“I read somewhere that a high-fat diet can damage your gut bacteria and promote weight gain,” writes this week’s house call. “Should I be concerned if I’m eating a high-fat diet?”

It is true that what you eat can affect your gut bacteria, for better and for worse, and changes in your gut bacteria or microbiome cause weight gain. Indeed, some studies demonstrate that high-fat diets can adversely affect your gut flora and promote inflammation and weight gain. However, it’s important to note that the type of fat you eat matters! Most of these studies are focused on diets that incorporate high levels of inflammatory, refined omega 6 vegetable oils like soybean oil.

Refined omega-6 rich vegetable oils fall into the “bad fats” category and should be avoided. While most of us have been convinced, by the food industry and our government, that vegetable oils are safe and a heart-healthy alternative to saturated fats, we now know differently.

Polyunsaturated fats from soybean, canola, and other seed oils are inflammatory. Avoid them if you want to be healthier. Even if you consume some omega 3 fats while consuming these inflammatory oils, you won’t reap the healthy fat benefits.

For most of human history, we consumed a much higher ratio of omega 3 fats to omega 6 fats. Wild foods like grass-fed beef and wild-caught fish provide a great source of omega 3s, but these foods are not a big part of our modern diet. Unfortunately, the factory-farmed animals that do make up much of our modern diet have almost zero omega 3 fats.

The vast quantities of omega 6 fats in our diet contribute to heart disease, diabesity, and cancer. Studies also link high omega 6 fat consumption to depression, suicide, and other major health problems due to increased inflammation.

To reverse these and other problems and create optimal health, replace these damaging omega 6 fats with healthy ones – like coconut oil, avocados, grass-fed butter, fish rich in omega 3s, and extra-virgin olive oil.

Interestingly, when we look at studies that use the healthy, anti-inflammatory omega 3 fats, we see just the opposite effect. These healthy fats promote healthier gut bugs, lower inflammation levels, and increased weight loss.

I said it before and I’ll say it again: the types of fat we eat matters. The wrong fats increase inflammation, promote the growth of bad bugs, and create resistance to weight loss. The right fats decrease inflammation and help with weight loss.

Why Is Gut Health So Important?

Optimal gut health has become a prominent focus in 21st century health. Having too many bad critters hanging out in the gut has been linked to numerous problems – including autism, obesity, diabetes, allergies, autoimmunity, depression, cancer, heart disease, fibromyalgia, eczema, and asthma. The links between chronic illness and an imbalanced microbiome (or gut bacteria) keep growing every day.

Many scientists have begun to refer to the gut as our second brain, an idea that is reflected in amazing books like The Good Gut, Brainmaker, The Microbiome Solution, and The Gut Balance Revolution.

Having a healthy gut should mean more to you than being annoyed by a little bloating or heartburn. It becomes central to your entire health and connected to everything that happens in your body. That’s why I almost always start treating my patients’ chronic health problems by fixing their guts first.

You can begin to understand the importance of gut health when you consider there are 500 species and three pounds of bacteria in your gut. There are trillions of bacteria in your gut, and they collectively contain at least 100 times as many genes as you do. The bacterial DNA in your gut outnumbers your own DNA by 100 times. You have about 20,000 genes, but there are 2,000,000 (or more) bacterial genes!

Altogether, your gut is a huge chemical factory that helps to digest food, produce vitamins, regulate hormones, excrete toxins, produce healing compounds and keep your gut healthy.

Intestinal health could be defined as the optimal digestion, absorption, and assimilation of food. But that is a big job that depends on many other factors. For example, the bugs in your gut are like a rain forest – a diverse and interdependent ecosystem. They must be in balance for you to be healthy.

Too many of the wrong ones (like parasites, yeasts or bad bacteria) or not enough of the good ones (like Lactobacillus or Bifidobacteria), can lead to serious damage to your health.

Optimal gut balance begins with your diet, which directly affects that balance. You want to eat a diet with lots of fiber, healthy protein, and healthy fats.

Good fats, including omega 3 fats and monounsaturated fats – such as extra-virgin olive oil, avocados or almonds – improve healthy gut flora, while inflammatory fats, like omega 6 vegetable oils, promote growth of bad bugs that cause weight gain and disease.

Even obesity has been linked to changes in our gut ecosystem, resulting from an intake of inflammatory omega 6s and not enough anti-inflammatory omega 3s. Bad bugs produce toxins called lipopolysacchardies (LPS) that trigger inflammation, insulin resistance or pre-diabetes and therefore, promote weight gain.

Lack of sleep and chronic stress also contribute to gut imbalance, In fact, your gut flora listens to and becomes influenced by your thoughts and feelings. So be sure to get 7 to 8 hours of quality sleep and remember to practice your favorite stress reduction activities daily.

8 Ways to Optimize Gut Flora

The best way to grow a healthy inner garden and make your gut bugs happy begins with your diet. Here are 9 ways to build healthy gut flora starting with your next forkful:

  1. Eat whole, unprocessed, unrefined foods. One of the best ways to maintain gut health involves cutting out the sugar and refined carbs and jacking up gut-supporting fiber.
  2. Make 75 percent of your plate be vegetables and plant-based foods. Your gut bugs really love these high-fiber plant foods.
  3. Eat good fats and get an oil change. The good fats we mentioned earlier (like omega 3 fats and monounsaturated fats, such as extra-virgin olive oil) will help with decreasing inflammation, giving healthy gut bugs a chance to flourish.
  4. Supplement smartly. Beyond the numerous benefits (including reducing inflammation), studies find omega 3 fatty acids can support healthy gut flora. You should definitely supplement with an essential fatty acids formula, if you’re not regularly eating wild-caught fatty fish. You can find professional-quality formulas in my store. Take a good probiotic supplement. This helps reduce gut inflammation while cultivating health and the growth of good bacteria.
  5. Add more coconut. Studies demonstrate anti-inflammatory and weight loss benefits from adding Medium Chain Triglyceride or MCT oils. One of my favorite fats, coconut oil and coconut butter, contains these fabulous fat-burning MCTs.
  6. Remove inflammatory fats. Cut out bad, inflammatory omega 6 rich fats like vegetable oils. Replace these with healthier oils like extra-virgin olive oil and coconut oil.
  7. Add fiber-rich foods. Nuts, seeds, and a special fiber called glucomannan provide prebiotics and feed our healthy bacteria.
  8. Add fermented foods. Sauerkraut, kimchi, tempeh, and miso contain good amounts of probiotics so your healthy gut bugs can be fruitful and multiply.

The above recommendations are not miracle cures. They are the actions that lead to normalized gut function and flora through improved diet, increased fiber intake, daily probiotic supplementation, the use of nutrients that repair the gut lining, and the reduction of bad bugs in the gut with herbs or medication.

Yes, inflammatory fats will definitely damage your gut bacteria. But the right fats, including omega 3s and extra-virgin olive oil combined with a whole, real food diet can actually repair your gut and even increase good bacteria.

My new book, Eat Fat, Get Thin, challenges conventional wisdom about what constitutes healthy oils and documents the research that debunks our old ideas about fat.

For some people on a diet, the pounds just seem to fall off, while others have a much harder time losing weight. Now, a new, small study finds that people’s gut bacteria may play a role in determining how easy, or difficult, it is for them to lose weight.

The study suggests that, among people who have a hard time losing weight, their gut bacteria tend to be better at using carbohydrates, which provide people’s bodies with more energy. This is usually a good thing, as people need energy to fuel their bodies. But for some people trying to lose weight, the ability of their gut bacteria to provide energy may be a weight-loss deterrent, the researchers said.

The study “tells us gut bacteria are likely an important determinant of the degree of weight loss attained following lifestyle and dietary intervention,” said Dr. Purna Kashyap, a gastroenterologist at the Mayo Clinic in Rochester, Minnesota, and co-senior author of the study.

The researchers stressed that the findings are preliminary and need to be confirmed with larger studies. But the study suggests the “need to take the microbiome into account in clinical studies ; and it also provides an important direction to pursue in terms of providing individualized care in obesity,” Kashyap told Live Science.


Studying stool

For the new study, the researchers analyzed data from 26 overweight or obese people enrolled in an obesity-treatment program that involved diet, exercise and behavioral changes aimed at helping people lose weight. The researchers also analyzed the participants’ stool samples, which were collected at the start of the study and after three months on the weight-loss program.

