MealEnders Blog

Maintaining Your Microbiome for Health and Weight Loss

By MealEnders
July 18, 2017

Microbiome diet

Chances are, you’ve heard of probiotics: the beneficial bacteria that naturally inhabit the human gut. They’re found naturally in several food products, like yogurt, kefir, kimchi, and miso, as well as in supplement form; but they’re also popping up in processed food products like chips, juices, and snack bars. Research has shown that probiotics can boost health in a number of ways, from improving digestive health to boosting mood. And in the past few years, research has found that probiotics may also play a role in body weight and metabolism.

First, a refresher: probiotics are just one group of bacteria that make up your microbiome, the collection of microorganisms (both good and bad) that live in and on the human body. A well-balanced microbiota plays a variety of roles in the human body, including providing immune support, inhibiting the colonization of harmful pathogens, breaking down indigestible carbohydrates, synthesizing vitamins, moderating mood and cognition, and metabolism of nutrients. Alterations to the microbiome, including antibiotic use, quality and diversity of diet, exercise, and smoking, can upset this balance, leading to dysbiosis. An altered microbiome has been implicated in a number of consequences, including inflammatory bowel disease and obesity.

Several studies1,2,3 led by Peter Turnbaugh, PhD and Assistant Professor at UCSF studying the impact of the human gut microbiome on pharmacology and nutrition, have found that the microbiomes of normal weight adults versus obese adults are very different. The studies looked at two of the most prevalent families of bacteria in the gut: bacteroidetes and firmicutes. Specifically, obese individuals tend to have more firmicutes and fewer bacteroidetes than normal weight people. What’s more, when obese individuals followed low calorie diets and lost weight, their microbiome began to resemble that of a normal-weight person’s.1 Another study found that when obese individuals added a probiotic drink into their diet, they showed significant reductions in body weight, BMI, waist and hip circumference, and body fat mass.4

How exactly can probiotics regulate weight? It used to be a commonly held belief that weight loss was a matter of calories in and calories out: if you burn more calories than you eat, you’ll lose weight. But it turns out that it’s not so simple: there are factors that affect how your body metabolizes those calories that are coming in. One of those factors may be the microbiome: your gut flora may play a role in how your body extracts calories from food. For example, one strain of probiotics–Lactobacillus gasseri SBT2055–has been found to inhibit the absorption of dietary fat, thereby reducing the amount of calories your body absorbs.4,5,6 Other studies suggest that probiotics may also influence hormones, like glucagon-like peptide 1 (GLP-1). GLP-1 inhibits gastric secretion and motility, delaying the absorption of carbohydrates and thus contributing to satiety.7 In addition, obesity has been linked with inflammation–and probiotics can moderate inflammation.8 Despite these suggested mechanisms, more research is needed to explore the ways by which probiotics affect nutrient absorption.

Further complicating matters is the fact is that not all strains of probiotics are beneficial. In fact, some research implies that certain strains may promote weight gain, not loss. Certain lactobacillus strains, including L. acidophilus and L. fermentum, were associated with weight gain in both humans and animals.9 L. acidophilus is a strain that is particularly prevalent in the US and is found in acidophilus milk (meant for lactose intolerant individuals) and some yogurts. And many studies fail to show any weight-reducing benefits of probiotics whatsoever.10

It’s important to remember that much of this research is new, and more studies should be done to replicate these findings. And, of course, adding probiotics to your diet isn’t the silver bullet for weight loss. If you are thinking of adding probiotics–in food or supplement form–here are our recommendations:

Choose a strain with research to back it up. Lactobacillus gasseri is one of the most promising strains for weight loss. In one human study, adults who drank milk with L. gasseri for 12 weeks experienced reductions in weight, visceral fat, and waist and hip circumference.4 When they stopped taking the supplement, however, they gained back the weight–indicating that supplementation should be constant. L. gasseri can be found in many fermented foods, including miso, kefir, sauerkraut, and tempeh. Another product that has promising research behind it is VSL#3, a probiotic supplement made of 8 different strains. VSL#3 may actually help protect against weight gain: in a 2015 study, non-obese participants who supplemented with VSL#3 and ate a high-fat, hypercaloric diet–which required them eating 1,000 extra calories per day–gained less fat and total weight compared with those who did not take the probiotic strain.11 VSL#3 probiotic supplement is a proprietary combination of beneficial bacteria and is not found naturally in foods (although its 8 strains appear in a number of fermented foods); currently it’s available online and at certain pharmacies

Eat plenty of fiber. In order for probiotics to thrive, they need a constant supply of prebiotics, indigestible food components that act as food for and stimulate the growth of probiotics. Prebiotics are a type of fiber that remain undigested as they travel through the upper GI tract; in the lower GI tract, they are fermented by probiotics. Rich sources of prebiotics include chicory root, dandelion greens, and jerusalem artichoke, but they’re also found in more commonly eaten foods like oats, barley, bananas, asparagus, apples, leeks, onions, and garlic. If you’re already eating a diet high in vegetables, whole grains, and legumes, you’re likely already getting enough prebiotics in your diet. If you’re not, aim to increase your fiber intake to reach the recommended minimum amount of 25 and 38 grams per day for women and men, respectively. If you’re working up to this amount, start slowly–adding too much fiber at once can cause GI distress and bloating!

