inulin: Present in garlic, onions, leeks, and asparagus.
3. Intermittent Fasting - Akkermansia has a unique characteristic: when food is not present, it feeds on the gut's own mucus. This, far from being harmful, stimulates goblet cells to produce new, fresh mucus, which keeps the intestinal barrier young and thick. Respecting fasting windows (such as the 16/8 or 17/7 schedule) is one of the most effective ways to increase its presence.
4. Berberine: Several studies have shown that it significantly increases the abundance of Akkermansia. Berberine is an ingredient found in many plant species, including Oregon grape and barberry. It has been used to treat many conditions, including diarrhea, diabetes, and high cholesterol.
Thank you, Leynia. ❤ I think Paul Marik's report is a fundamental basis because it contextualizes the relationship between microbiota, metabolism, inflammation, immunity, and cancer, and allows us to understand, for example, why Akkermansia muciniphila can be so relevant within this complex ecosystem. 👍👌
My comment about Akkermansia muciniphila was simply intended to complement that information with some additional mechanisms and references. I believe that's precisely where the value of the report lies: it provides a framework that we can translate from theory to practice.
For example, Marik's report can be used as a kind of "roadmap":
--Analyze the microbiome: don't just look at Akkermansia, but also at diversity, potentially relevant bacteria, and overall balance.
--Look at function, not just species: potential production of butyrate and other SCFAs, fiber metabolism, mucin, bile acids, etc.
--Relate microbiota to diet: use the results to ask ourselves which dietary components could promote a healthier ecosystem. -- Identify potentially beneficial foods: polyphenols from coffee, tea, berries, pomegranate, cocoa, vegetables, etc.
- Evaluate fiber/prebiotics and determine which are tolerated and which are not, because more fiber is not necessarily better for everyone.
- Conduct longitudinal follow-up: repeating the analysis after months of dietary changes can be much more insightful than a single snapshot.
- Relate the gut microbiota to metabolic context: glucose, insulin sensitivity, inflammation, body composition, etc.
- And most interestingly, it allows for the development of practical strategies and then observation of how the gut ecosystem responds: diet, polyphenols, fiber, prebiotics, physical activity, fasting, etc.
Thank you for taking the time to write all this. The structure of Dr. Marik's article, its overall concepts, seem sensible to me also, although my knowledge is minimal. As to its details, about which I know even less, they seem to match what people are saying these days.
Guillermou, for some reason I am unable to “like” more than a comment or two on Substack, but please know I appreciate everything you write. I have found that good gut health is everything. I especially appreciate you listing the foods that promote microbiome health.
Last year and this year I undertook a gut cleanse to get rid of all the nasties and then started to rebuild my gut (and wall) including taking a good quality probiotic. More recently I have been taking a very good quality fermented goats’ milk with kefir grains. Amongst other things I take Butyrate and Akkermansia.
My go-to bible is a book, by the biochemist, Chris Woollams ’Heal your Gut - Heal your Body’. Incredibly readable.
The American Gut Project (AGP) was one of the largest citizen science projects on the human microbiome, with tens of thousands of participants. Its data continue to be used in recent studies to investigate relationships between diet, medications, obesity, food intolerances, and microbial diversity. Recent findings based on data from the American Gut Project:
1. Dietary fiber after antibiotics
A study published in 2016 analyzed nearly 2,000 AGP participants who had taken antibiotics. Individuals with higher fiber intake showed a more diverse microbiota and bacterial profiles consistent with better recovery after antibiotic-induced disruption.
An analysis of more than 7,000 people from the American Gut Project (AGP) found an association between lower gut bacterial diversity and higher BMI, reinforcing the hypothesis that microbial richness is related to metabolic health.
Researchers used AGP data to identify microbial differences between people with and without lactose intolerance. They detected specific alterations in several bacterial genera and suggest that the microbiome could influence the intensity of symptoms.
4. Relationship with pesticides and the microbiome
Recent research shows that numerous pesticides, food additives, and environmental pollutants can alter beneficial gut bacteria. This is relevant because it helps explain why environmental factors could modify the patterns observed in large cohorts.
The latest research is shifting from simply studying "what bacteria are present" to analyzing "what functions they perform." The results suggest that the metabolic activity of the microbiome may be more important for cardiovascular and metabolic health than its bacterial composition alone.
