Fitting into Your Skinny Jeans: Why This Second Set of Genes May Be Making It Difficult

“I’m nowhere near the finish line,” my patient said during our fifth consultation, sighing vacantly as she stared at the floor. With a waist circumference of 38 inches, triglycerides of 300, and fasting blood sugar of 110, I had diagnosed her with metabolic syndrome at her initial checkup.

Over three months and as many follow-ups, I had exhausted my arsenal of strategies to help normalize her blood sugar. She removed processed carbohydrates, utilized blood sugar-balancing nutrients like chromium and lipoic acid, got sufficient sleep, and incorporated burst training and weight resistance into her fitness routine.

All those strategies helped move the needle a little, yet my patient sat discouraged that day, still carrying about 25 extra pounds.

Around that time, I was learning more about the microbiome. I initially felt skeptical, yet copious research revealed an emerging science around gut health and disease, with connections to numerous problems including cancer, autoimmune diseases, and obesity.

During our next visit, at a loss for conventional strategies to treat metabolic syndrome, I suggested microbiome testing. Her results revealed a double whammy of bad gut bugs and a lack of gut diversity that, despite doing everything else correctly, held my client’s weight hostage.


Why Your Second Genome Becomes First Priority For Optimal Health

Joshua Lederberg coined the phrase microbiome to describe your microorganism “community.” Think of your microbiome as a second genome: A blueprint or foundation for all your gut bacteria.

Microbiota, on the other hand, are those actual inhabitants. About 100 trillion microbial cells populate the human microbiome, outnumbering cells ten to one.

It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about ten resident microbes,” says Michael Pollan in a brilliant 2013 New York Times Magazine essay. “To the extent that we are bearers of genetic information, more than 99 percent of it is microbial.”

Most of that gut community comes from your parents and stabilizes in early childhood, Pollan says, yet environment also plays a role in microbiota population and diversity. As the old saying goes, genetics load the gun but environment pulls the trigger. Youhave control maintaining a healthy gut.

Only recently have scientists begun considering how your microbiome impacts health and illness, describing it as a “newly discovered organ.” 

A diverse, healthy array of microbiota has become such a big deal, in fact, that in 2008, the National Institutes of Health launched The Human Microbiome Project, a five-year, $115 million project intended to explore microbial flora in healthy and not-so-healthy folks.

The results so far have been fascinating to better understand health and disease. Far from being dormant little critters in your gut, healthy microbiota or gut flora are workhorses that, among other roles, keep out pathogens and other foreign invaders as well as manufacturer vitamins and other things that affect immunity and metabolism.

While you’ll always have some bad guys hanging out, you want mostly good flora, and you want a diverse species of those good guys. “More diversity is probably better than less, because a diverse ecosystem is generally more resilient —and diversity in the Western gut is significantly lower than in other, less-industrialized populations,”writes Pollan.

Bluntly put, if you live in the U.S., you’ve probably got less-than-stellar gut flora. Environmental toxins dwindle diversity and ramp up bad flora; so do antibiotics. Yet probably the most destructive link to a damaged microbiome involves–you guessed it – the sugary, heavily processed foods many Americans eat.


The Gut-Breast Cancer Connection

Claudia Plottel, MD, a Clinical Associate Professor at N.Y.U., and her team look at how microbiome affects estrogen circulation, and how certain microbes adversely affect cancer –specifically, breast cancer –risk.

Patient Check-up to Lose Weight and Fasting Blood SugarPlottel believes your microbiota species can create enzymes that increase estrogen–clinically called estrogen dominance – and, therefore, estrogen-related cancers. Estrobolome are your genes that code these enzymes that metabolize estrogen.

Dysbiosis, or a preponderance of bad gut flora, can “lower circulating lymphocytes, and increase neutrophil to lymphocyte ratio, a finding which has been associated with a decreased survival in women with breast cancer,” researchers argue in a study published in ISRN Oncology. “Dysbiosis also plays a role in the recycling of estrogens via the entero-hepatic circulation, increasing estrogenic potency in the host, which is another leading cause of breast malignancy.”

A more recent study in PLOS One confirmed that dysbiosis could increase breast cancer risk.

Not only was unhealthy microbiota increasing that and other risks; it also provided the missing link to better understand my patient’s weight loss resistance.


How Bad Gut Flora Can Be Keeping You From Losing Weight

Excessive amounts of bad gut flora ramps up estrogen, increasing your risk for certain cancers but also stalling fat loss by –among other obstacles –messing with fat-regulating hormones.

Interestingly, obese people have different types of microbes than lean people, and when they lose weight, their mircobiota change. This makes sense when you consider how these microbes behave.

Concept of Diet and Lose Weight“The bacteria themselves appear to [produce] signaling chemicals that regulate our appetite, satiety and digestion,” Pollan says. Bad bacteria coupled with a lack of diversity create a surefire way to create hormonal havoc.

