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Race/Ethnicity and the Microbiome

January 7, 2018 4:19 pm / Leave a comment

1800 words

The microbiome is the number and types of different microorganisms and viruses in the human body. Racial differences are seen everywhere, most notably in the phenotype and morphology. Though, of course, there are unseen racial differences that then effect bodily processes of different races and ethnic groups. The microbiome is one such difference, which is highly heritable (Goodrich et al, 2014; Beaumont et al, 2016; Hall, Tolonen, and Xavier, 2017) (though they use the highly flawed twin method, so heritabilities are most likely substantially lower). They also show that certain genetic variants predispose individuals to microbial dysbiosis. However, diet, antibiotics and birth mode can also influence the diversity of microbiota in your biome (Conlon and Bird, 2015; Bokulich et al, 2017; Singh et al, 2017) and so while the heritability of the microbiome is important (which is probably inflated due to the twin method), diet can and does change the diversity of the biome.

It used to be thought that our bodies contained 90 percent bacteria and only 10 percent human cells (Collen, 2014), however that has been recently debunked and the ratio is 1.3 to 1, human to microbe (Sender, Fuchs, and Milo, 2016). (Collen’s book is still an outstanding introduction to this subject despite the title of her book being incorrect.) Though the 10:1 microbe/human cell dogma is debunked, in no way does that lessen the importance of the microbiome regarding health, disease and longevity.

Lloyd-Price, Abu-Ali, and Huttenhower (2016) review definitions for the ‘healthy human microbiome’ writing “several population-scale studies have documented the ranges and diversity of both taxonomic compositions and functional potentials normally observed in the microbiomes of healthy populations, along with possible driving factors such as geography, diet, and lifestyle.” Studies comparing the biomes of North and South America, Europe and Africa, Korea and Japan, and urban and rural communities in Russia and China have identified numerous different associations that are related to differences in the microbiome between continents that include (but are not limited to) diet, genetics, lifestyle, geography, and early life exposures though none of these factors have been shown to be directly causal regarding geographic microbiome diversity.

Gupta, Paul, and Dutta (2017) question the case of a universal definition of a ‘healthy microbiome’ since it varies by geographic ancestry. Of course, ancestry and geographic location influence culture which influences diet which influences microbiome diversity between populations. This, of course, makes sense. why have a universal healthy microbiome with a reference man that doesn’t reflect the diversity of both the individual and group differences in the microbiome? This will better help different populations with different microbiomes lose weight and better manage diseases in certain populations.

The microbiome of athletes also differs, too. Athletes had enhanced microbiome diversity when compared to non-athletes (Clarke et al, 2016). In a further follow-up study, it was found that microbial diversity correlated with both protein consumption and creatine kinase levels in the body (Clarke et al, 2017) are proxies for exercise, and since they’re all associations, causality remains to be untangled. Nevertheless, these papers are good evidence that both lifestyle and diet leads to changes in the microbiome.

Fortenberry (2013: 165) notes that American racial and ethnic classifications are “social and political in origin and represent little meaningful biologic basis of between-group racial/ ethnic diversity“. It is also known that eating habits, differing lifestyles and metabolic levels also influence the diversity of the microbiome in the three ‘races’* studied (Chen et al, 2016), while deep sequencing of oral microbiota has the ability to classify “African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity” (Mason et al, 2014). The infant microbiome, furthermore, is influenced by maternal diet and breastfeeding as well as the infant’s diet (Stearns et al, 2017). This is why differences in race/ethnicity call into question the term of ‘healthy human microbiota’ (Gupta, Paul, and Dutta, 2017). These differences in the microbiome also lead to increased risk for colorectal cancer in black Americans (Goyal et al, 2016; Kinross, 2017).

Further, the healthy vagina “contains one of the most remarkably structured microbial ecosystems, with at least five reproducible community types, or “community state types” (Lloyd-Price, Abu-Ali, and Huttenhower 2016). The diversity of the microbiome in the vagina also varies by race. It was found that 80 percent of Asian women and 90 percent of white women harbored a microbiota species named Lactobacillus, whereas only about 60 percent of ‘Hispanics’ and blacks harbored this species. The pH level, too, varied by race with blacks and ‘Hispanics’ averaging 4.7 and 5.0 and Asians and whites averaging 4.4 and 4.2. So, clearly, since Asians and whites have similar vaginal pH levels, then it is no surprise that they have similar levels of vaginal Lactobacillus, whereas blacks and ‘Hispanics’, with similar pH levels have similar vaginal levels of Lactobacillus.