During this three-month period, the participants lost an average of 8.2 lbs. (3.7 kilograms). Nine of the participants lost at least 5 percent of their body weight, which the researchers considered a “successful” weight loss. The other 17 participants lost less than 5 percent of their body weight. Among the “successful” weight-loss group, participants lost an average of 17.4 lbs. (7.9 kg), compared with 3.3 lbs. (1.5 kg) in the “unsuccessful” group.

Next, using the stool samples, the researchers analyzed the participants’ gut microbiome for bacterial genes that play a role in breaking down carbohydrates. They found that, in the unsuccessful weight-loss group, there was an increased number of these bacterial genes, compared with the successful weight- loss group.

“A gut microbiota with increased capability for carbohydrate metabolism appears to be associated with decreased weight loss,” the researchers wrote in the study, published online today (Aug. 1) in the journal Mayo Clinic Proceedings.

What’s more, the study also found that people in the successful weight-loss group had higher amounts of a bacterium called Phascolarctobacterium, while those in the unsuccessful weight-loss group had higher amounts of a bacterium called Dialister. (Still, it’s unclear whether Dialister bacteria specifically use carbohydrates in a way that could hinder weight loss, the researchers noted.)

Future avenues

The new study is “supportive of things we’re learning about the microbiome,” said Dr. Vijaya Surampudi, a physician with the Risk Factor Obesity Weight Management Program at UCLA Health who was not involved in the study.

Indeed, the findings agree with other recent studies that suggest gut bacteria may play a role in obesity and weight loss. For example, a 2013 study in mice found that mice who received a “gut bacteria transplant” from an obese human gained more weight and fat mass than those who received bacteria from a lean human. And a 2015 study in people found that bariatric surgery may lead to long-term changes in people’s gut bacteria that could contribute to weight loss.

However, Surampudi agreed that the new study was small, and that more research is needed to confirm the findings.

One day, it might be possible to identify people who would respond, or not, to a given diet, Surampudi said. For example, if the new findings turn out to be true, it may mean that people who have more carbohydrate-using bacteria would respond better to a low-carb diet, she said.

“We use the microbiome to help us navigate which diet approach would be better for people,” Surampudi told Live Science, though more research is needed before this approach could be used in patients.

Kashyap agreed that if future studies confirm the findings, “we may need to modify the weight loss plan based on an individual’s gut bacteria; or try to change the makeup of the gut bacteria using targeted approaches like probiotics before instituting a weight loss program.”

Original article on Live Science.

These gut bacteria prevent mice from becoming obese — what could that mean for us?

Published online in the journal Science on July 25, the study shows that healthy mice have plenty of Clostridia — a class of 20 to 30 bacteria — but those with an impaired immune system lose these microbes from their gut as they age. Even when fed a healthy diet, the mice inevitably become obese. Giving this class of microbes back to these animals allowed them to stay slim.

June Round, Ph.D., an associate professor of pathology at U of U Health, is the study’s co-senior author along with U of U Health research assistant professor W. Zac Stephens, Ph.D. Charisse Petersen, Ph.D., a graduate student at the time, led the research.

“Now that we’ve found the minimal bacteria responsible for this slimming effect, we have the potential to really understand what the organisms are doing and whether they have therapeutic value,” Round says.

Results from this study are already pointing in that direction. Petersen and colleagues found that Clostridia prevents weight gain by blocking the intestine’s ability to absorb fat. Mice experimentally treated so that Clostridia were the only bacteria living in their gut were leaner with less fat than mice that had no microbiome at all. They also had lower levels of a gene, CD36, that regulates the body’s uptake of fatty acids.

These insights could lead to a therapeutic approach, Round says, with advantages over the fecal transplants and probiotics that are now being widely investigated as ways to restore a healthy microbiota. Therapeutics such as these, that are based on transferring living microbiome to the gut, won’t work for everyone due to differences in diet and other factors that influence which bacteria can survive and thrive.


The current study found that one or more molecules produced by Clostridia prevented the gut from absorbing fat. The next step is to isolate these molecules and further characterize how they work to determine whether they could inspire focused treatments for obesity, type 2 diabetes, and other related metabolic disorders.

“These bacteria have evolved to live with us and benefit us,” Petersen says. “We have a lot to learn from them.”

A Good Defense Is the Best Offense

Finding that mice with a compromised immune system couldn’t help but become obese was a discovery that almost didn’t happen. Serendipity brought Petersen into the lab at the right time to see that mice genetically engineered to lack myd88, a gene central to the immune response, were “as fat as pancakes.” She had let the rodents age longer than usual, revealing an unappreciated link between immunity and obesity.

Still, the observation didn’t answer the question why the animals became overweight.

Based on previous research she had carried out in the Round lab, she suspected the microbiome was involved. She had helped demonstrate that one role of the immune system is to maintain balance among the diverse array of bacteria in the gut. Impairing the body’s defenses can cause certain bacterial species to dominate over others. Sometimes, the shift negatively impacts health.

Following a similar logic, Petersen and colleagues determined that the obesity observed in immune-compromised mice stemmed from the failure of the body’s defense system to appropriately recognize bacteria. These mice produced fewer of the antibodies that ordinarily latch onto the microbiome like target-seeking missiles. This change made the gut less hospitable for Clostridia, leading to more fat absorption and excessive weight gain. Over time, the mice also developed signs of type 2 diabetes.

Round points out that research by others have shown that people who are obese similarly lack Clostridia, mirroring the situation in these mice. There are also some indications that people who are obese or have type 2 diabetes may have a suboptimal immune response. The hope is that understanding these connections will provide new insights into preventing and treating these pervasive health conditions.

“We’ve stumbled onto a relatively unexplored aspect of type 2 diabetes and obesity,” Round says. “This work will open new investigations on how the immune response regulates the microbiome and metabolic disease.”

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Antibiotics have done wonders for extending human life by killing off deadly pathogens. But they target “a particular disease the way a nuclear bomb targets a criminal, causing much collateral damage,” says Karen Kaplan in the Los Angeles Times. Incidental victims include a whole host of microbes that actually help us, and “our friendly flora never fully recover,” argues New York University microbiologist Martin Blaser in the journal Nature. The unintended targets of antibiotics might also include our waistlines, according to new theories linking the drugs to a sharp rise in obesity. Here’s what you need to know:

How do antibiotics hurt us?
Bacteria have lived in and on us as long as there have been humans, creating a symbiotic relationship. But that’s changed over the past 80 years, Blaser says, because the development of antibiotics started disrupting the population of mostly beneficial bacteria that help us digest our food, metabolize vitamins and nutrients, and even fight off invading organisms. “Antibiotics kill the bacteria we do want, as well as those we don’t,” he notes.

And there’s evidence of this?
Blaser points to Helicobacter pylori, a bacterium he’s worked with for 26 years. Discovered in 1982, H. pylori “has been the dominant ancient organism of the human stomach since time immemorial,” he tells The Scientist. Now it’s disappearing. In the early 1900s, it thrived in the guts of all people; today, fewer than 6 percent of American, Swedish, and German kids have any trace of H. pylori. A likely cause, says Blaser, is antibiotics: A single course of amoxicillin or other antibiotics used to clear up, say, an ear infection, also wipes out H. pylori up to 50 percent of the time.

Is losing a little bacteria really so bad?
In the case of H. pylori, it appears to be a mixed blessing: The bacterium promotes gastric cancer and ulcers, which have gotten rarer along with the microbe. But Blaser’s lab has also shown that kids lacking H. pylori are more prone to asthma, hay fever, and skin allergies. “And H. pylori is just one bacterium!” says Karen Kaplan in the L.A. Times.

Wait, what does this have to do with obesity?
H. pylori also affects the behavior of two stomach-producing hormones that control hunger — ghrelin, which tells the brain you’re hungry, and leptin, which tells it you’re full. If those hormones are thrown out of balance, your appetite probably is, too. Blaser says the rise in antibiotic use tracks with sharp increases in obesity. (Half of U.S. adults will be obese by 2030, according to a new study published in the journal The Lancet.) That’s not proof the two trends are related, he concedes, but it’s a fertile path for exploration.

