The traditional belief that fiber is the exclusive source of short-chain fatty acids (SCFAs), particularly butyrate, has been challenged by recent research. While the colon has long been regarded as the primary site for SCFA production, it has become apparent that substrates other than fiber can fuel colonic cells. The findings referenced in the study suggest that beta-hydroxybutyrate, acetoacetate, and even long-chain fatty acids can be utilized to fuel colonic cells, indicating that SCFAs need not be exclusively derived from fiber.
Moreover, it has been observed that both long- and short-chain fatty acids are oxidized in the colon, with an inverse relationship suggesting a preference for short-chain fatty acids, particularly butyrate. This preference shifts based on the abundance of SCFAs, highlighting the dynamic nature of colonic cell metabolism.
A notable revelation from the study is the role of bile, which contains medium and long-chain fatty acids in the form of acyl carnitines. During fasting, these acyl carnitines can be utilized by epithelial cells in the colon, leading to increased circulation. This challenges the prior belief that energy could only be derived from the lumen side of the colon.
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The adverse impact of dietary patterns on gut health has been a subject of significant academic interest, particularly in discerning the repercussions of specific macronutrient combinations. Contrary to conventional understanding, the most detrimental diet combination appears to arise from high sugar and high seed oil consumption, rather than solely from low fiber intake. This insight challenges the prevailing beliefs regarding the primary factors influencing gut health and underscores the multifaceted nature of dietary influences on the gastrointestinal ecosystem.
Furthermore, the emergence of a ketogenic diet, characterized by low sugar, moderated protein, and fat, has garnered attention for its potential to enhance gut health even in the absence of fiber. Notably, an exclusive clinical study in humans revealed that patients following a zero-fiber ketogenic diet exhibited the most favorable health outcomes. This discovery not only prompts a reevaluation of the established associations between fiber intake and gut health but also underscores the potential therapeutic benefits of specific dietary regimens in clinical settings.
In the broader context of gut function, the increased prevalence of the Bilophila bacteria in a carnivore diet has garnered attention due to its role in degrading trimethylamine (TMA) to dimethylamine (DMA), thereby impeding the conversion of TMA to trimethylamine-N-oxide (TMAO) at elevated levels. This elucidation sheds light on the intricate interplay between dietary patterns and gut microbiota composition, emphasizing the need for a comprehensive understanding of microbial dynamics in the digestive milieu.
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The impact of diet on gut microbiome composition and function is also substantial. For instance, a ketogenic diet, which is low in sugar and moderate in protein and fat, has shown improvements in gut health even in the absence of fiber. The study noted that patients on a zero-fiber diet displayed the best health outcomes.
Furthermore, the interplay between diet and gut microbiome diversity is evident, with factors such as sun exposure and certain food types influencing alpha diversity. Notably, the diversity of gut microbes was found to be similar in urban Italians following a Paleolithic diet to non-western populations, including the Hadza, contrasting with those adhering to a Mediterranean diet. This supports the notion that the composition and function of the gut microbiome are heavily influenced by dietary choices.
“Human gut bacteria in the genus Bilophila have genomic signatures for genetic code expansion that could enable them to metabolize both TMA and its precursors without production of TMAO. We uncovered evidence that the Bilophila demethylation pathway is actively transcribed in gut microbiomes and that animal-based diets cause Bilophila to rapidly increase in abundance" (Schnorr et al., 2014)
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Bilophila is a bacteria that in a carnivore diet increases. It's been shown to degrade TMA (TMA converts to TMAO) to DMA so conversion to TMAO in high levels does not happen. (Kivenson, V. Giovannoni, S.J,. 2020)
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Recent findings indicate that the detrimental impact of dietary habits on gut health goes beyond the conventional focus on low fiber consumption. High sugar and high seed oil consumption have emerged as significant contributors to compromised gut health. Conversely, a ketogenic diet, characterized by low sugar, moderate protein, and fat content, has been associated with improvements in gut health even in the absence of fiber, as evidenced by the most promising health outcomes observed in patients on a zero-fiber regimen in the sole clinical study conducted in humans.
Further observations on gut function have revealed the influence of dietary patterns on microbial dynamics.