A control group and experimental group were both given PEG and antibiotics. The experiment’s value is therefore specific to the conditions resulting, conditions that can affect not only the gut in more ways than we know, but other aspects of physiology about whch we know even less. The experiment is therefore okay in itself, but the prep drugs are not a valid stand-in for general conclusions about the gut and nutrition.
Leynia. Also: there is growing evidence of the beneficial effects of dietary fiber intake on human health. Mechanistic research has shown that the physiological functions of different dietary fibers depend largely on their physicochemical characteristics, one of which is solubility. Compared to insoluble dietary fiber, soluble dietary fiber is readily accessible and metabolized by microorganisms in the gut, producing a range of beneficial and functional metabolites.
In a study based on the significant abundance of potential pathogens, the gut microbiota of the non-vegetarian group showed an abundance of potential pathogens such as Bilophila wadsworthia, Escherichia coli, and E. hermannii, while the vegetarian group's microbiota contained only Klebsiella pneumoniae. These results suggest that the gut microbiota of those who consume many vegetables, with a high abundance of P. copri and a low variety of potential pathogens, could be a way to maintain good health.
Both polyphenols and dietary fiber play a crucial role in protecting human health and can produce butyrate through fermentation by the gut microbiota. The interaction of polyphenols with dietary fiber affects their bioaccessibility in the upper and lower digestive tracts. Dietary fiber, polyphenols, their conjugates, and their metabolites modulate the population and diversity of the gut microbiome. Consuming dietary fibers rich in polyphenols, such as pomegranate, cranberry, berries, and tea, improves gut health.
It is important to note that in recent years, our understanding of the mechanisms involved has deepened, highlighting the crucial role of the gut microbiota in this process through the production of short-chain fatty acids (SCFAs) and other functional metabolites. The decline in dietary fiber intake over centuries has fostered a gut microbiota detrimental to human health, leading to a global epidemic of diabetes, cancer, and other non-communicable diseases. The gut microbiota's response to increased dietary fiber availability can vary depending on the type, level, and duration of intake, demonstrating specific cutoff thresholds for each type of dietary fiber.
Dietary fiber can be classified into three types based on the physiological properties of its resistant carbohydrate polymerization with 3 to 9 monomeric units (MU): 1) non-starch polysaccharides (NSPs) (MU ≥ 10); 2) resistant starches (RS) (MU ≥ 10); and 3) resistant/non-digestible oligosaccharides (ROSs) (MU: 3–9). NSPs primarily include cellulose, hemicellulose, pectins, inulin, and various hydrocolloids. Inulin is a fructan containing 2 to 60 fructose units. When MU < 10, inulin is also recognized as a fructooligosaccharide (FOS), a well-documented prebiotic. Reactive sugars (RS) can be further classified into RS 1 to RS 5, which can be derived from ground grains and seeds (RS 1), raw potatoes, corn, and green plantains (RS 2), cooked and cooled potatoes and corn flakes (RS 3), bakery products (RS 4), and fried rice chips (RS 5). Reactive oxygen species (ROS) consist of 3–9 MU, many of which are named after polymerized monosaccharides, such as galactooligosaccharides (GOS), xylooligosaccharides (XOS), and galactosides. Dietary fibers escape digestion in the upper gastrointestinal tract and are fermented by bacteria in the colon. The degree of polymerization, particle size, solubility, viscosity, and other characteristics of dietary fiber can influence fiber fermentability and bacterial specificity. Fibers with a low degree of polymerization can be broken down into small molecules in the intestine with rapid fermentation; Small particles are more likely to be exposed to microbial enzymes; whereas soluble and viscous fibers, with a high capacity for water retention and stool formation, and therefore limited exposure to microbes, are resistant to fermentation. The various interactions between monomer chains and enzymes influence bacterial growth, resulting in fiber-specific gut microbiota.
Dietary fibers escape digestion in the upper gastrointestinal tract and are fermented by bacteria in the colon. The degree of polymerization, particle size, solubility, viscosity, and other characteristics of dietary fiber can influence fiber fermentability and bacterial specificity. Fibers with a low degree of polymerization can be broken down into small molecules in the intestine with rapid fermentation; small particles are more likely to be exposed to microbial enzymes. In contrast, soluble and viscous fibers, with a high water-holding capacity and fecal-forming capacity, and therefore limited exposure to microbes, are resistant to fermentation. The various interactions between monomer chains and enzymes influence bacterial growth, resulting in fiber-specific gut microbiota.