White subjects also have more diverse species of microbiota than non-white subjects while also having a different microbiota structure (Chen et al, 2015). Caucasian ethnicity/race was also shown to have a lower overall microbiome diversity, but higher Bacteroidetes scores, while white babes also had lower scores of Proteobacteria than black Americans (Sordillo et al, 2017). This comes down to both diet and genetic factors (though causation remains to be untangled).

Differences in the skin microbiome also exist between the US population and South Americans (Blaser et al, 2013). They showed that Venezuelan Indians had a significantly different skin biome when compared to US populations from Colorado and New York, having more Propionibacterium than US residents. Regarding the skin microbiota in the Chinese, Leung, Wilkins, and Lee (2015) write “skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households.” Skin microbiota also becomes similar in cohabitating couples (Ross, Doxey, and Neufeld, 2017) and even cohabitating family members and their dogs (Song et al, 2013; Cusco et al, 2017; Torres et al, 2017).

Differences between the East and West exist regarding chronic liver disease, which may come down to diet which may influence the microbiota and along with it, chronic liver disease. (Nakamoto and Schabl, 2016). The interplay between diet, the microbiome and disease is critical if we want to understand racial/ethnic differentials in disease acquisition/mortality, because the microbiome influences so many diseases (Cho and Blaser, 2012; Guinane and Cotter, 2013; Bull and Plummer, 2014; Shoemark and Allen, 2015; Zhang et al, 2015; Shreiner, Kao, and Young, 2016; Young, 2017).

The human microbiome has been called our ‘second genome’ (Zhu, Wang, and Li, 2010; Grice and Seger, 2012) with others calling it an ‘organ’ (Baquero and Nombela, 2012; Clarke et al, 2014; Brown and Hazen, 2015). This ‘organ’, our ‘second genome’ can also influence gene expression (Masotti, 2012; Maurice, Haiser, and Turnbaugh, 2013; Byrd and Seger, 2015) which could also have implications for racial differences in disease acquisition and mortality. This is why the study of the microbiome is so important; since the microbiome can up- and down-regulate gene expression—effectively, turning genes ‘on’ and ‘off’—then understanding the intricacies that influence the microbiome diversity along with the diet that one consumes will help us better understand racial differences in disease acquisition. Diet is a huge factor not only regarding obesity and diabetes differences within and between populations, but a ‘healthy microbiome’ also staves off obesity. This is important. The fact that the diversity of microbiota in our gut can effectively up- and down-regulate genes shows that we can, in effect, influence some of this ourselves by changing our diets, which would then, theoretically, lower disease acquisition and mortality once certain microbiome/diet/disease associations are untangled and shown to be causative.

Finally, the Hadza have some of the best-studied microbiota, and since they still largely live a hunter-gatherer lifestyle, this is an important look at what the diversity of microbiota may have looked like in our hunter-gatherer ancestors (Samuel et al, 2017). The fact that they noticed such diverse changes in the microbiome—some species effectively disappearing during the dry season and reappearing during the wet season—is good proof that what drives these changes in the diversity of the microbiota in the Hadza are seasonal changes in diet which are driven by the wet and dry seasons.

Gut microbiota may also influence our mood and behavior, and it would be interesting to see which types of microbiota differ between populations and how they would be associated with certain behaviors. The microbes are a part of the unconscious system which regulates behavior, which may have causal effects regarding cognition, behavioral patterns, and social interaction and stress management; this too makes up our ‘collective unconscious’ (Dinan et al, 2015). It is clear that the microbes in our gut influence our behavior, and it even may be possible to ‘shape our second genome’ (Foster, 2013). Endocrine and neurocrine pathways may also be involved in gut-microbiota-to-brain-signaling, which can then alter the composition of the microbiome and along with it behavior (Mayer, Tillisch, and Gupta, 2015). Gut microbiota also plays a role in the acquisition of eating disorders, and identifying the specific microbiotal profiles linked to eating disorders, why it occurs and what happens while the microbiome is out of whack is important in understanding our behavior, because the gut microbiome also influences our behavior to a great degree.