I believe we’ve hit the tip of a big iceberg understanding microbiome and hormonal interaction, but some patterns are already emerging. Martin Blaser, a physician and microbiologist at New York University, believes a dwindling H. pylori bacteria population interferes with ghrelin, your hunger hormone.

Blaser also believes antibiotics could adversely affect your microbiome and contribute to obesity. Along with a plethora of processed foods and food intolerances like gluten and dairy prevalent in the Western diet, you’ve set the stage for gut permeability and inflammation.

A vicious cycle ensues, and overall it isn’t a pretty picture.

One study in the journal Nature looked at 123 non-obese and 169 obese Danish individuals. Researchers found those with low amounts of healthy bacteria had more marked overall adiposity, insulin resistance, dyslipidemia (altered fat metabolism), and inflammation compared with healthy-gut folks.

“The obese individuals among the lower bacterial richness group also gain more weight over time,” researchers noted.

Looking at all this research, my patient’s problem became all too apparent: Faulty gut flora created her weight loss resistance. So I designed these well-researched strategies to healthily repopulate and diversify her microbiota.


Strategies to Improve Your Microbiome

Pollan says “while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.” That’s good news if you want to reduce your risk for numerous chronic illnesses and eliminate weight loss resistance.

The biggest way to repopulate and diversify microbiota is with your fork. One study in the journal Nature looked at how short-term dietary alterations can affect your microbiome. The good news is that researchers found your gut rapidly responds to an altered diet.

“We don’t know a lot, but we probably know enough to begin taking better care of it,” says Pollan. “We have a pretty good idea of what it likes to eat, and what strong chemicals do to it. We know all we need to know, in other words, to begin, with modesty, to tend the unruly garden within.”

You can positively impact your microbiome starting with your very next meal. “Your microbiome changes with every bite of food,” says my friend Dr. Mark Hyman.


Here are five ways to positively impact your microbiome:

1. Try resistant starch.

Resistant starch is a unique fiber that –as its name suggests –resists digestion, remaining intact until it hits your colon, which converts that resistant starch to short-chain fatty acids for energy. Resistant starch has an impressive resume benefiting everything from increased insulin sensitivity to colorectal cancer to improved gut microbiome. Legumes, potatoes, and plantains are among the numerous foods that contain resistant starch.

Likewise, consider using Bob’s Red Mill Potato Starch or another resistant starch to thicken foods or otherwise supplement with this crucial fiber.

2. Incorporate prebiotic- and probiotic-rich foods.

Kimchi, raw, unpasteurized sauerkraut, and (if you’re not dairy intolerant) unsweetened Greek yogurt provide excellent sources of probiotics to rebalance healthy gut flora.

Inulin and Jerusalem artichoke are excellent sources of prebiotics, the food your gut flora graze on. One study in the Journal of Clinical Gastroenterology concluded prebiotics and probiotics “serve to elicit changes in the gut microbiota composition that increase populations of purported beneficial gut bacterial genera.”

3. Eat one pound of cruciferous vegetables each day.

Beyond providing an excellent fiber source, broccoli and other cruciferous veggies provide cancer-fighting compounds like indole-3-carbinol as well as numerous nutrients. One study in the Journal of Agricultural and Food Chemistry concluded whole foods like cruciferous vegetables could help up-regulate beneficial bacteria. Gradually increase your intake until you’ve hit a pound every day.

Broccoli stir-fried in coconut oil and garlic or Brussels sprouts with onions and nitrate-free bacon make delicious ways to meet that quota.

4. Remove all sugar. Bad gut flora love sugar.

Refusing to feed your enemy can help healthy flora proliferate while the bad guys die out. I’m not just talking obvious sugar sources here. You’ll also want to eliminate sugary dressings, sauces, and numerous other places sugar hides. This strategy alone helped my patient lose 10 pounds in her first month, dramatically reduce bloating, and trim waist from 38 to 34 inches, thereby reversing metabolic syndrome.

5. Get 35 –45 grams of fiber each day.

Most scientists Pollan interviewed agreed lack of fiber in the Western diet adversely affects microbiome. Rather than go from zero to 60 (or, um, 45), gradually increase your fiber five grams a day until you’ve met your quota. Otherwise, bloating, gas, and other unpleasant consequences can ensue.

Microbiome is a newly emerging science, and I believe scientists will continue to unravel fascinating discoveries about how this “second genome” affects wellness and well-being.

As we better understand the numerous roles it plays in health and disease, healthcare experts have increased focus on nourishing and healing the gut.

What strategies have you taken to boost gut health?

Share your thoughts below or on my Facebook fan page.


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DC Savage, “Microbial ecology of the gastrointestinal tract,”Annual Review of Microbiology 31 (1977):107-33.

I Shapira et al., “Evolving Concepts: How Diet and the Intestinal Microbiome Act as Modulators of Breast Malignancy,” ISRN oncology 2013 (2013).

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