Inulin-like fructans (ITFs) were hydrolyzed extracellularly by Bifidobacteria in the human colon, releasing monosaccharides and/or oligosaccharides accessible to butyrate producers, the secondary degraders. During the utilization and metabolism of polysaccharides by bacteria, multiple metabolites were generated, including gases (e.g., H₂, CH₄, CO₂), lactate, succinate, and short-chain fatty acids (SCFAs).
The most abundant SCFAs are acetate, propionate, and butyrate. SCFAs can be used by intestinal mucosal cells as energy sources, with butyrate being the preferred energy substrate for colonocytes. Furthermore, absorbed SCFAs are transferred to the circulation via the hepatic portal vein to act as signaling molecules and can activate complex downstream molecular pathways in the liver, brain, lungs, pancreas, bones, adipose tissue, and other organs. Short-chain fatty acids (SCFAs) play crucial regulatory roles in host metabolic homeostasis, immunological processes, maintenance of intestinal barriers, neurobiology, skeletal functions, and the suppression of inflammation and carcinogenesis, and have been shown to be beneficial to human health. SCFAs have multiple beneficial effects on the epithelial, immune, nervous, and vascular systems. A decrease in the production of these metabolites has been linked to several diseases, including intestinal inflammation, diabetes, liver cirrhosis, and atherosclerosis. SCFAs play a crucial role in improving gastrointestinal health by acting locally in the gut. These metabolites help preserve the integrity of the intestinal barrier, which aids in nutrient absorption and blocks pathogens and harmful substances. Hypotheses about the possible mechanisms of fiber's anti-inflammatory effects include a direct impact on immune cells (e.g., for pectin), fermentation to short-chain pleiotropic fatty acids (for fermentable fiber only), modulation of the gut microbiome towards greater diversity, changes in bile acid metabolism, differential release of intestinal hormones (such as glucose-dependent insulinotropic peptide [GIP]), and improved insulin resistance.
Furthermore, the contribution of phytate-mediated antioxidant and immunomodulatory mechanisms should be considered. The gut microbiota plays a vital role in the synthesis of neurotransmitters such as serotonin, dopamine, and norepinephrine, as well as metabolites like short-chain fatty acids (SCFAs). Alterations in the composition of the microbiota are called dysbiosis, which has been associated with systemic inflammation and chronic stress.
The microbiomes of soil, plants, animals, and humans are interconnected. Soil microorganisms influence plant microbiomes and, through food and contact with nature, can affect humans.
Numerous studies show that herbicides, fungicides, and insecticides can reduce soil microbial diversity or alter its composition, affecting important ecological functions. Exposure to pesticides can also directly alter the gut microbiome.
A systematic review published in 2026 concluded that pesticide exposure is associated with changes in the gut microbiota (dysbiosis) in both animals and humans. The findings indicate that prenatal pesticide exposure is linked to adverse fetal developmental outcomes. Furthermore, pesticide exposure affects metabolic, immune, and nervous system function due to alterations in the composition of the gut microbiota and membrane permeability.
The "microbial biodiversity" theory proposes that the loss of diversity in ecosystems decreases human exposure to beneficial environmental microorganisms, which could influence immunological and inflammatory diseases.
Current evidence supports a plausible chain of influence: This is the chain of events: Pesticides alter the soil microbiome, leading to changes in plants and food, and consequently, changes in human microbial exposure, influencing the human microbiome and health.
Dear Guillermou, It is nice to see you back in the saddle here with backed up info since Mercola stopped allowing comments. You always had helpful research for those who wanted more in-depth info. 🙏
Thank you Dr. Marik, for presenting Sabine Hazan's work. All of the ancient methods of supporting human health seem to remain in force.
I also appreciated Dr. Kory's story of the take-downs of IV vitamin-C for sepsis-survival, and your provision of life-saving patient care in-hospital during COVID. He describes your ambush by the lockstep hospital-admin overriding your prescriptive orders. ;-(
Professor Paul Marik Identified The Cure for Sepsis. I Watched Medicine Bury It.