Is there any way to reverse this trend?
A general reduction in the use of antibiotics is a good first step, Blaser says, but we also need to develop a new generation of antibiotics that more surgically target specific pathogens. And someday, he tells The Scientist, doctors will find what microbes infants are lacking, “and just as a child gets their immunizations, they’ll get a dose of the missing bacteria so that they can get the early life benefits just as all their forebears have.”

Sources: Gizmodo, LiveScience, Los Angeles Times, The Scientist, Waleg, Washington Post

Pop an antibiotic recently? While it may be useful for treating your strep throat, it could also be packing on pounds.

In a recent study, researchers found that lean people have a more diverse community of gut flora (meaning there’s a greater variety of healthful bacteria taking up shop in their stomachs) than plumper folks.

So what does that have to do with our jeans feeling extra snug?

Researchers aren’t clear on why antibiotics may contribute to weight gain. In fact, all they know for sure is that lean people have different gut flora than their plumper counterparts — and antibiotics have a dramatic impact on gut flora.

However, in a study published by the European Molecular Biology Organization, researchers suggest that healthful gut bacteria is responsible for how much fat we pack on. Gut flora “has a metabolic activity equal to a virtual organ within an organ,” they write, and “improved understanding of this hidden organ will reveal secrets that are relevant to human health” — including possibly how to prevent obesity.

Thomas R. Clark, director of clinical affairs at the American Society of Consultant Pharmacists, says the possible connection between gut flora and obesity needs further exploration. But he maintains that the overuse of antibiotics and the growth of bacteria that are resistant to antibiotics is a major concern.

“There is still too much of a casual attitude toward antibiotics on the part of some consumers and prescribers,” says Clark. “Use of antibiotics should be limited to situations where they are clearly needed.” What are those situations? Infections! But only infections caused by bacteria, fungi and certain parasites — not things like viruses, colds and flu.

If you feel like you’re packing a few extra pounds and you’ve been on and off antibiotics throughout your life, it may be time to ease off the meds. Never take antibiotics without a prescription. If, for whatever reason, you have antibiotics leftover from a time when you were previously sick, do not take them unless your doctor tells you it’s OK.

Then, start popping probiotics (in the form of yogurt, kefir and other bacteria-spiked foods or supplements), which may help restore gut flora.

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A malnourished child with kwashiorkor.Lyle Conrad/Wikimedia Commons

In the early 2000s, malnutrition got a squishy new peanut-flavored enemy. Kids fed a calorie-rich paste of peanuts, sugar, milk, and the whole alphabet of vitamins and minerals recovered at rates nearly twice that for previous treatments. However, some 15 percent of the severely malnourished children still didn’t recover on the ready-to-use therapeutic food (RUTF), puzzling and frustrating doctors. A pair of studies in Malawi recently published in the New England Journal of Medicine and Science suggest a clue: bacteria living in the kids’ guts.

The first study, led by peanut-based food therapy pioneer Mark Manary, found that antibiotics plus RUTF cut mortality among severely malnourished children by 36 to 44 percent compared to RUTF alone. The WHO is now planning to recommend wider antibiotic use for malnutrition, which kills a million kids each year.

“We were completely shocked,” says the study’s first author Indi Trehan. The researchers initially thought their study would prove cutting antibiotics saves money. The antibiotics were a holdover from the old milk-based malnutrition therapy that required kids to spend weeks in the hospital, which left them susceptible to hospital-acquired infections. RUTF, on the other hand, comes in packets easily distributed at home and should have eliminated that problem.

Why antibiotics helped these kids is still unknown. Trehan says it may ease chronic infections in these malnourished and immunodeficient kids. In addition, the intestinal linings of malnourished children break down, so bacteria normally harmless in the gut enter the bloodstream and cause trouble. Antibiotics could help those infections.

A mother feeding her kids peanut-based RUTF in Malawi. Indi Trehan

A second study in Science suggests that imbalance in the gut microbiome causes kwashiorkor, an extreme form of malnutrition characterized by swelling. Identical twins could eat the same diet, the authors puzzled, but only one would have the bloated belly associated with kwashiorkor. So they looked at 13 discordant twin pairs in Malawi and found their gut microbes were markedly different. RUTF helped in the short term, but the kids with kwashiorkor reverted to abnormal microbiota at the end of treatment. And over time, the microbiota of kids with kwashiorkor didn’t mature like their twins’—a finding that suggests kwashiorkor is a permanent condition.

Back in St. Louis, Washington University professor Jeffrey Gordon transplanted the Malawi twins’ gut bacteria into sterile mice, a technique he’s used before to study links between the gut microbiome and obesity (PDF). These mice were then fed either a protein-poor Malawian diet or regular chow. Only the mice with both kwashiorkor microbiota and Malawian diets lost significant weight. This suggests that RUTF longer than the normal nine weeks may help correct the bacterial imbalance. An additional set of experiments looking at metabolites in mice urine and feces found that kwashiorkor microbiota messes with proper nutrient absorption.

This study solves some of the mystery of kwashiorkor and points toward a possible cure. “If you think of the microbiota as an organ, then repair requires microbes that can fill different ‘professions,’” says Gordon. Thus, in addition to longer RUTF, treatment could directly target the bacteria, either in the form of probiotics to replace a missing microbe or a fecal transplant that repopulates the entire community.

In light of what we know about the opposite problem, obesity, it makes perfect sense that antibiotics and the gut microbiome play a role in starvation. Obese mice (and humans) have altered microbial communities compared to their normal counterparts. And antibiotics in early childhood has been linked to higher body mass.

The antibiotics study may also echo the process that of fattening up animals with regular doses of antibiotics (which my colleague Tom Philpott wrote about here), but Trehan cautions lumping against them together in one biological mechanism. The kids are given only one dose of antibiotics, rather than continual doses over a whole lifetime. This also mitigates the problem of resistance, as the antibiotics are selectively doled out to malnourished kids rather than everyone in a particular town. “I spend half my time telling people to stop taking antibiotics as a pediatric fellow ,” says Trehan, but “in an underfunded healthcare system, access to antibiotics is pretty rare.”

Trehan’s comment highlights the obvious gulf between healthcare in Malawi and St. Louis. The microbiome is one of the hottest areas in biomedicine right now, but research about its disease implications has focused on decidedly First World problems like obesity, high blood pressure, and autoimmune disorders. An age-old and seemingly simple problem like malnourishment can benefit from cutting-edge science, too.

Changing your gut microbes may not help you lose belly fat.

In a preliminary study, obese people got either capsules containing gut microbes from a lean person or placebo pills. Microbes from the lean donor took hold in the guts of the obese recipients. But early results suggest that the bacteria didn’t change the volunteers’ weight or levels of a hormone that helps signal fullness, gastroenterologist Jessica Allegretti reported May 8 at a news conference.

People with obesity often have different types of gut microbes than lean people do. And previous studies with lab animals and anecdotal evidence from people have suggested that transfers of intestinal bacteria and other microbes — collectively known as the gut microbiome — from a donor to a recipient may lead to weight loss or gain, depending on whether the donor was lean or obese. So the researchers reasoned that giving obese people gut microbes from a lean person, known as a fecal or intestinal microbiome transplant, might help overweight people control appetite and shed pounds.

In the study, 11 obese people swallowed 30 capsules containing gut microbes from the same lean donor. Another 11 obese people got identical-looking capsules that contained no gut bacteria. At four weeks and again at eight weeks after the initial dose, the volunteers downed 12 additional capsules. Twelve weeks after the experiment’s start, the researchers measured changes in the people’s gut microbe mix, their weight, levels of a protein called GLP-1 and bile acid production.

When people eat fiber, gut microbes process that fiber into short chain fatty acids. Those molecules cause the small intestine to make GLP-1, which in turn tells the brain that the person has had enough to eat. Other weight loss studies have indicated that GLP-1 levels change as people lose weight.

Allegretti and colleagues thought that changing the gut microbe mix might boost GLP-1 production. Instead, they found no change in the satiety protein between the transplant and placebo groups. There was also no indication that the bacteria led to weight loss.

But people who got the lean microbes increased production of certain bile acids, which help break down fats. Providing new gut microbes that make bile-acid-processing enzymes may alter the metabolism of fat in obese patients, says Allegretti, who directs the fecal microbiome transplant program at Brigham and Women’s Hospital in Boston.