The debate on whether or not racial/ethnic differences in microbiome diversity differs due to ‘nature’ or ‘nurture’ (a false dichotomy in the view of developmental systems theory) remains to be settled (Gupta, Paul, and Dutta, 2017). However, like with all traits/variations in traits, it is due to a complex interaction of the developmental system in question along with how it interacts with its environment. Understanding these complex disease/gene/environment/microbiotal pathways will be a challenge, as will untangling direct causation and what role diet plays regarding the disease/microbiota/dysbiosis factor. As we better understand our ‘second genome’, our ‘other organ’, and individual differences in the genome and how those genomic differences interact with different environments, we will then be able to give better care to both races/ethnies along with individuals. Just like with race and medicine—although there is good correlative data—we should not jump to quick conclusions based on these studies on disease, diet, and microbiotal diversity.

The study of ethnic/racial/geographic/cultural/SES differences in the diversity of the microbiome and how it influences disease, behaviors and gene expression will be interesting to follow in the next couple of years. I think that there will be considerable ‘genetic’ (i.e., differences out of the womb; I am aware that untangling ‘genetic’ and ‘environmental’ in utero factors is hard, next to impossible) differences between populations regarding newborn children, and I am sure that even the microbiota will be found to influence our food choices in the seas of our obesogenic environments. The fact that our microbiota is changeable with diet means that, in effect, we can have small control over certain parts of our gene expression which may then have consequences for future generations of our offspring. Nevertheless, things such as that remain to be uncovered but I bet more interesting things never dreamed of will be found as we look into the hows and whys of both individual and populational differences in the microbiome.

Is Obesity Caused by a Virus?

August 12, 2017 10:33 pm / 6 Comments on Is Obesity Caused by a Virus?

2150 words

I’ve recently taken a large interest in the human microbiome and parasites and their relationship with how we behave. There are certain parasites that can and do have an effect on human behavior, and they also reduce or increase certain microbes, some of which are important for normal functioning. What I’m going to write may seem weird and counter-intuitive to the CI/CO (calories in/calories out) model, but once you understand how the diversity in the human mirobiome matters for energy acquisiton, then you’ll begin to understand how the microbiome contributes to the exploding obesity rate in the first world.

One of the books I’ve been reading about the human microbiome is 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness. P.h.D. in evolutionary biology Alanna Collen outlines how the microbiome has an effect on our health and how we behave. Though one of the most intriquing things I’ve read in the book so far is how there is a relationship with microbiome diversity, obesity and a virus.

Collen (2014: 69) writes:

But before we get too excited about the potential for a cure for obesity, we need to know how it all works. What are these microbes doing that make us fat? Just as before, the microbiotas in Turnbaugh’s obese mice contained more Firmicutes and fewer Bacteroidetes, and they somehow seemed to enable the mice to extract more energy from their food. This detail undermines one of the core tenets of the obesity equation. Counting ‘calories-in’ is not as simple as keeping track of what a person eats. More accurately, it is the energy content of what a person absorbs. Turnbaugh calculated that the mice with the obese microbiota were collecting 2 per cent more calories from their food. For every 100 calories the lean mice extracted, the obese mice squeezed out 102.

Not much, perhaps, but over the course of a year or more, it adds up. Let’s take a woman of average height. 5 foot 4 inches, who weights 62 kg (9st 11 lb) and a healthy Body Mass Index (BMI: weight (kg) /(height (m)^2) of 23.5. She consumes 2000 calories per day, but with an ‘obese’ microbiota, her extra 2 per cent calorie extraction adds 40 more calories each day. Without expending extra energy, those further 40 calories per day should translate, in theory at least, to a 1.9 kg weight gain over a year. In ten years, that’s 19 kg, taking her weight to 81 kg (12 st 11 lb) and her BMI to an obese 30.7. All because of just 2 percent extra calories extracted from her food by her gut bacteria.