Becoming Paul Marik's close colleague was the most inspiring turn my career ever took, until the same partnership got us both excommunicated from academic medicine and ended his career at the bedside.
This is not an easy one to answer. It is a balance. Perhaps alternating may help.
Yes. Doxycycline does affect the intestinal microbiome, but generally less profoundly than many broad-spectrum antibiotics, particularly β-lactams, clindamycin, and fluoroquinolones. Its effects are complex and depend on dose, duration, route of administration, diet, and the individual's baseline microbiome.
Your question about Bifidobacterium is particularly important because this genus has been associated with immune homeostasis and, in several studies, with improved responses to immune checkpoint inhibitors.
Does doxycycline reduce Bifidobacterium? The answer is yes, it can, but the effect is variable.
Several human and animal studies have shown that doxycycline or other tetracyclines can:
Reduce the abundance of Bifidobacterium
Reduce Lactobacillus
Decrease overall bacterial diversity during treatment
Increase the relative abundance of some opportunistic organisms
However, these changes are often less dramatic than those produced by antibiotics such as clindamycin or ciprofloxacin. Importantly, recovery of the microbiome frequently begins after the antibiotic is discontinued, although recovery may be incomplete after prolonged or repeated courses.
Practical implications for your metabolic oncology protocol
This is an important consideration because doxycycline is one of the cornerstone agents for targeting mitochondrial function and cancer stem cells in your protocol. Rather than abandoning doxycycline because of microbiome concerns, a reasonable approach would be to actively support the microbiome during treatment.
For patients receiving prolonged doxycycline, I would consider:
A diet rich in diverse plant fibers (as tolerated)
Daily fermented foods or a thoughtfully selected probiotic
Consideration of periodic microbiome recovery phases if clinically appropriate
Avoidance of additional unnecessary antibiotics
Monitoring for gastrointestinal symptoms that may suggest significant dysbiosis
From a biological perspective, this represents a trade-off: doxycycline may transiently reduce beneficial organisms such as Bifidobacterium, yet it also targets mitochondrial metabolism in cancer cells and cancer stem cells. Optimizing both anti-tumor efficacy and microbiome health may therefore offer the greatest overall benefit.
Thanks.
Great information and presentation! 👍👌
Increasing levels of the bacteria Akkermansia muciniphila is one of the most interesting strategies in current digestive health, as this bacterium is responsible for strengthening the colon's mucus barrier, leading to better immune balance and reduced systemic inflammation.
Akkermansia lives in the mucous layer of the intestine, right in the intestinal wall. Unlike many other microbes that feed on food, Akkermansia helps regenerate the intestinal mucosa, keeping it strong, resilient, and able to protect against inflammation and imbalance. This is why Akkermansia is so vital for overall health: it literally strengthens the intestinal barrier, which is essential for absorbing nutrients, maintaining a healthy metabolism, and keeping toxins at bay.
Studies have shown that people with higher levels of Akkermansia tend to have less body fat, better insulin sensitivity, and better weight regulation; it has earned the nickname "the slimming bug." Here are the fundamental pillars to nourish and stimulate its growth:
1. Foods Rich in Polyphenols: Unlike other bacteria, Akkermansia loves antioxidant compounds that the body doesn't easily absorb in the small intestine.
--- Red and dark fruits: Blueberries, raspberries, blackberries, and especially pomegranate (rich in ellagitannins).
--- Beverages: Green tea and coffee are excellent allies.
--- Nuts: Walnuts and pistachios provide polyphenols that promote its proliferation.
--- Apple peel, naturally rich in pectin and polyphenols, is a favorite energy source for Akkermansia.
--- Broccoli is useful for reducing weight, blood glucose levels, fat accumulation, and insulin resistance associated with AHGSD, relieving inflammation and liver and ileal damage, and improving the body's antioxidant capacity. Furthermore, broccoli can optimize the structure of the gut flora, promote the growth of Allobaculum, Muribaculaceae, Akkermansia, Eubacterium, and Bacteroides, and reduce bile acid deposition.
2. Specific Prebiotics. Certain fibers act as direct "fuel" for these bacteria:
---Resistant starch: Found in legumes, raw oats, or potatoes that have been cooked and then cooled (retrogradation process).
