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This post will explain how the gut microbiota can affect your weight.


What Are Short Chain Fatty Acids (SCFA)?

Short-chain fatty acids (SCFAs; acetic, propionic and butyric acid) are formed during bacterial fermentation of carbohydrates in the colon.

SCFAs cause low intestinal pH from the ileum (end of the small intestine) to the cecum (beginning of large intestine), which prevent the overgrowth of bad bacteria (like Enterobacteriaceae and Clostridia) (R).

SCFAs help fix ‘leaky gut‘, strengthening the intestinal wall by increasing the secretion of mucin-2 (MUC-2), which then prevents LPS from crossing the barrier (R).

Composition of SCFAs In Our Gut

Out of the total SCFAs present in the colon, 90%-95% are acetate, propionate, and butyrate in healthy people.

  • Acetate=60%,
  • Propionate=25%,
  • Butyrate=15%,

Most of the SCFAs are absorbed in the colon, being exchanged with bicarbonate (R).

SCFAs are acidic, while bicarbonate is alkaline.

Short Chain Fatty Acids (SCFA) and Obesity


There is some conflicting information on SCFAs and weight.

On the one hand, they increase caloric utilization, which means you absorb more calories. On the other hand, they have some anti-obesity effects.

Overall, however, butyrate is antiobesity, propionate has mixed effects, and acetate seems to promote weight gain (R).

The fecal concentration of SCFAs is 20% higher in obese individuals than their lean counterparts. But this may reflect a compensatory protective mechanism against obesity, in which a greater amount is eliminated from the stool (R).

This would prevent the increased accumulation of SCFA in the intestines, which may cause weight gain (mainly from acetate) (R).

SCFAs, like butyrate and propionate, increase the formation of the gut hormones glucagon-like peptide-1 (GLP-1) and polypeptide YY (PYY). It reduces food intake by decreasing appetite (R).

PYY increases gut flow (R).


Butyrate reduces food intake and causes weight loss.

Butyrate has so many benefits.  It combats autoimmunity, cancer, and psychological disorders.  It also changes the epigenetics in our brain (R).

Butyrate is mainly produced by Firmicutes (R).

Butyrate is mostly not absorbed because it is primarily used by colon cells, where is serves as a major source of energy for them (R).

Butyrate production is determined by the level of bacteria that produce butyrate, and the pH of the large intestine (R).

Butyrate-producing bacteria seem to thrive in a more acidic environment (lower pH), whereas acetate and propionate bacteria seem to thrive in a more alkaline environment (higher pH) (R).

In the mitochondria of colon cells, 70% to 90% of butyrate is oxidized into acetyl-CoA, which is subsequently processed through the tricarboxylic acid cycle to generate a large quantity of ATP (R).

Butyrate (in summary):

  • Is a major energy source for colon cells
  • Has anti-cancer effects
  • Increases mitochondrial activity
  • Prevents toxins from crossing gut barrier
  • Prevents activation of intestinal glucose production
  • Improves insulin sensitivity
  • Increases energy expenditure by improving mitochondrial function, reducing obesity
  • Increases intestinal barrier function – an anti-inflammatory potential
  • Protects against diet-induced obesity without necessarily causing a reduction in caloric intake (mediated through gut hormones).
  • Increases the synthesis of leptin (which reduces appetite)


Propionate also reaches the liver via portal circulation and produces glucose (in the liver) (R).

Propionate possesses both pro- and anti- obesity effects, but overall it seems to be protective against obesity.

Acetate and propionate are the main products of Bacteroidetes (R).

Proprionate (in summary):

  • Increases the synthesis of leptin (which reduces appetite)
  • Protects against diet-induced obesity without causing a reduction in caloric intake (mediated through gut hormones).
  • Decreases cholesterol synthesis (by inhibiting acetyl-CoA synthetase, the enzyme that converts acetate to acetyl-CoA)
  • Is a precursor for glucose generation by the liver, which decreases the synthesis of cholesterol
  • Inhibits resistin in human fat tissue


Of all the three SCFAs, acetate seems to cause the most weight gain.  However, it also has some properties that protect against obesity.

Acetate causes obesity outside of the brain. But it has been shown that it can also control weight gain in the hypothalamus (arcuate nucleus) by increasing GABA (R).

A substantial part of acetate is readily absorbed and reaches liver (via portal circulation), where it’s used to create cholesterol (RR2).

Human studies have shown that when lactulose (metabolized by microbiota to produce high amounts of acetate) was administered to the diets of six volunteers for two weeks, there was a significant increase in both total and LDL cholesterol, ApoB and blood levels of acetate (R).

Acetate and propionate are the main products of Bacteroidetes (R).

Acetate (in summary):

  • Acts as a fuel for fat creation and cholesterol synthesis in the liver and other tissues
  • Protects against diet-induced obesity without causing a reduction in caloric intake

Bacterial Species and Obesity


Obese animals and people have a lower microbiome diversity, a lower percentage of Bacteroides, Verrucomicrobia, Faecalibacterium prausnitzii and a higher percentage of Firmicutes and Actinobacteria.  Some of these results were not reproduced (R).