The study was small, and mainly designed to determine whether such microbiome transplants are safe and if a lean donor’s microbes could settle in in an obese person’s guts. “We did not expect to answer the question. ‘Does work to treat obesity?’ from this first step,” Allegretti says. But “I’ve seen enough from this data that makes me want to continue exploring it further.” She will report more results from the study May 20 in San Diego at the Digestive Disease Week 2019 medical conference.

In the United States, the Food and Drug Administration allows intestinal microbiome transplants for treating people with infections with Clostridium difficile for whom other treatments have failed. C. diff is a severe bacterial infection that takes hold when people’s normal gut microbes have been ravaged by antibiotics. The bacteria can cause symptoms ranging from diarrhea to life-threatening inflammation of the intestines and other organs. In those instances, intestinal microbe transplants can save lives.

So far, gut microbe transplants to treat diabetes have made some obese people with the disease more sensitive to insulin. But that hasn’t really helped them lose weight, says Alexander Khoruts, a gastroenterologist at the University of Minnesota in Minneapolis. Khoruts was not involved in new study, but has experience with transplanting gut microbes from one person to another. Most studies in humans, including an unpublished trial Khoruts and his colleagues conducted, have found only minuscule changes in waist circumference, weight or body mass index in obese people who have gotten gut microbes from someone lean.

Still, the new work is the first to compare gut microbe transplants to placebo, says Vincent Young, an infectious disease physician at the University of Michigan Medical School in Ann Arbor. That alone is “potential progress,” he says.

But it’s still too early to determine what role the microbiome plays in obesity. Researchers aren’t yet sure what a healthy microbiome is, for example. Nor do they know or whether the microbes in the colon (those are the ones transferred in this and other fecal microbiome transplants) or those in the small intestine play a bigger role in determining body weight.

For now, swapping gut microbes doesn’t seem to be an easy cure for obesity, Allegretti says. The team may need to alter the dose of lean microbes or tweak the treatments in other ways to maximize the results.

How Your Gut Bacteria Can Help You Lose Weight

Photo: Susanne Alfredsson / EyeEm / Getty Images

What if you could enjoy a chocolate bar without taking in all its calories? This isn’t just wishful thinking. It may already be happening, thanks to the trillions of microbes in your digestive system.

Until recently, the assumption was that the bacteria huddling in your intestine pretty much mind their own business. But now a growing body of research suggests that your internal community of bacteria, known as a microbiota, could be influencing your metabolism and, surprisingly, affecting your weight. Turns out, the gut bacteria-weight-loss connection is a pretty fascinating one. (Here’s what you should be eating for a healthy gut.)

What Scientists Know About Gut Bacteria and Weight Loss

For example, having a greater abundance of a recently discovered type of bacteria called Christensenellaceae in your gut is associated with being slim, while having less of the bacteria is linked to being obese, a study in the journal Cell shows. “How much you have is partially determined by genetics,” says lead study author Julia Goodrich, a graduate student at Cornell University. The good news is that most of us harbor the bacteria—it was detected in 96 percent of the study samples—and it may be possible to alter our levels of gut bacteria for weight loss.

Christensenellaceae isn’t the only gut bacteria that might affect weight loss. A diverse mixture of microbes in the gut seems to be one key to staying slim, says Jeffrey Gordon, M.D., the director of the Center for Genome Sciences and Systems Biology at the Washington University School of Medicine, who was one of the first researchers to link intestinal bacteria and obesity. In fact, research found that lean people have 70 percent more gut bacteria and therefore a more diverse microbiota than that of their overweight peers. Other findings have found that people in the United States, who have a high rate of obesity, have less-diverse gut microbes than people from less developed parts of the world do. The correlation is consistent enough that in a study of twins, “we could predict whether one was lean or obese based solely on their gut microbes,” says Rob Knight, Ph.D., a cofounder of the American Gut Project. (Related: Nutritious Juice Shots for Gut Health)

The impact of the gut bacteria-weight loss link isn’t known yet, but many researchers believe that your gut microbiota plays a role in processing food and helping to determine how many calories and nutrients your body absorbs. Certain intestinal microbes may also alter your sensitivity to insulin—the hormone that moves sugar out of your blood—so that your body burns fat it would have otherwise stored. Interestingly, it only takes a few days of eating high-fat foods to disturb the balance of good and bad bacteria in the gut, which throws off an important process of breaking down undigested macros.

Your gut bacteria might affect how hungry you are too. One key microbe appears to be Helicobacter pylori, the bacterium that’s involved in causing ulcers and stomach cancer. Antibiotic treatments have helped cut H. pylori infection rates in half in recent decades, which is good news for ulcer sufferers-but which could be bad news for our waistlines. H. pylori also dials back the stomach’s production of the hunger hormone ghrelin. “When you wake up in the morning and you’re hungry, it’s because ghrelin is telling you to eat,” says Martin Blaser, M.D., a professor of medicine and microbiology at New York University and the author of the book Missing Microbes. “When you eat breakfast, your level of ghrelin usually goes down, but if you don’t have Helicobacter in your system, it doesn’t.” The end result: You could eat more. (Related: 8 Tips to Absorb More Nutrients From Your Food)

The Impact of Antibiotics on Gut Bacteria and Weight Loss

You might not even have to take antibiotics to feel their effects on your gut bacteria. The heavy reliance on antibiotics by the food industry, which routinely uses the drugs in feed to keep livestock healthy, may be fueling the rise of obesity by disrupting the fine balance of our intestinal microbes, some experts believe. “The obesity epidemic really took off in the last 20 years in the U.S. So the question is, what happened then? What was a large segment of the population exposed to that could account for this massive weight gain?” asks Lee Riley, M.D., a professor of epidemiology at the University of California, Berkeley. He points out that that’s when the number of large-scale densely packed factory farms expanded, which also increased the use of antibiotics in livestock feed. Today, 80 percent of the antibiotics sold in the United States go toward helping animals remain healthy and gain more weight in crowded conditions. “Counties with the highest prevalence of obesity are those counties with large concentrated animal feeding operations,” he says.

Not to mention that antibiotics are often used when they shouldn’t be, as when doctors prescribe them for viral infections or because patients demand them. (Sometimes a full course of antibiotics isn’t necessary.) The exact repercussion on human health is still being debated, but Dr. Blaser says that the gut bacteria-weight loss link in laboratory studies is pretty clear. “If you put mice on a high-fat diet, they get fat,” he says. “If you put them on antibiotics, they get fat. And if you put them on both, they get very fat.”

While some of your gut bacteria is determined by genetics, life­style and dietary habits can have a dramatic impact on your mix of beneficial and harmful microbes. A study in the journal Nature found that when people switched from their normal diet to one consisting primarily of meat and cheese, there was an almost immediate increase in Bilophila, a type of bacteria that has been linked to colitis, but that a plant-based diet decreased the levels.

4 Ways to Keep Your Gut Bacteria Healthy

Eat more fiber. It’s the number-one thing you can do to better your gut bacteria (and hopefully help with weight loss), says Justin Sonnenburg, Ph.D., an assistant professor of microbiology and immunology at Stanford University. Research suggests that fiber nourishes your microbes, making them diverse and more likely to help keep you at a healthy weight. Avoid the temptation to buy processed foods that have added fiber. Instead, eat vegetables, fruits, and whole grains. Aim for at least two to three servings each of produce and whole grains and 20 to 30 grams of fiber a day, says Mark Moyad, M.D., a urologist and the author of The Supplement Handbook. These foods also provide prebiotics, which are essentially a type of fiber that your gut bacteria flourishes on. Some plants, like sunchokes, garlic, and leeks, are packed with prebiotics. Bananas and whole-wheat breakfast cereals are other good sources. (Related: This Study About Fiber-Rich Carbs Might Make You Rethink the Keto Diet)

Snack smarter. The fact that we consume so much added sugar—more than 22 teaspoons a day for the average person—could actually be starving our gut flora, says Sonnenburg. Bacteria need complex carbohydrates, like legumes and whole grains, in order to thrive. So when you get too many calories from sweets, you’re leaving your microbes hungry. They either die or adapt by feeding on the mucus inside your intestine, which, experts hypothesize, could contribute to low-level inflammation, a condition that has been linked to obesity. Instead of grabbing a cookie when your stomach starts growling at 3:00 p.m., reach for a handful of nuts or an apple. Check labels for hidden sugars in foods like pasta sauce and salad dressing. And choose brown rice and whole-grain pasta instead of white.