As mentioned, the proliferation of Bilophila, a bacterium linked to carnivorous diets, has been associated with the degradation of trimethylamine (TMA) to dimethylamine (DMA), thus mitigating the conversion to the proatherogenic compound trimethylamine-N-oxide (TMAO). Moreover, animal models have demonstrated that antibiotic usage and induced inflammation can lead to escalated levels of enterobacter aca, encompassing well-known pathogens such as E. coli, Klebsiella, and Salmonella, alongside other pathogens. Notably, the production of butyrate, especially prevalent in carnivorous species, is attributed to corprocascus, which exhibits a high tolerance to bile, among other microorganisms.
ALPHA DIVERSITY IN THE DARK AGES STILL
In an exploratory assessment of gut microbial composition, metagenomic sequencing, also known as shotgun sequencing, has revealed the presence of a substantial proportion of unidentified microbes, termed "dark matter," which some researchers speculate might include viral entities. This contrasts with the less detailed 16S sequencing method, which entails a broader analysis of stool samples, encompassing viruses, fungi, microbes, and bacteria.
When you do metagenomic sequencing (also called shotgun sequencing) is where researchers take a gut DNA sample, grind it all up and sequence it. Then compare it to a database of known microbes. Between 50% upto 70% of the results are unknown. A so-called 'dark matter' in the gut that some researchers believe may even be viruses.
16s sequencing is much less nuanced
Essentially this is taking poop and studying it. So you'll get everything, viruses, fungi, microbes, bacteria etc.
Moreover, the administration of a ketogenic diet or ketone esters has been linked to elevated levels of beta-hydroxybutyrate in the gut lumen and colon tissues. Additionally, it has demonstrated a potential protective role in th17 cells, which are frequently implicated in autoimmune disorders, while also contributing to the preservation of the gut mucus layer, even in the absence of fermentable carbohydrates. These discernments underline the multifaceted interplay between dietary patterns, microbial ecology, and gut health.
The administration of a ketogenic diet or ketone esters has been linked to elevated levels of beta-hydroxybutyrate in the gut lumen and colon tissues. Additionally, it has demonstrated a potential protective role in th17 cells, which are frequently implicated in autoimmune disorders, while also contributing to the preservation of the gut mucus layer, even in the absence of fermentable carbohydrates. These discernments underline the multifaceted interplay between dietary patterns, microbial ecology, and gut health.
In summary, the intricate relationship between diet, gut microbiome, and gut health has unveiled a more nuanced understanding of colonic cell metabolism and microbial function. This dynamic interplay necessitates a comprehensive approach to maintaining gut health, considering not only the sources of SCFAs but also broader dietary influences on gut microbiome composition and function.
High insulin leads to water retention which in turn results in dysregulation of sodium and uric acid levels.
This high water retention will mean endothelial cells will 'bulge' and decrease the internal circumference of the arteries. This has a deleterious impact on the gut lining.
Definition of a healthy microbiome.
There is no one ‘healthy’ microbiome. If you're healthy then the microbiome you have is probably a good one!
Is the name given to how diverse the gut microbes are. Having higher diversity is thought to indicate better health but eating a diverse range of foods does not necessarily lead to better alpha diversity. In studies even diets of meat, organs and honey can lead to a near 100% top rating in alpha diversity.
What does increase alpha diversity?
This study shows urban Italians on a Paleolithic diet had gut diversity similar to three non-western populations, including the Hadza, whereas the Italian people on a 'mediterranean' diet did not have anywhere near the diversity.
This is a cross sectional study and keep in mind those choosing a Paleolithic diet might exhibit healthy user bias. Meaning that someone deliberately choosing to eat healthier will also improve other areas of their life to achieve their goals, so you can't 100% attribute improvements to diet alone. All participants were considered 'healthy' with daily contact with nature. The Paleolithic group did not eat bread, grains or processed foods.
Even sunlight exposure increases alpha and beta diversity
Skin Exposure to Narrow Band Ultraviolet (UVB) Light Modulates the Human Intestinal Microbiome
Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context
In an interventional study increasing fiber intake from 20% to 40% of calories saw no change in microbial status.
Interestingly eating fermentable foods did see a slight change in microbiome species. So drinking pickle juice may be beneficial for some people. Remember those in the study were eating a standard western diet. Fermentation can increase histamines so proceed with caution.
In the study yogurt seemed beneficial in those that can tolerate whey and casein. Others seemed to be tolerating fermented vegetables in brine. Only those with good alpha diversity did well though. For others autoimmune issues increased, which reflects real world data where patients increase these food items but feel worse.