Microbiota in normal gut Microbiota in obesity (R).
Firmicutes phylum Increase in Firmicutes phylum
Bacteriodetes phylum Reduced abundance of Bacteroidetes
Actinobacteria phylum A higher level of Actinobacteria phylum
Verrucomicrobia phylum Lower proportion of Verrucomicrobia
Faecalibacterium prausnitzii species Reduced abundance of Faecalibacterium prausnitzii species

My Ubiome Results:

As a whole, I was pretty happy with the results. According to Ubiome, my gut sample is more diverse than 74 percent of the population, which is accordance with being fit. But there’s always room for improvement.


I have 1.29X higher Firmicutes compared to all of their samples.

Firmicutes help us to digest fat that our bodies need for energy. An oversupply of Firmicutes has been linked to a higher risk of obesity, as a result of increased calorie absorption.

The increased population of Firmicutes has been found to raise the number of lipid droplets, thereby proportionately intensifying fatty acid absorption (R).

The first settlers of Europe needed to be able to better digest fat so they would have enough energy to survive brutal winters.


I have 34% fewer Bacteroides.

Bacteroidetes are thought to help protect against obesity because they do not digest fat well.


I have 1.17X higher Actinobacteria.

Actinobacteria are important to a healthy microbiome.

People with psoriasis have less of these bugs but people with ulcerative colitis tend to have more. 


I have 91% fewer proteobacteria than other people.

People with inflammatory bowel disease seem to have more Proteobacteria and fewer varieties of other bacteria.

Other Bacterial Species and Obesity

The following bacteria have less evidence in causing obesity:

Methane-producing Archaea have been found to be present in greater abundance in obese mice and humans compared with lean subjects (R).

Cocolonization of M. smithii with B. thetaiotaomicron led to the fermentation of dietary fructans to acetate, resulting in a significant increase in fat creation (R).

M. smithii is found in 70% of human beings. It generates methane. It has been found to enhance the fermentation of polysaccharides and other carbohydrates by removing hydrogen atoms, leading to greater production of SCFAs and hence, their increased absorption. These SCFAs function as an extra source of energy which contributes towards weight gain and subsequent obesity (R).

The numbers of hydrogen-producing Prevotellaceae (a Bacteroidetes) and Methanobacteriales (Archaea, which are hydrogen-oxidizing methanogens), were at a higher level in obese individuals compared with lean subjects and with those after gastric bypass. The investigators hypothesized that hydrogen was reduced, which allowed greater production of SCFAs.  This leads to more energy that is absorbed across the intestines (was not reproduced) (R).

Prevotellaceae is a source of LPS (R), which causes inflammation.

C. ramosum in the mucosa of the small intestine of mice increase body fat as a result of an increase in intestinal absorption of glucose and lipids (R).

The intestines of obese humans and mice have been found to contain (R):

  • Low relative proportions of Bacteroides vulgatus
  • High Erysipelotrichi (Firmicutes)
  • High Clostridium ramosum (part of Erysipelotrichi)
  • High Lactobacillus spp. – was positively correlated with hs-CRP
  • High Lactobacillus reuteri
  • High Staphylococcus species (linked with increased caloric intake in children) (R)
  • Oscillibacter and Clostridium clusters XIVa and IV (found in obese-prone mice and were totally absent from their obese-resistant counterparts).
  • High Ruminococcus (most of its species fall under several Clostridium clusters, including Clostridium clusters IV and XIVa).
  • Clostridium leptum (cluster IV) has been found to be associated with both obesity and weight loss.
  • F. prausnitzii – linked with alteration in the inflammatory state and diabetes (R). The presence of F. prausnitzii species is directly associated with the reduction in low-grade inflammation state in obesity and diabetes (independent of calorie intake) (R, R2).

How to Increase Butyrate

I use all 3 of these sources for butyrate.

You’ll need the Hi-Maize for butyrate in your large intestine, and the butyrate pills for your stomach and small intestine.

The pills provide calcium and magnesium.

I use HMB mainly for its synergistic effects with Resveratrol in activating SIRT1.

  • Hi-maize Resistant Starch
  • Butyrate (IHERB)

Health Tools I Wish I Had When I Was Sick

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  • BrainGauge – a device that detects subtle brain changes and allows you to test what’s working for you
  • SelfHacked VIP – an area where you can ask me (Joe) questions about health topics

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  • Nejc

    Fiberfin but it is expensive because it is Norwegian.

  • Steve

    Thank you for the article and for your efforts but some points you make in this article have confused me and I hope you can help me figure it out.

    You write that a greater amount of firmicutes compared to bacteroidetes (according to Ubiome) is correlated with obesity (or more weight gain) and that greater amounts of bacteroidetes correlate to being leaner.

    In the same article you write that butyrate is associated with less weight gain and is created by bacteria in the frmicutes phylum and that acetate is associated with more weight gain and is created by bacteria in the bacteroidetes phylum.

    There seems to be a contradiction here.

    Could you clarify please?

    Thank you

  • pamojja

    Anyone in the known of a hi maize retailer in Europe?


  • Relentless

    The hi maize on iherb has been discontinued for 3-4 months now, so its not sold there anymore.. 🙁

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