Pick probiotic foods. If prebiotics are like fertilizer for your microbial garden, probiotics are like seeds. The best way to get them is by regularly eating fermented foods such as yogurt, kefir, sauerkraut, and miso. And about yogurt, that probiotic rock star: A landmark study in the New England Journal of Medicine reported that among all foods studied, yogurt was the one most strongly correlated with weight loss. The average person gained almost a pound a year, but people who regularly ate yogurt actually lost weight. Choose plain Greek yogurt and mix in pomegranate seeds or your favorite berries for a hit of fiber. (Related: 5 Legit Benefits of Probiotics)

Move your body. Your bacteria might benefit from a good workout as much as you do. Exercisers with a normal BMI had more diverse microbes than exercisers with a high BMI, according to an Irish study of male rugby players. They also had higher levels of Akkermansiaceae, a type of bacteria that has been linked to lower obesity rates. So sweat daily to trim your gut—and to boost your gut bacteria.

  • By Laura Beil and Renee Cherry

Do gut bacteria inhibit weight loss?

Ask the doctor

Published: January, 2018

Q. I just can’t lose weight. A friend says that my problem might be due to the types of bacteria that live in my gut. That sounds crazy to me, but is it true, and can I do something about it?

A. Ten years ago, I also would have thought your friend was crazy. Today, I’d say she could well be right. Here’s why. We’ve known for a century that bacteria live in our intestines, but we’ve assumed that they did little to affect our health. We thought that they were just mooching off of us — taking advantage of the warmth and nutrients in our gut.

In the past decade, however, remarkable breakthroughs have allowed scientists to count and characterize the genes in our gut bacteria. The results have been astonishing. Our gut bacteria have 250 to 800 times more genes than we have human genes. Even more remarkable, these bacterial genes make substances that get into the human bloodstream, affecting our body chemistry. That means it is entirely plausible that the bacteria in our gut could be affecting our health.

How could they affect our weight? When we eat food, our gut breaks it down into small pieces. Only the smallest pieces get absorbed into our blood. The rest is eliminated as waste material. In other words, not all of the calories in the food we eat get into our body and increase our weight. The gut bacteria help break down food. Some bacteria are better able to chop food into those smallest pieces that get digested, add calories to our body and thereby tend to increase our weight. Theoretically, if our guts have more of those kinds of bacteria, it should be harder to lose weight.

But is there evidence that it really is true? Several studies in animals, and some in humans, say that it is. For example, scientists transferred bacteria from the guts of two strains of mice — one that naturally becomes obese and one that naturally stays lean — into a third lean strain raised from birth to have no gut bacteria. Gut bacteria transferred from the naturally obese mice made the germ-free mice become fat, but gut bacteria transferred from the naturally lean mice kept them lean.

Then scientists took bacteria from the guts of human identical twins, one of whom was obese and one of whom was lean, and transferred those bacteria into the guts of lean, germ-free mice. Bacteria from the obese twin made the mice become fat, but bacteria from the lean twin did not.

We are just beginning to understand the role of gut bacteria in obesity, and the science hasn’t led yet to treatments that will make it easier to lose weight. However, I believe that day is coming.

— by Anthony L. Komaroff, M.D.
Editor in Chief, Harvard Health Letter

Based on a solid foundation of current nutrition science, Harvard’s Special Health Report Healthy Eating: A guide to the new nutrition describes how to eat for optimum health.

Image: © ChrisChrisW/Thinkstock

As a service to our readers, Harvard Health Publishing provides access to our library of archived content. Please note the date of last review on all articles. No content on this site, regardless of date, should ever be used as a substitute for direct medical advice from your doctor or other qualified clinician.

Weight loss is easier with a friend…so how about a few trillion of them?

Granted, these particular friends aren’t very sociable, and they probably won’t like any of your meal photos on Instagram. But they sure can help you lose weight in the least painful way possible.

If you haven’t figured it out by now, the “friends” are the bacteria (and other wee beasties, but they’re mostly bacteria) that live in your gut. They’re also called the gut microbiota, the gut flora, or “gut bugs.” You can learn all about them at our gut portal here.

Gut bacteria affect your weight in a couple ways. This review is free to read and runs through all of them exhaustively if you want to really get into it, but here’s the short version:

  • They change how much energy you get from your food. Some people “waste” a lot of calories from their food because they have gut bacteria that are really inefficient.
  • They affect inflammation. Inflammation drives fat accumulation in ways that are too complicated to go into detail about here, but here’s a whole paper on it if you’re interested.
  • They affect feelings of hunger and fullness.
  • They affect insulin sensitivity and metabolic health.

So if you’re trying to lose weight, you really want all these guys on your side. Here are 6 ways to make that happen:

1. Go to Bed

Sleep deprivation is one of the worst things you can do for your gut bacteria. In this study, researchers took normal-weight men and let them sleep only from 2:45 to 7 AM (that’s about 4 hours) for two nights in a row. After just two nights of partial sleep deprivation, the men had a bunch of changes in their gut bacteria that are associated with different metabolic problems. They also had lower insulin sensitivity.

This study was in mice but still interesting. The researchers subjected the poor mice to chronic “sleep fragmentation,” otherwise known as “having a really terrible night of sleep where you kept waking up.” At the end of 2 weeks, their gut bacteria looked bad. And to go with their gut problems, they had more inflammation in their fat tissue, more fat tissue, lower insulin sensitivity, and significant gut barrier disruption. Ouch. Don’t be these mice: get enough sleep!

This study took another approach: it linked shift work to obesity through the gut bacteria. It’s well-known that shift work is associated with obesity, and this study offers some evidence that the reason has to do with the gut bacteria. Because shift workers sleep for less time on average, their gut bacteria are disturbed, making them more susceptible to weight gain and metabolic disease.

Long story short: if you want your gut on your side for weight loss, go to bed.

2. Consider Intermittent Fasting

The bacteria that live in your gut have a circadian cycle – different species are more prominent at different types of day. In obesity, that cycle is blunted. (If that sounds familiar, it might be because the circadian rhythm of the hormone cortisol is also often blunted in obesity). But it turns out you might be able to get the circadian gut cycle up and running normally again with some clever food timing.

In this study, the researchers first took a bunch of mice and made them really fat by feeding them junk food. Then they tried a time-restricted diet, where the mice were only allowed to eat during their natural feeding periods (for mice, that’s night time, but for humans, the equivalent would be only eating during the day – no midnight snacking). The time-restricted feeding partly restored the normal circadian cycle of gut bacteria, especially species involved in metabolism. And it helped reduce body fat percentage in the time-restricted mice.

It’s one mouse study. It’s not conclusive proof of anything – but there are also all kinds of other benefits to intermittent fasting, or at least not eating a lot of junk food at night. It might be worth considering as an addition to your weight-loss plan.

3. Eat a Variety of Vegetables

When they first start out with Paleo, some people like to make the same meals all the time. It’s easy, it’s pretty mindless, it saves time on prep and shopping, and it builds a healthy routine. But meals based on this template tend to revolve around a limited set of vegetables. And that can be less than ideal, because it means that you’re getting a pretty repetitive diet where fiber is concerned.

Even all-stars need a team supporting them to actually win the game.

Fiber is food for your gut bacteria. Whatever types of bacteria you feed, those are the types that will grow. So if you’re always eating the same type of fiber, you’ll get a fairly limited range of gut bacteria. Unfortunately, bacterial diversity is probably best for weight loss, and one of the best ways to get there is to eat a wide variety of fiber types.

Here’s a way to do that without adding a lot of difficulty to your cooking routine: group vegetables by how you like to cook them. For example:

  • Roasting vegetables: beets, squash, cauliflower, eggplant…
  • Pan-frying vegetables: onions, mushrooms, spinach, kale…
  • Raw vegetables: carrots, salad greens…

You can adjust the categories as necessary or put one vegetable in more than one category. But the idea is to plan your meals based on category, not on a specific vegetable type. For example, Thursday dinner could be “chicken thighs + roasting vegetable,” not specifically chicken thighs with beets. That way you can get more diversity in vegetables without changing much about your cooking routine or adding any difficulty.

(The obvious caveat to this: some people have sensitivities to certain carbohydrates, like FODMAPs carbohydrates. In that case, it may be better to hold off on those until your gut can handle them.)