---Inulin: Present in garlic, onions, leeks, and asparagus.
3. Intermittent Fasting - Akkermansia has a unique characteristic: when food is not present, it feeds on the gut's own mucus. This, far from being harmful, stimulates goblet cells to produce new, fresh mucus, which keeps the intestinal barrier young and thick. Respecting fasting windows (such as the 16/8 or 17/7 schedule) is one of the most effective ways to increase its presence.
4. Berberine: Several studies have shown that it significantly increases the abundance of Akkermansia. Berberine is an ingredient found in many plant species, including Oregon grape and barberry. It has been used to treat many conditions, including diarrhea, diabetes, and high cholesterol.
https://pmc.ncbi.nlm.nih.gov/articles/PMC4856456/ (2016).--
https://pmc.ncbi.nlm.nih.gov/articles/PMC6164842/ (2018).—
https://pmc.ncbi.nlm.nih.gov/articles/PMC6924600/#:~:text=of%20paired%20data.-,A.,Lactobacillus%20spp.(2019).-
https://healthpath.com/gut-health/akkermansia-muciniphila-overview/#:~:text=Some%20of%20them%20aren't,polyphenols%20up%20and%20supercharge%20their (2020).—
https://pmc.ncbi.nlm.nih.gov/articles/PMC8624415/#:~:text=Based%20on%20the%20fresh%20weight,red%20onions%20(Table%201).(2021).-
https://www.researchgate.net/publication/359643751_Mucin_foraging_enables_Akkermansia_muciniphila_to_compete_against_other_microbes_in_the_gut_and_to_modulate_host_sterol_biosynthesis (2022).--
https://pmc.ncbi.nlm.nih.gov/articles/PMC10301191/ (2023).--
https://pmc.ncbi.nlm.nih.gov/articles/PMC9959343/ (2023).—
https://www.mdpi.com/2304-8158/13/10/1550 (2024).--
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1595527/full (2025).--
https://pmc.ncbi.nlm.nih.gov/articles/PMC12156470/#:~:text=This%20classification%20is%20based%20on,phenolic%20compounds)%20and%20its%20significant (2025)
https://www.mdpi.com/2072-6643/17/3/562 (2025).-
https://pubs.rsc.org/en/content/articlelanding/2025/fo/d4fo03731f/unauth (2025).-
Thanks Guillermo
👍❤️
Thank you for providing an interpretation that, imo, should have been a major part of the article.
Thank you, Leynia. ❤ I think Paul Marik's report is a fundamental basis because it contextualizes the relationship between microbiota, metabolism, inflammation, immunity, and cancer, and allows us to understand, for example, why Akkermansia muciniphila can be so relevant within this complex ecosystem. 👍👌
My comment about Akkermansia muciniphila was simply intended to complement that information with some additional mechanisms and references. I believe that's precisely where the value of the report lies: it provides a framework that we can translate from theory to practice.
For example, Marik's report can be used as a kind of "roadmap":
--Analyze the microbiome: don't just look at Akkermansia, but also at diversity, potentially relevant bacteria, and overall balance.
--Look at function, not just species: potential production of butyrate and other SCFAs, fiber metabolism, mucin, bile acids, etc.
--Relate microbiota to diet: use the results to ask ourselves which dietary components could promote a healthier ecosystem. -- Identify potentially beneficial foods: polyphenols from coffee, tea, berries, pomegranate, cocoa, vegetables, etc.
- Evaluate fiber/prebiotics and determine which are tolerated and which are not, because more fiber is not necessarily better for everyone.
- Conduct longitudinal follow-up: repeating the analysis after months of dietary changes can be much more insightful than a single snapshot.
- Relate the gut microbiota to metabolic context: glucose, insulin sensitivity, inflammation, body composition, etc.
- And most interestingly, it allows for the development of practical strategies and then observation of how the gut ecosystem responds: diet, polyphenols, fiber, prebiotics, physical activity, fasting, etc.
Thank you for taking the time to write all this. The structure of Dr. Marik's article, its overall concepts, seem sensible to me also, although my knowledge is minimal. As to its details, about which I know even less, they seem to match what people are saying these days.
😊❤️🌹
Guillermou, for some reason I am unable to “like” more than a comment or two on Substack, but please know I appreciate everything you write. I have found that good gut health is everything. I especially appreciate you listing the foods that promote microbiome health.
