How ApoE Genes Impact Your Gut Health and Cognition

February 21, 2022 6 min read

How ApoE Genes Impact Your Gut Health and Cognition - Layer Origin Nutrition

Despite receiving a bad rap for much of the 1990s and early 2000s, lipids like dietary fats and cholesterol are critical nutrients without which biological life would be impossible. Cholesterol is the precursor to all steroid hormones and bile acids and serves as an essential component of cellular membranes. Meanwhile, fats are converted into bioactive signaling molecules, assembled into membranes, and serve as a direct primary fuel source for all the organs in the body outside of the brain. Moreover, the cellular breakdown of long chain fatty acids is the primary source of metabolic heat in all warm-blooded animals and is what allows us to maintain a stable body temperature.


Introduction to Lipoproteins

Following their consumption, dietary fats and cholesterol undergo transport into the circulation by particles known as lipoproteins. Although they themselves are composed primarily of cholesterol and fat, lipoproteins are responsible for shuttling cholesterol, phospholipids (a special kind of fat that is used to construct membranes), triglycerides (the storage form of fatty acids), and fat-soluble vitamins between organs. Lipoproteins are also adorned with special proteins known as apoproteins, with each lipoprotein having a unique apoprotein signature.

There are four primary lipoproteins: chylomicrons, very-low-density lipoproteins (VLDLs), low-density lipoproteins (LDLs), and high-density lipoproteins (HDLs).



Chylomicrons are the largest of the four particles and are constructed by the small intestine. They are responsible for transporting dietary fat and cholesterol directly from the small intestine to the circulation. The primary function of chylomicrons is to deliver fats to organs to support tissue energy production in the post-prandial (fed) state. With a half-life of 15 to 20 minutes, chylomicrons are rapidly cleared from the blood by the liver. A half-life is the amount of time it takes for the number of particles in the bloodstream to be reduced by half.



Following their clearance from the circulation, any triglycerides and cholesterol that remain inside the chylomicrons are repackaged into VLDLs by the liver and excreted into the circulation. The primary function of VLDLs is to deliver fats to organs to support energy production in the post-absorptive (fasted) state. VLDLs have a half-life between 4 and 6 hours.



After this time, the VLDLs will return to the liver and be repackaged once more as LDLs which are excreted into the blood where they will remain for about 3 days. LDLs are the most cholesterol-rich of the lipoprotein particles, and the lab measurement for LDL cholesterol, LDL(c), is frequently used by medical professionals to estimate the number of LDL particles in the blood.



Unlike the other lipoproteins which transport fat and cholesterol to the tissues of the body, HDLs are primarily responsible for transporting cholesterol away from the tissues of the body and back to the liver for processing and excretion. This so called “reverse cholesterol transport” is believed to be cardioprotective by slowing down the development of atherosclerosis (hardening of the arteries). The half-life of HDLs is about 5 days.


The Role of Apolipoprotein E (APOE) in Lipid Transport

ApoE is one of over a dozen apoproteins and can be found on chylomicrons, VLDLs, and some HDLs. It promotes the clearance of chylomicrons and VLDLs from the circulation by allowing them to bind tightly to lipoprotein receptors on the surface of liver cells. This is, in part, why chylomicrons and VLDLs have such short half-lives compared to LDLs. In the brain, which can’t access circulating lipoproteins due to the presence of the blood brain barrier, ApoE directly serves as the primary lipid transporter, shuttling cholesterol and phospholipids between cells.


An Overview of the ApoE Variants

Genetically, there are three variants of ApoE within the human population: ApoE2, ApoE3, and ApoE4. Each variant, or isoform, differs by only one or two amino acids (the building blocks of proteins), however the structural and functional consequences of these differences is significant. ApoE3 is the dominant isoform of ApoE and is considered to be the “normal” form of this protein. Around 77% of the population possesses one or two copies of E3.

ApoE4 is the second-most dominant isoform with about 15% of the population possessing one or two copies. It preferentially binds to VLDLs in the circulation, whereas E2 and E3 bind preferentially to HDLs. ApoE4 binds even more tightly to certain lipoprotein receptors than does E3. Individuals with two copies of ApoE4 have a significantly higher risk of developing cognitive decline, neuroinflammation, and late-onset Alzheimer’s disease (AD).  In fact, E4 is the strongest genetic risk factor for AD currently identified. Individuals with one copy (i.e. carriers) of E4 also have a higher risk of developing AD, but to a lesser extent than those with two copies. The precise role of ApoE4 in AD progression has not yet been well-characterized.

ApoE2 is the least common isoform, with about 8% of the population possessing one or two copies. E2 is only capable of binding to lipoprotein receptors in the liver at 2% the efficacy of the E3 isoform. As a result, E2 is no longer able to effectively facilitate the clearance of chylomicrons and VLDLs from the circulation. The result, for individuals with two copies of E2, is a condition known as type III hyperlipoproteinemia, which presents as extremely elevated levels of chylomicrons and VLDLs. As these lipoproteins remain in the circulation, they begin concentrating cholesterol and contribute to the development of atherosclerosis and accelerated cardiovascular disease. On the flipside, ApoE2 confers a protective benefit against AD.


ApoE and Gut Microbiome

Interestingly, the ApoE isoforms an individual possesses are linked to specific shifts in the composition of the gut microbiome. These shifts are believed to contribute, at least partially, to the deleterious physiological effects associated with ApoE4. Higher levels of the bacteria Prevotellaceae have been observed in E3/E3 individuals relative to other genotypes, and higher levels of Ruminococcaceae have been observed in E2/E3 individuals relative to ApoE4 carriers. In alignment with these findings, clinical reports note a depletion of these two bacterial families in the microbiomes of individuals with Parkinson’s disease and AD.