4. Be Consistent About Your Diet

As this review discusses, short-term dietary interventions do change gut bacterial composition…in the short term. You can put people on any kind of extreme diet and watch their gut bacterial composition go crazy. But the short-term changes don’t last. Gut bacteria are remarkably resilient and always happy to go back to “normal” – which in this case is based on whatever you usually eat.

This means that cultivating healthy gut bacteria takes consistency. Whatever diet works for your gut, eat that way consistently and regularly. It takes a while to get your gut bacteria to recognize something as the “new normal.”

5. Go to the Gym

There are all kinds of reasons why exercise is good for you. It’s great for weight loss even though it doesn’t burn a lot of calories – burning calories isn’t the point. But one of the many reasons why exercise is helpful is that it makes your gut bacteria happy. There’s not a lot of research studying this in humans – mostly just this study finding that exercise is associated with greater microbial diversity in the gut, which is great, but it’s one study and it’s just proving an association. There’s a lot more evidence from rat studies and mouse studies showing that exercise alters the composition of the gut microbiome in ways that help the rats and mice stay lean (or lose weight, if they’re already obese).

But the reason that exercise makes it onto this list is this study. It was in mice, but the results suggested that the benefits of exercise are totally different from the benefits of changing your diet. So there’s at least some evidence that exercise and diet aren’t just interchangeable in this regard, which is a pretty good argument for doing both.

6. Take a Probiotic with Lactobacillus Strains

N.B. all the usual caveats about supplements apply to probiotics – there’s a huge amount of fraud out there, so don’t waste your precious money on junk and fakes.

Probiotics basically add some healthy bacteria to your gut. There’s an enormous range of probiotic species available in supplement form, but this review suggests that Lactobacillus strains are probably the ones to look for. Those are the probiotics that get results like reductions in body weight, and more importantly, body fat. Or better cholesterol profiles in people with Type 2 diabetes.

As the name suggests, Lactobacilli are mostly associated with fermented dairy products, but you can get them in dairy-free probiotic supplements, too.

What are your strategies for getting your gut bacteria on board with your weight loss efforts?


While we’ve long looked to our poop to find out about our microbiome, a new study makes that link actionable by identifying the bacteria responsible for weight loss. “Human intestinal bacteria have been linked to the increasing prevalence of overweight and obesity, and scientists have started to investigate whether the intestinal bacteria can play a role in the treatment of being overweight,” explained the study’s author, professor Arne Astrup, head of the Department of Nutrition, Exercise, and Sports at the University of Copenhagen, Denmark (he shared many of the findings of his remarkable weight-loss research with mbg back in April). “But it is only now that we have a breakthrough demonstrating that certain bacterial species play a decisive role in weight regulation and weight loss.”

The study divided 54 people into two groups. For 26 weeks, one of these groups ate the New Nordic Diet, while the other consumed a standard Danish Diet. The New Nordic Diet (similar to a Mediterranean eating plan) focuses on plant-based foods, seafood, and canola oil, while the Danish Diet limits to only two food groups—protein and vegetables—and cuts out all fruit, whole grains and dairy products. The group eating the New Nordic Diet lost roughly double the weight of the other group.

Here’s where it gets interesting: The subjects were then divided by their level of gut bacteria. People with a high proportion of Prevotella bacteria in relation to Bacteroides bacteria lost 3.5 kg more during the duration of the study by eating the New Nordic Diet, while subjects with a low proportion of Prevotella didn’t lose any weight. Roughly 50 percent of the population has the bacteria makeup identified to aid weight loss in the study.

“The study shows that only about half of the population will lose weight if they eat in accordance with the Danish national dietary recommendations and eat more fruit, vegetables, fibers, and whole grains. The other half of the population doesn’t seem to gain any benefit in weight from this change of diet,” explained assistant professor Mads Fiil Hjorth, who co-authored the study.

While we haven’t yet identified the role of all of the bacteria in the gut, the study shows a glimpse of a future where people can use personalized bacteria profiles (garnered, likely, from their feces) to custom tailor their diets for maximum health results. Bacteria profiling is already available (our health editor had her microbiome sequenced—here’s what she found out), and scientists are making strides in identifying new correlations daily.

Want a great poop every time? Sip this gut-healing apple cider vinegar tonic daily.

Is There A Link Between Gut Bacteria And Weight Loss?

There’s no such thing as skinny bacteria or fat microbes, but your gut bugs still help regulate metabolism, nutrient absorption, and weight management.

It can be frustrating to watch friends eat whatever they like, do very little exercise, and still look fit. Yet, it might not just be amazing metabolic powers, because gut bacteria and body weight are linked in many ways. Read on to find out how.

Table of contents

  • Gut bacteria and weight loss 101
  • Microbes for weight loss: do they exist?
  • How to change your gut bacteria to lose weight
  • Gut health and weight gain: food matters
  • Bad gut bacteria and weight gain: antibiotics
  • How to improve gut bacteria for weight loss
  • Colourful foods for microbiome and metabolism
  • Gut flora weight loss: the hard and honest truth
  • The microbiome acts indirectly on body weight

Gut bacteria and weight loss 101

Your gut microbes may help you to maintain a healthy body shape and even hold the answer to why some of us are protected from obesity.

Your large intestine is a haven for trillions of mutually beneficial microbes that make up your gut microbiota. These gut bacteria form an ecosystem involved in vital functions like metabolism, hunger, and digestion.

Even though it doesn’t always receive the recognition it deserves because humanity has feared microbes since their discovery, your microbiome is important for many aspects of your body, including your weight.

In particular, a diverse gut microbiome is beneficial for your health. That’s because different types of bacteria perform a variety of jobs in your colon, and thus, microbial diversity helps control your metabolism and in turn, your body weight.

However, if your intestinal environment is imbalanced, it can cause what is known as dysbiosis, and that’s not good for anyone. It can mean that you have lower levels of beneficial bacteria, more opportunistic pathogens, or reduced diversity – all of which can have an impact on your body.

Altogether, this can negatively impact your health and may even explain why you put on weight more easily than other people. But like your weight, gut microbial health is also influenced by your lifestyle. That’s right, food and exercise are also important for the diversity of your gut bacteria.

Microbes for weight loss: do they exist?

Search for skinny gut bacteria and you’ll actually read about microbes that reinforce the gut lining and modulate your metabolism.

Two gut bacteria are associated with lean body weight. Akkermansia muciniphila and Christensenella minuta are good gut bacteria for weight loss because they are linked with preventing weight gain and are often found in slim individuals.

Akkermansia can feed on the mucus that lines your gut, promoting its production which strengthens your intestinal barrier (a weaker gut lining is detected in people with obesity). These microbes also produce acetate, a short-chain fatty acid that helps regulate body fat stores and appetite.

You can try boost the abundance of A. muciniphila with prebiotic foods that fuel their activities. You probably eat some of these anyway, but increasing your intake could help the growth of Akkermansia in your gut and enhance your protection against obesity.

Foods to boost Akkermansia

  • Cranberries
  • Concord grapes
  • Black tea
  • Fish oil
  • Bamboo shoots
  • Flaxseeds
  • Rhubarb extract

Christensenella is also an emerging gut microbe associated with weight control. Like Akkermansia, it is abundant in the microbiomes of lean people, and scientists think it could be promising for preventing obesity, which is now considered a global health epidemic.

Christensenella is associated with your genetic makeup, meaning that to some extent, you have higher chances of finding this bacterium in your gut if your relatives have them too. Some people don’t have them, and that’s okay.

Only a microbiome test can accurately check your gut bacteria

So if your Atlas Microbiome Test didn’t detect any, don’t worry. You can still have a healthy microbiome without them because there are lots of other beneficial and probiotic bacteria that help regulate your metabolism.

However, strictly speaking, there are no weight loss bacteria. Instead, there is evidence that microbes indirectly act on our body fat composition. Researchers are already investigating how to manipulate gut health for weight loss purposes, so more findings are likely to emerge very soon.

☝️FACT☝️There’s no such thing as fat bacteria or skinny bacteria, what matters is microbiome composition, beneficial microbes, and functions.

How to change gut bacteria to lose weight

Beneficial gut microbes are happy to trade plant-based foods and healthy fats for their health-promoting services.

Getting 30g of fiber every day from plants of different colours (think red peppers, orange pumpkin, purple carrots, etc.) may also help diversify your microbiota which is good for your overall health.