Outstanding comment. Thank you.
Thanks for that!
Last year and this year I undertook a gut cleanse to get rid of all the nasties and then started to rebuild my gut (and wall) including taking a good quality probiotic. More recently I have been taking a very good quality fermented goats’ milk with kefir grains. Amongst other things I take Butyrate and Akkermansia.
My go-to bible is a book, by the biochemist, Chris Woollams ’Heal your Gut - Heal your Body’. Incredibly readable.
The American Gut Project (AGP) was one of the largest citizen science projects on the human microbiome, with tens of thousands of participants. Its data continue to be used in recent studies to investigate relationships between diet, medications, obesity, food intolerances, and microbial diversity. Recent findings based on data from the American Gut Project:
1. Dietary fiber after antibiotics
A study published in 2016 analyzed nearly 2,000 AGP participants who had taken antibiotics. Individuals with higher fiber intake showed a more diverse microbiota and bacterial profiles consistent with better recovery after antibiotic-induced disruption.
https://link.springer.com/article/10.1186/s13104-026-07708-7?utm_source=chatgpt.com (2026)
2. Microbial Diversity and Body Mass Index
An analysis of more than 7,000 people from the American Gut Project (AGP) found an association between lower gut bacterial diversity and higher BMI, reinforcing the hypothesis that microbial richness is related to metabolic health.
https://www.researchgate.net/publication/403987299_Association_Between_Gut_Microbial_Alpha_Diversity_and_Body_Mass_Index_Evidence_from_the_American_Gut_Project (2026)
3. Lactose Intolerance
Researchers used AGP data to identify microbial differences between people with and without lactose intolerance. They detected specific alterations in several bacterial genera and suggest that the microbiome could influence the intensity of symptoms.
https://www.reddit.com/r/IBSResearch/comments/1fujltk/gut_microbiome_and_serum_metabolome_alterations/?utm_source=chatgpt.com (2026)
4. Relationship with pesticides and the microbiome
Recent research shows that numerous pesticides, food additives, and environmental pollutants can alter beneficial gut bacteria. This is relevant because it helps explain why environmental factors could modify the patterns observed in large cohorts.
https://nypost.com/2025/12/06/health/food-additives-and-pesticides-may-be-harming-gut-health-study-says/?utm_source=chatgpt.com (2025)
5. What's Emerging in 2025-2026
The latest research is shifting from simply studying "what bacteria are present" to analyzing "what functions they perform." The results suggest that the metabolic activity of the microbiome may be more important for cardiovascular and metabolic health than its bacterial composition alone.
https://link.springer.com/article/10.1186/s40168-025-02258-9?utm_source=chatgpt.com (2025)
A control group and experimental group were both given PEG and antibiotics. The experiment’s value is therefore specific to the conditions resulting, conditions that can affect not only the gut in more ways than we know, but other aspects of physiology about whch we know even less. The experiment is therefore okay in itself, but the prep drugs are not a valid stand-in for general conclusions about the gut and nutrition.
Leynia. Also: there is growing evidence of the beneficial effects of dietary fiber intake on human health. Mechanistic research has shown that the physiological functions of different dietary fibers depend largely on their physicochemical characteristics, one of which is solubility. Compared to insoluble dietary fiber, soluble dietary fiber is readily accessible and metabolized by microorganisms in the gut, producing a range of beneficial and functional metabolites.
In a study based on the significant abundance of potential pathogens, the gut microbiota of the non-vegetarian group showed an abundance of potential pathogens such as Bilophila wadsworthia, Escherichia coli, and E. hermannii, while the vegetarian group's microbiota contained only Klebsiella pneumoniae. These results suggest that the gut microbiota of those who consume many vegetables, with a high abundance of P. copri and a low variety of potential pathogens, could be a way to maintain good health.
Both polyphenols and dietary fiber play a crucial role in protecting human health and can produce butyrate through fermentation by the gut microbiota. The interaction of polyphenols with dietary fiber affects their bioaccessibility in the upper and lower digestive tracts. Dietary fiber, polyphenols, their conjugates, and their metabolites modulate the population and diversity of the gut microbiome. Consuming dietary fibers rich in polyphenols, such as pomegranate, cranberry, berries, and tea, improves gut health.