Turnbaugh et al (2006) showed that differing microbiota contributes to differing amounts of weight gain. The obese microbiome does have a greater capacity to extract more energy out of the same amount of food in comparison to the lean microbiome. This implies that obese people would extract more energy eating the same food as a lean person—even if the so-called true caloric value on the package from a caloriometer says otherwise. How much energy we absorb from the food we consume comes down to genes, but not the genes you get from your parents; it matters which genes are turned on or off. Our microbes also control some of our genes to suit their own needs—driving us to do things that would benefit them.

Gut microbiota does influence gene expression (Krautkramer et al, 2016). This is something that behavioral geneticists and psychologists need to look into when attempting to explain human behavior, but that’s for another day. Fact of the matter is, where the energy that’s broken down from the food by the microbiome goes is dictated by genes; the expression of which is controlled by the microbiome. Certain microbiota have the ability to turn up production in certain genes that encourage more energy to be stored inside of the adipocite (Collen, 2014: 72). So the ‘obese’ microbiota, mentioned previously, has the ability to upregulate genes that control fat storage, forcing the body to extract more energy out of what is eaten.

Indian doctor Nikhil Dhurandhar set out to find out why he couldn’t cure his patients of obesity, they kept coming back to him again and again uncured. At the time, an infectious virus was wiping out chickens in India. Dhurandhar had family and friends who were veteraniarians who told him that the infected chickens were fat—with enlarged livers, shrunken thymus glands and a lot of fat. Dhurandhar then took chickens and injected them with the virus that supposedly induced the weight gain in the infected chickens, and discovered that the chickens injected with the virus were fatter than the chickens who were not injected with it (Collen, 2014: 56).

Dhurandhar, though, couldn’t continue his research into other causes for obesity in India, so he decided to relocate his family to America, as well as studing the underlying science behinnd obesity. He couldn’t find work in any labs in order to test his hypothesis that a virus was responsible for obesity, but right before he was about to give up and go back home, nutrional scientist Richard Atkinson offered him a job in his lab. Though, of course, they were not allowed to ship the chicken virus to America “since it might cause obesity after all” (Collen, 2014: 75), so they had to experiment with another virus, and that virus was called adenovirus 36—Ad-36 (Dhurandhar et al, 1997; Atkinson et al, 2005; Pasarica et al, 2006; Gabbert et al, 2010; Vander Wal et al, 2013; Berger et al, 2014; Pontiero and Gnessi, 2015; Zamrazilova et al. 2015).

Atkinson and Dhurandhar injected one group of chickens with the virus and had one control group. The infected chickens did indeed grow fatter than the ones who were not infected. However, there was a problem. Atkinson and Dhurandhar could not outright infect humans with Ad-36 and test them, so they did the next best thing: they tested their blood for Ad-36 antibodies. 30 percent of obese testees ended up having Ad-36 antibodies whereas only 11 percent of the lean testees had it (Collen, 2014: 77).

So, clearly, Ad-36 meddles with the body’s energy storage system. But we currently don’t know how much this virus contributes to the epidemic. This throws the CI/CO theory of obesity into dissarray, proving that stating that obesity is a ‘lifestyle disease’ is extremely reductionist and that other factors strongly influence the disease.

On the mechanisms of exactly how Ad-36 influences obesity:

The mechanism in which Ad-36 induces obesity is understood to be due to the viral gene, E4orf1, which infects the nucleus of host cells. E4orf1 turns on lipogenic (fat producing) enzymes and differentiation factors that cause increased triglyceride storage and differentiation of new adipocytes (fat cells) from pre-existing stem cells in fat tissue.

We can see that there is a large variation in how much energy is absorbed by looking at one overfeeding study. Bouchard et al (1990) fed 12 pairs of identical twins 1000 kcal a day over their TDEE, 6 days per week for 100 days. Each man ate about 84,000 kcal more than their bodies needed to maintain their previous weight. This should have translated over to exactly 24 pounds for each individual man in the study, but this did not turn out to be the case. Quoting Collen (2014: 78):

For starters, even the average amount the men gained was far less than maths dictates that it should have been, at 18 lb. But the individual gains betray the real failings of applying a mathematical rule to weight loss. The man who gained the least managed only 9 lb — just over a third of the predicted amount. And the twin who gained the most put on 29 lb — even more than expected. These values aren’t ’24 lb, more or less’, they are so far wide of the mark that using it even as a guide is purposeless.