This was shown by the results of the American Gut Project, in which people who ate 30 plant foods of different colours per week had the greatest microbiota diversity. You can read more about these foods in our guides:

  • Red Foods: Guide To Health Facts, Food Lists And Recipes
  • Orange Foods: Guide To Health Facts, Food Lists And Recipes

Rainbow plant foods contain many different phytonutrients, like polyphenols, that help the body prevent free radical damage and inflammation. They also contain a variety of fibers for gut health. Both of these also nourish beneficial bacteria in the microbiota.

Gut health and weight gain: food matters

So, we now know two types of bacteria that prevent obesity, but what about gut bacteria and weight gain? Simply put, what you eat is a huge factor. In fact, changing your diet won’t just change your weight, it’s the fastest way to change your microbes too.

There are links between gut bacteria and weight. The gut microbiota of individuals who are overweight show patterns of dysbiosis compared to healthy individuals.

Ultimately, this is associated with inflammation and increased blood sugar levels because there is a greater extraction of energy from food. Equally, these two factors are linked to being overweight or obese, and so to is the Western diet because of its high levels of sugar and fat.

Research has also shown that following a natural plant-based diet reduces calorie intake, increases weight loss, and lowers metabolic markers. It also nourishes beneficial gut bacteria because plants contain lots of different prebiotic fibers.

In a study involving type II diabetes patients, a vegan diet was shown to be more effective at controlling blood sugar levels than a usual diabetic diet. And, in the plant diet group, calorie intake was lower, which meant weight loss was more rapid. Interestingly, the beneficial bacteria that thrive on plant foods are also associated with better blood sugar control.

Bad gut bacteria and weight gain: antibiotics

Dysbiosis of the gut microbiome can result from other factors too, like antibiotics. This type of medication is linked to weight gain because they disrupt the microbial communities in your gut, either by preventing and slowing bacterial growth, or killing them.

Yet, the link between antibiotics and weight gain isn’t really a secret. Industrial agriculture has known for decades that low doses of antibiotics can encourage animals destined for meat consumption to gain weight faster.

This experiment that has been replicated in mice, who share many similar microbiome and biological traits with humans. These findings have led scientists to believe that antibiotics help explain the striking increase in childhood obesity in recent years.

What is obesity and overweight by Mia Nacamulli for Ted Ed

Indeed, there’s plenty of evidence indicating that the microbial disruptions caused by antibiotic use is linked to the world’s obesity problem. Research has shown that being exposed to antibiotics early on in life can lead to long-term disruptions in the gut microbiome, causing metabolic changes as you grow and develop.

That’s because antibiotics don’t only act on a specific type of bacteria. So when your doctor prescribes them for a bacterial infection (if you follow the instructions carefully) the bacteria making you sick should be eliminated, but it can also affect your other microbes, including the beneficial ones.

☝️FACT☝️ Antibiotics can induce changes in the gut microbiome that can be detected 6 months and even two years after taking them.

How to improve gut bacteria for weight loss

Now that you know why diet counts for body weight and your gut bacteria, it’s time to talk about physical activity. Because when it comes to exercise, people who lead a sedentary lifestyle tend to have a microbiome which lacks diversity compared to people who regularly get their sweat on.

Aerobic exercises, the ones that get your heart pumping – like walking, jogging, swimming, cycling, and dancing – increase the abundance of health-promoting bacteria like Bifidobacteria, Faecalibacterium prausnitzii, and Akkermansia muciniphila.

By doing so, you support gut barrier function, which can help prevent inflammation. These microbes also maintain the gut environment which provides stability for good gut bacteria and deters potential pathogens, all of which reduce the risk of dysbiosis and help alleviate gut microbial imbalances that are associated with being overweight.

Exercise also helps stabilise your metabolic markers, like blood glucose and blood lipids, at healthy levels and trains your muscles to consume more energy. This also helps regulate your body fat. That’s why regular physical activity helps you lose weight and stay lean.

Eat the rainbow for good gut bacteria

Put more colour in your diet to achieve a diverse microbial community in your gut, and at the same time, keep your metabolism in check too!

Eating plenty of fruits, vegetables, and whole grains is vital for your health, yet many of us are not eating enough. In fact, the western diet is so low in fiber that 73% of British people consume less than the recommended 400g of fruit and vegetables per day according to a 2014 study.

It’s called a phytonutrient gap. These natural plant chemicals are beneficial to our health and beneficial gut microbes. Fortunately, with a little effort, these foods can be easy to incorporate into your diet.

Colourful foods for microbiome and metabolism

Colour Foods Benefits
Red Apples, cherries, cranberries, red onion, tomatoes, red cabbage Anti-inflammatory properties, antioxidants, immune system support, abundance of good gut bacteria
Yellow Apples, bananas, lemons, ginger, yellow onions, corn Antioxidant properties, increase gastric emptying, healthy gut microbiome, reduces blood sugar balance
Orange Oranges, apricots, mangoes, carrots, turmeric, yams Antioxidant effects in fat soluble tissues, abundance of healthy gut bacteria, fertility
Green Brussels sprouts, green tea, olives, green apples, artichokes, greens, cabbage Antioxidant properties, healthy blood circulation, abundance of good gut bacteria
Blue-purple Blueberries, blackberries, prunes, purple grapes, purple cabbage, purple kale, plums Antioxidant properties, sustenance for beneficial gut bacteria

There is a lot of research that shows long-term weight gain is associated with a gut microbiome that lacks diversity – not consuming enough dietary fibre is a contributing factor to this. Luckily, by increasing your intake of rainbow foods, you can support your whole body, a healthy weight, and your gut microbes all at once.

Gut flora weight loss: the hard and honest truth

It’s not as simple as change your gut flora and lose weight. Rather, it’s the impact these microbes have on your body that affects weight loss.

Your gut bacteria have roles in your digestion, fat storage, and hunger, all of which can have major impacts your weight. But you can’t simply change gut bacteria and lose weight. No matter what you’ve read elsewhere, we’ve done the research, and it’s not a quick fix solution.

Changing gut bacteria to lose weight

Let’s face it, you’ve probably already googled “which gut bacteria cause weight loss”, and found a whole list of bacteria names or tips. But take it from us and our team of microbiome researchers (who have PhDs and many published scientific papers to their names), healthy and sustainable weight loss can be achieved with healthy eating habits, no by starvation diets and supplements.

There’s no magic bullet, spend your time and money on real food instead

Sadly, it’s true. There’s no such thing as a weight loss gut bacteria supplement (so please don’t buy one). The fastest way to have a significant and lasting positive impact on your microbiome is to eat a healthier diet with lots of fruit and veg, and importantly, less refined sugar, artificial sweeteners, and meat.

Basically, gut bacteria won’t directly cause you to lose weight. Instead, it’s the effects of their activities rippling through your body which can help lose, gain, or maintain your weight because they help determine how much energy your body absorbs, and also how hungry or full you feel.

The microbiome acts indirectly on body weight

Research shows that the composition of our gut microbiome has a role in regulating our body weight. It is estimated that 60% of the variation in our microbiota (compared to other people’s) is a product of your environment, especially diet and antibiotics.

Plus, there are distinct differences in the composition of the microbiomes of healthy people and those who are obese, or have another metabolic disorder like type 2 diabetes. For example, diabetic individuals tend to have lower abundances of butyrate-producers in their gut.

These microbes break down dietary fibre and turn it into the short-chain fatty acids, some of which have anti-inflammatory functions. However, the western diet is notoriously high in refined sugar, animal fat, and very little plant-based sustenance.

Research also shows that butyrate has an important role in protecting us from inflammation, maintaining a healthy gut lining, and most importantly, regulating our metabolism and food intake. It does this by stimulating the release of gut hormones which signal to our brain that we feel full.

If you don’t have a gut rich in butyrate producers, it may actually be telling you you’re hungry, making you eat more (potentially unhealthy) foods to satisfy your hunger. Over the long term, this can encourage symptoms like high blood sugar levels and insulin resistance.

Gut flora and weight loss: The Take Home Message

Your gut microbiome is pretty special, and it’s completely unique to you. Ultimately, that means you have a great level of control over its composition and diversity. So when it comes to gut bacteria, weight is a modifiable factor.

Your lifestyle has a real impact on the diversity of your gut microbiome and your susceptibility to weight gain and obesity. Eating more plant-based foods, prebiotic fibres, and doing more physical activity can enhance your gut microbial function.