It is important to note that in recent years, our understanding of the mechanisms involved has deepened, highlighting the crucial role of the gut microbiota in this process through the production of short-chain fatty acids (SCFAs) and other functional metabolites. The decline in dietary fiber intake over centuries has fostered a gut microbiota detrimental to human health, leading to a global epidemic of diabetes, cancer, and other non-communicable diseases. The gut microbiota's response to increased dietary fiber availability can vary depending on the type, level, and duration of intake, demonstrating specific cutoff thresholds for each type of dietary fiber.
Dietary fiber can be classified into three types based on the physiological properties of its resistant carbohydrate polymerization with 3 to 9 monomeric units (MU): 1) non-starch polysaccharides (NSPs) (MU ≥ 10); 2) resistant starches (RS) (MU ≥ 10); and 3) resistant/non-digestible oligosaccharides (ROSs) (MU: 3–9). NSPs primarily include cellulose, hemicellulose, pectins, inulin, and various hydrocolloids. Inulin is a fructan containing 2 to 60 fructose units. When MU < 10, inulin is also recognized as a fructooligosaccharide (FOS), a well-documented prebiotic. Reactive sugars (RS) can be further classified into RS 1 to RS 5, which can be derived from ground grains and seeds (RS 1), raw potatoes, corn, and green plantains (RS 2), cooked and cooled potatoes and corn flakes (RS 3), bakery products (RS 4), and fried rice chips (RS 5). Reactive oxygen species (ROS) consist of 3–9 MU, many of which are named after polymerized monosaccharides, such as galactooligosaccharides (GOS), xylooligosaccharides (XOS), and galactosides. Dietary fibers escape digestion in the upper gastrointestinal tract and are fermented by bacteria in the colon. The degree of polymerization, particle size, solubility, viscosity, and other characteristics of dietary fiber can influence fiber fermentability and bacterial specificity. Fibers with a low degree of polymerization can be broken down into small molecules in the intestine with rapid fermentation; Small particles are more likely to be exposed to microbial enzymes; whereas soluble and viscous fibers, with a high capacity for water retention and stool formation, and therefore limited exposure to microbes, are resistant to fermentation. The various interactions between monomer chains and enzymes influence bacterial growth, resulting in fiber-specific gut microbiota.
Dietary fibers escape digestion in the upper gastrointestinal tract and are fermented by bacteria in the colon. The degree of polymerization, particle size, solubility, viscosity, and other characteristics of dietary fiber can influence fiber fermentability and bacterial specificity. Fibers with a low degree of polymerization can be broken down into small molecules in the intestine with rapid fermentation; small particles are more likely to be exposed to microbial enzymes. In contrast, soluble and viscous fibers, with a high water-holding capacity and fecal-forming capacity, and therefore limited exposure to microbes, are resistant to fermentation. The various interactions between monomer chains and enzymes influence bacterial growth, resulting in fiber-specific gut microbiota.
Inulin-like fructans (ITFs) were hydrolyzed extracellularly by Bifidobacteria in the human colon, releasing monosaccharides and/or oligosaccharides accessible to butyrate producers, the secondary degraders. During the utilization and metabolism of polysaccharides by bacteria, multiple metabolites were generated, including gases (e.g., H₂, CH₄, CO₂), lactate, succinate, and short-chain fatty acids (SCFAs).
The most abundant SCFAs are acetate, propionate, and butyrate. SCFAs can be used by intestinal mucosal cells as energy sources, with butyrate being the preferred energy substrate for colonocytes. Furthermore, absorbed SCFAs are transferred to the circulation via the hepatic portal vein to act as signaling molecules and can activate complex downstream molecular pathways in the liver, brain, lungs, pancreas, bones, adipose tissue, and other organs. Short-chain fatty acids (SCFAs) play crucial regulatory roles in host metabolic homeostasis, immunological processes, maintenance of intestinal barriers, neurobiology, skeletal functions, and the suppression of inflammation and carcinogenesis, and have been shown to be beneficial to human health. SCFAs have multiple beneficial effects on the epithelial, immune, nervous, and vascular systems. A decrease in the production of these metabolites has been linked to several diseases, including intestinal inflammation, diabetes, liver cirrhosis, and atherosclerosis. SCFAs play a crucial role in improving gastrointestinal health by acting locally in the gut. These metabolites help preserve the integrity of the intestinal barrier, which aids in nutrient absorption and blocks pathogens and harmful substances. Hypotheses about the possible mechanisms of fiber's anti-inflammatory effects include a direct impact on immune cells (e.g., for pectin), fermentation to short-chain pleiotropic fatty acids (for fermentable fiber only), modulation of the gut microbiome towards greater diversity, changes in bile acid metabolism, differential release of intestinal hormones (such as glucose-dependent insulinotropic peptide [GIP]), and improved insulin resistance.