This shows that, obviously, the composition of the individual microbiome contributes to how much energy is broken down in the food after it is consumed.

One of the most prominent microbes that shows a lean/obese difference is one called Akkermansia micinphilia. The less Akkermensia one has, the more likely they are to be obese. Akkermansia comprise about 4 percent of the whole microbiome in lean people, but they’re almost no where to be found in obese people. Akkermansia lives on the mucus lining of the stomach, which prevents the Akkermansia from crossing over into the blood. Further, people with a low amount of this bacterium are also more likely to have a thinner mucus layer in the gut and more lipopolysaccharides in the blood (Schneeberger et al, 2015). This one species of microbiota is responsible for dialing up gene activity which prevents LPS from crossing into the blood along with more mucus to live on. This is one example of the trillions of the bacteria in our microbiome’s ability to upregulate the expression of genes for their own benefit.

Everard et al (2013) showed that by supplementing the diets of a group of mice with Akkermensia, LPS levels dropped, their fat cells began creating new cells and their weight dropped. They conclude that the cause of the weight gain in the mice was due to increased LPS production which forced the fat cell to intake more energy and not use it.

There is evidence that obesity spreads in the same way that an epidemic does. Christakis and Fowler (2007) followed over 12000 people from 1971 to 2003. Their main conclusion was that the main predictor of weight gain for an individual was whether or not their closest loved one had become obese. One’s chance of becoming obese increased by a staggering 171 percent if they had a close friend who had become obese in the 32 year time period, whereas among twins, if one twin became obese there was a 40 percent chance that the co-twin would become obese and if one spouse became obese, the chance the other would become obese was 37 percent. This effect also did not hold for neighbors, so something else must be going in (i.e., it’s not the quality of the food in the neighborhood). Of course when obesogenic environments are spoken of, the main culprits are the spread of fast food restaurants and the like. But in regards to this study, that doesn’t seem to explain the shockingly high chance that people have to become obese if their closest loved ones did. What does?

There are, of course, the same old explanations such as sharing food, but by looking at it from a microbiome point of view, it can be seen that the microbiome can and does contribute to adult obesity—due in part to the effect on different viruses’ effects on our energy storage system, as described above. But I believe that introducing the hypothesis that we share microbes with eachother, which also drive obesity, should be an alternate or complimentary explanation.

As you can see, the closer one is with another person who becomes obese, the higher chance they have of also becoming obese. Close friends (and obviously couples) spend a lot of time around each other, in the same house, eating the same foods, using the same bathrooms, etc. Is it really an ‘out there’ to suggest that something like this may also contribute to the obesity epidemic? When taking into account some of the evidence reviewed here, I don’t think that such a hypothesis should be so easily discarded.

In sum, reducing obesity just to CI/CO is clearly erroneous, as it leaves out a whole slew of other explanatory theories/factors. Clearly, our microbiome has an effect on how much energy we extract from our food after we consume it. Certain viruses—such as Ad-36, an avian virus—influence the body’s energy storage, forcing the body to create no new fat cells as well as overcrowding the fat cells currently in the body with fat. That viruses and our diet can influence our microbiome—along with our microbiome influencing our diet—definitely needs to be studied more.

One good correlate of the microbiomes’/virsuses’ role in human obesity is that the closer one is to one who becomes obese, the more likely it is that the other person in the relationship will become obese. And since the chance increases the closer one is to who became obese, the explanation of gut microbes and how they break down our food and store energy becomes even more relevant. The trillions of bacteria in our guts may control our appetites (Norris, Molina, and Gewirtz, 2013; Alcock, Maley, and Atkipis, 2014), and do control our social behaviors (Foster, 2013; Galland, 2014).

So, clearly, to understand human behavior we must understand the gut microbiome and how it interacts with the brain and out behaviors and how and why it leads to obesity. Ad-36 is a great start with quite a bit of research into it; I await more research into how our microbiome and parasites/viruses control our behavior because the study of human behavior should now include the microbiome and parasites/viruses, since they have such a huge effect on eachother and us—their hosts—as a whole.