By doing so, you can increase the abundance of health-promoting bacteria, as well as their beneficial functions. And it’s this which will enable you to maintain a healthy weight, because your gut barrier will work effectively to protect you from inflammation and rising metabolic markers.

☝TIP☝Discover your gut bacteria’s butyrate, dietary fiber, and obesity protection levels with the Atlas Microbiome Test.

The Microbiome and Weight Gain: Everything We Know So Far


In our grandparents’ times, obesity was a rare occurrence. This has changed over the past four decades. According to the World Health Organization, obesity has almost tripled since 1975. Today, more than one-third of the world’s population is either overweight or obese. While this was more prevalent in first-world countries, it is now common in most parts of the world. Currently, obesity and being overweight kills more people than undernourishment. There is also an alarming rise in obesity among children. It has become a global epidemic.

Our understanding of obesity until the last decade indicated that it was a function of lifestyle choices. It is true that obesity is more prevalent in the western world. Immigrants and indigenous populations show higher rates of obesity after being introduced to a western diet. Until recently, obesity was only associated with an individual’s food choices. This implied that obesity was a matter of choice alone.

Recent studies say that there may be more to obesity than a simple choice. Researchers examined the gut microbiome of obese and non-obese individuals. They found that the gut microbiome of obese and non-obese individuals is different. This difference dictates how the body uses energy from the food we consume. It also indicates that obesity is not just a matter of food choices. It is instead a matter of how gut bacteria process that food. This shifts how we look at obesity, as a disease rather than a consequence of poor food choices.

To understand how the gut microbiome and obesity are connected, let’s take a closer look.

The gut microbiome

Our gut is home to trillions of microorganisms. There are 300 to 500 different kinds of bacteria living in our digestive tract. These contain almost 2 million genes. These bacteria, along with other microorganisms like virus and fungi, make up our gut microbiome. The gut microbiome plays a key role in digesting the food we eat and absorbing and synthesizing nutrients from our food. Several factors influence the composition of the gut microbiome in each individual. These factors include the microbiome we inherit from our mother’s body, our diets, and our lifestyle. The microbiome, in turn, affects different aspects of our body like our metabolism, mood, and immune system. Find out what your gut microbiome looks like.

The link between weight gain and the gut microbiome

Recent research into the role of the gut microbiome in obesity has uncovered some fascinating links. One study exploring this link examined the gut bacteria in obese and lean mice and human volunteers. They found that the relative abundance of two dominant types of bacteria, Bacteroidetes and Firmicutes, was different in obese and lean subjects. They further investigated the effect of this difference in gut microbiota in mice. They found that changes in gut microbiota affected metabolism. The microbiome in obese mice could harvest more energy from food than their lean counterparts. They also found that this effect could be transmitted. Colonizing lean mice with microbiota from obese individuals significantly increased total body fat. This study indicates that the gut microbiome plays an important role in obesity. (1,2) It shows that changes in the gut microbiome have a significant impact on metabolic function.

Several other studies show the effects of the gut microbiome on insulin resistance, inflammation, and fat deposition in the body (3). They also show that gut microbiota responds to weight loss (4).

It is clear that the microbiome regulates several vital functions in the body, and alterations in gut microbiota have significant effects on health and well-being. What alters the gut microbiome? Dietary composition and caloric intake seem to affect gut microbial function quickly. Antibiotic use has been shown to decrease gut bacterial communities. (5) The mode of delivery during childbirth also influences the gut microbiome.

What this means for you

We know that environmental factors alter the gut microbiome. An altered gut microbiome can lead to changes in metabolic function and, as a result, cause obesity. To find out what your gut microbiome looks like, order your Gut Intelligence Test and find out what foods are right for your body in order to optimize your gut microbiome.

  1. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031

  2. Ley, Ruth E et al. Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America vol. 102,31 (2005): 11070-5.

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Gut Bacteria and Weight Loss: What You Need to Know

  • Your gut is full of more than 1,000 species of bacteria. Research shows that obese and lean people have different types of bacteria in their gut.
  • Changes in your gut bacteria impact your metabolism, how effectively your body turns food into energy, and your overall body fat.
  • If your gut bacteria are causing inflammation and hormonal imbalances, it’ll show up on the scale.
  • To support your gut health, follow a low-toxin, high-nutrient diet and experiment with gut-healing synbiotic supplements.

Not losing weight? Blame your stubborn gut bacteria. A growing body of research says that your gut microbiome affects your entire body, from your hormones to your metabolism. If your gut is out of whack, those stubborn bacteria can hamper your weight loss efforts and keep you from feeling your best. Here’s what you need to know, plus tips to take back control of your gut health.

The science behind gut bacteria and weight loss

Your gut is full of more than 1,000 species of bacteria, all of which work together to digest your food, keep your immune system strong, and remove toxins. Everyone has a unique gut microbiome, which is affected by everything from your diet to your genes. Your weight is another key factor.

Research has found that obese and lean people actually have different types of bacteria in their gut. In a 2016 study, researchers compared the gut microbiomes of obese and lean volunteers. The lean group had more diverse, anti-inflammatory gut bacteria. In comparison, the obese group had significantly more inflammatory gut bacteria and less bacterial diversity.

Other researchers have found similar results. One study put genetically-similar mice on a high fat diet. The mice gained or lost weight depending on the types of bacteria in their gut. Another study looked at 77 pairs of twins — one twin was obese, the other wasn’t. The researchers found that the obese twin had different gut bacteria — as well as less bacterial diversity — than their non-obese twin.

How your gut controls your waistline

As more and more research points to the relationship between your gut health and your weight, the next natural question is: Why? How can a bunch of microscopic organisms decide whether or not you fit into your pants?

Changes in your gut bacteria impact your metabolism, how effectively your body turns food into energy, and your overall body fat.Studies have found that a diverse mix of bacteria in the gut is key to staying thin, and naturally slender people have more of a bacteria from the Bacteroidetes phylum. Obese people have more Firmicutes bacteria in their guts, which is correlated with weight gain.

Here are some possible explanations:

  • Firmicutes consume more energy than Bacteroidetes, which means obese people may absorb more calories from food than lean people — even without a change in diet.
  • If your gut bacteria are causing inflammation, that’ll show up on the scale. Inflammation can lead to digestive conditions like leaky gut, autoimmune disease, and even mood disorders.
  • Hormonal imbalances can impact how full you feel after meals, drive you to binge on foods when you’re stressed, and even make you store fat. Learn more about what your body type says about your hormones.

How to hack your gut bacteria for weight loss

Good news: You have the power to take control of your gut and support a thriving, healthy digestive system.

If you think your gut microbiome is off-kilter, , a downloadable guide to troubleshooting your microbiome. You can take a quick quiz to find out what’s throwing you off, and get a clear action plan on how to fix it. Remember, if you’re dealing with chronic digestive issues, talk to your doctor.

Eat your vegetables (and chocolate)

Help your beneficial Bacteroidetes bacteria thrive by eating foods bursting with antioxidants called polyphenols. Polyphenols are found in brightly colored vegetables, coffee, and chocolate.

You’ll also want to cut the sugar and starch to starve the bad gut bacteria. Here’s why: Gut microbes make a hormone called FIAF (fasting-induced adipose factor) which tells the body to stop storing fat and burn it instead. To ramp up FIAF production, ditch the candy and white bread. When bacteria are “hungry,” they make more FIAF, and you burn fat.

A low-toxin, anti-inflammatory, high-nutrient diet will help good bacteria thrive and keep the bad guys at bay. The Bulletproof Diet is a great place to start.

Experiment with synbiotics

You might have heard of probiotics, or gut-boosting microorganisms found in fermented foods like kefir and sauerkraut. Not a lot of people know that these microorganisms need to feed on prebiotics in order to flourish. Prebiotics are a type of fiber you can find in foods like asparagus and artichokes.

For the best of both worlds, add synbiotic supplements to your routine. Synbiotics combine probiotics and prebiotics into one gut-friendly supplement that helps good gut bacteria thrive. Taking care of your digestive health is a big deal in a world where everything from stress to industrial meat impacts your gut microbiome. Even something as simple as antibacterial soap can make bad bacteria more resilient.

These tips are just a start. Keep reading to learn how to balance your gut flora so you can feel awesome all day long.

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