Furthermore, the contribution of phytate-mediated antioxidant and immunomodulatory mechanisms should be considered. The gut microbiota plays a vital role in the synthesis of neurotransmitters such as serotonin, dopamine, and norepinephrine, as well as metabolites like short-chain fatty acids (SCFAs). Alterations in the composition of the microbiota are called dysbiosis, which has been associated with systemic inflammation and chronic stress.
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So sad most gastroenterologists don’t know this .
Or much of anything, in my experience, beyond the routine "If this symptom, do this".
Clown world 🤡
Nice to share comments with you again, Brandon is not your bro.
Yes, 🤨🤨❤️❤️
The microbiomes of soil, plants, animals, and humans are interconnected. Soil microorganisms influence plant microbiomes and, through food and contact with nature, can affect humans.
Numerous studies show that herbicides, fungicides, and insecticides can reduce soil microbial diversity or alter its composition, affecting important ecological functions. Exposure to pesticides can also directly alter the gut microbiome.
https://www.mdpi.com/2076-3298/12/12/492?utm_source=chatgpt.com (2025)
A systematic review published in 2026 concluded that pesticide exposure is associated with changes in the gut microbiota (dysbiosis) in both animals and humans. The findings indicate that prenatal pesticide exposure is linked to adverse fetal developmental outcomes. Furthermore, pesticide exposure affects metabolic, immune, and nervous system function due to alterations in the composition of the gut microbiota and membrane permeability.
https://pubmed.ncbi.nlm.nih.gov/41874112/ (2026)
The "microbial biodiversity" theory proposes that the loss of diversity in ecosystems decreases human exposure to beneficial environmental microorganisms, which could influence immunological and inflammatory diseases.
Current evidence supports a plausible chain of influence: This is the chain of events: Pesticides alter the soil microbiome, leading to changes in plants and food, and consequently, changes in human microbial exposure, influencing the human microbiome and health.
https://www.nature.com/articles/s41579-022-00779-w?utm_source=chatgpt.com (2022)
https://www.ncbi.nlm.nih.gov/books/NBK609362/?utm_source=chatgpt.com (2024)
https://pubmed.ncbi.nlm.nih.gov/41874112/ (2026)
Dear Guillermou, It is nice to see you back in the saddle here with backed up info since Mercola stopped allowing comments. You always had helpful research for those who wanted more in-depth info. 🙏
👍😊❤️🌹
Thanks for your honest comments.
I agree completely.
Good thought.. I agree.
Cool. Thanks.
I presume you are post postatectomy. I would continue the doxycycline.
Good question. I am not sure. And not sure the role of bifidiobacteria probiotics.
Thanks..
Thank you Dr. Marik, for presenting Sabine Hazan's work. All of the ancient methods of supporting human health seem to remain in force.
I also appreciated Dr. Kory's story of the take-downs of IV vitamin-C for sepsis-survival, and your provision of life-saving patient care in-hospital during COVID. He describes your ambush by the lockstep hospital-admin overriding your prescriptive orders. ;-(
https://pierrekorymedicalmusings.com/p/professor-paul-marik-identified-the
Professor Paul Marik Identified The Cure for Sepsis. I Watched Medicine Bury It.
Becoming Paul Marik's close colleague was the most inspiring turn my career ever took, until the same partnership got us both excommunicated from academic medicine and ended his career at the bedside.
Pierre Kory, MD, MPA
Jul 30, 2026
https://pierrekorymedicalmusings.com/p/professor-paul-marik-identified-the?utm_source=post-email-title&publication_id=645524&post_id=209013297&utm_campaign=email-post-title&isFreemail=true&r=ue9x3&triedRedirect=true&utm_medium=email