  • Reductions in Prevotellaceae negatively impact mucin synthesis (the major protein present in the gut mucosa) and results in increased gut permeability, aka “leaky gut”. This leakiness allows bacterial endotoxin to enter the bloodstream where it triggers off systemic inflammation in the body and brain.
  • On the other hand, Ruminococcaceaeare major producers of short chain fatty acids (SCFAs), like butyrate, in the colon. SCFAs exert anti-inflammatory effects in the gut, modulate immune cells to promote anti-inflammatory activities, and serve as key fuel sources for colon cells.


Gut Optimization Strategies for ApoE4 Individuals

In light of this information, it is advisable for ApoE4 carriers to implement dietary and/or supplementation strategies to support SCFA production and reduce gut permeability. Because Bifidobacteria produce key metabolites that feed SCFA-producing bacteria in the gut, bolstering their populations will allow individuals to optimize intestinal SCFA production. Bifidobacteria thrive on molecules known as human milk oligosaccharides such as 2’-fucosyllactose (2’FL), dark colored fruits like berries and pomegranate, as well as resistant starches like those found in semi-green bananas, raw oats, and beans. To reduce gut permeability, eating red apple skins or supplementing with an apple peel powder is prudent. A special pigment molecule in red apple skins feeds Akkermansia muciniphila, a species of bacteria that lives in the mucus layer of the gut and enhances the integrity of tight junctions (i.e., the connections between intestinal cells). Together, these nutritional strategies have the power to directly modulate the microbiome and help to mitigate the potential health consequences of ApoE4.


Written by: Dr. Alexis Cowan, a Princeton-trained PhD specializing in the metabolic physiology of nutritional and exercise interventions. Follow Dr. Cowan on Instagram: @dralexisjazmyn



Feingold KR. Introduction to Lipids and Lipoproteins. [Updated 2021 Jan 19]. In: Feingold KR, Anawalt B, Boyce A, et al., editors. Endotext [Internet]. South Dartmouth (MA):, Inc.; 2000-.

Jomard A and Osto E (2020) High Density Lipoproteins: Metabolism, Function, and Therapeutic Potential. Front. Cardiovasc. Med. 7:39. doi: 10.3389/fcvm.2020.00039

Huang Y, Mahley RW. Apolipoprotein E: structure and function in lipid metabolism, neurobiology, and Alzheimer's diseases. Neurobiol Dis. 2014 Dec;72 Pt A:3-12. doi: 10.1016/j.nbd.2014.08.025. Epub 2014 Aug 27. PMID: 25173806; PMCID: PMC4253862.

Liao, Fan et al. “Apolipoprotein E metabolism and functions in brain and its role in Alzheimer's disease.” Current opinion in lipidology vol. 28,1 (2017): 60-67. doi:10.1097/MOL.0000000000000383

Tran TTT, Corsini S, Kellingray L, Hegarty C, Le Gall G, Narbad A, Müller M, Tejera N, O'Toole PW, Minihane AM, Vauzour D. APOE genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer's disease pathophysiology. FASEB J. 2019 Jul;33(7):8221-8231. doi: 10.1096/fj.201900071R. Epub 2019 Apr 8. PMID: 30958695; PMCID: PMC6593891.

2 Responses

Layer Origin Customer Care
Layer Origin Customer Care

May 08, 2022

Reply to Lorie,

Hi Lorie, There are researches studying the gut microbiome composition in Parkinson’s’ patients, but mechanism illustrated on the bacteria part is not very conclusive. We wish we have a good answer for you, but we do not have it for now.


March 04, 2022

I’m quite interested in the prevention and reversal of cognitive decline – good article. Dr Cowan notes lower levels of Prevotellaceae and Ruminococcaceae in both ApoE4 individuals and those with Parkinsons and AD, but doesn’t explicitly make any connection to the species which your products directly benefit. Is there any known connection between cognitive decline and/or ApoE4 status and the species Bifidobacteria and Akkermansia muciniphila, which are increased with HMO and apple peels?

Leave a comment


The Human Milk Oligosaccharide - 2'-Fucosyllactose (2'-FL) Prevents Intestinal Inflammation Cover Image
The Human Milk Oligosaccharide - 2'-Fucosyllactose (2'-FL) Prevents Intestinal Inflammation, Study Finds

July 12, 2024 6 min read

Human milk oligosaccharides (HMOs), particularly the glycan known as 2’-Fucosyllactose (2’-FL), have been a cornerstone in neonatal nutrition, offering the first sweet taste and vital energy while establishing a thriving gut microbiome. Recent studies have expanded the understanding of these substances, with research showing 2’-FL's pivotal role in not only fostering beneficial gut bacteria but also in potentially mitigating adult conditions such as colitis. The Schalich et al. (2024) study further explores this by investigating 2’-FL's ability to modulate gut microbial metabolism, suggesting a promising future for HMOs in adult disease prevention and therapy, particularly for inflammatory bowel diseases like colitis.
Read More
How Akkermansia Survives and Thrives in the Gut?
How Akkermansia Survives and Thrives in the Gut?

June 27, 2024 6 min read

Discover some of the unique mechanisms Akkermansia employs to survive in the human gut and the genetics behind how this fascinating bacterium can maintain cholesterol homeostasis.
Read More
Study Finds Short-Term Cranberry Supplementation Has A Strong Bifidogenic Effect In The Human Gut - Blog Layer Origin
Study Finds Short-Term Cranberry Supplementation Has A Strong Bifidogenic Effect In The Human Gut

June 21, 2024 7 min read

Understand how cranberry extracts could improve the composition of the gut microbiome, increasing the abundance and activities of friendly bacteria and potentially offering a solution to combat the effects of the Western diet.
Read More