Limit added sugars and harmful fats. The health of your microbiome depends not only on the presence of probiotics, but also on the absence of harmful bacteria. Harmful bacteria thrive on food too: research has found that both high-fat and high-sugar diets can change the composition of the microbiome within just one day, leading to changes in microbiome gene expression and adiposity.12 Artificial sweeteners may also negatively influence the microbiome: in one study, the consumption of artificial sugars in both mice and humans increased the risk of glucose intolerance (elevated blood sugar levels that can be a precursor to diabetes), a characteristic of metabolic syndrome.13

In addition to supplements, add a wide range of probiotic-rich foods to your diet.  Beneficial bacteria found in foods and supplements frequently come from the genera Lactobacillus and Bifidobacterium. With probiotic supplements, you can select a single specific strain to add to your health regimen. Foods don’t offer that type of specificity, but typically provide more than one type of probiotic at varying levels of concentration.  For general health, a variety of probiotic-rich foods can support a healthy microbiome (plus, most probiotic-rich foods have other nutritional benefits).  In addition to yogurt, kefir, kimchi and miso, try adding tempeh, buttermilk, natto, pickles, kombucha, and sauerkraut to your diet.  Cheeses such as mozzarella, Gouda, cheddar and cottage cheese also contribute good bacteria to your system.

Augmenting your diet with probiotics could provide the extra boost you need to get the most out of a healthy, balanced diet, but it is unlikely to provide enough weight regulation power to counteract an unhealthy diet.  If you’re already eating a diet rich in fiber and plentiful fruits and vegetables, just incorporating a couple of the right probiotic-rich foods, or supplements, into your daily routine could be enough to have a positive impact on gut health, overall wellness, and, potentially, weight reduction.

To help you learn more about the microbiome and its impact on your health and weight, here are some excellent introductory articles:

Authority Nutrition: Why the Gut Microbiome is Crucial for Your Health

Authority Nutrition: 8 Surprising Things that Harm Your Gut Bacteria

• The Guardian: Yo-yo Weight Gain Driven by Gut Bacteria’s ‘Memory’ of Obesity, says Study


  1. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444(7122):1022-3.
  2. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE et al. A core gut microbiome in obese and lean twins. Nature. 2009; 457(7228):480-4.
  3. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122);1027-31.
  4. Kadooka Y, Sato M, Imaizumi K, Ogawa A, Ikuyama K, Akai Y et al. Regulation of abdominal adiposity by probiotics (Lactobacillus gasseri SBT2055) in adults with obese tendencies in a randomized controlled trial. Eur J Clin Nutr. 2010; 64:636-643.
  5. Ogawa A, Kobayashi T, Sakai F, Kadooka Y, Kawasaki Y. Lactobacillus gasseri SBT2055 suppresses fatty acid release through enlargement of fat emulsion size in vitro and promotes fecal fat excretion in healthy Japanese subjects. Lipids Health Dis. 2015; 14:30.
  6. Hamad EM, Sato M, Uzu K, Yoshida T, Higashi S, Kawakami H et al. Milk fermented by Lactobacillus gasseri SBT2055 influences adipocyte size via inhibition of dietary fat absorption in Zucker rats. Br J Nutr. 2009;101(4):716-24.
  7. Yadav H, Lee JK, Lloyd J, Walter P, Rane SG. Beneficial metabolic effects of a probiotic via butyrate-induced GLP-1 hormone secretion. J Biol Chem. 2013; 288(35):25088-97.
  8. Lescheid DW. Probiotics and inflammation: A review. Functional Foods in Health & Disease. 2014;4(7).
  9. Million M, Angelakis E, Paul M, Armougom F, Leibovici L, Raoult D. Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals. Microbial pathogenesis. 2012;53(2):100-108.
  10. Park S, Bae JH. Probiotics for weight loss: a systematic review and meta-analysis. Nutrition Research. 2015;35(7):566-575.
  11. Osterberg KL, Boutagy NE, McMillan RP, Stevens JR, Frisard MI, Kavanaugh JW. Supplementation attenuates increases in body mass and fat mass during high-fat diet in healthy young adults. Obesity. 2015;23(12):2364-70.
  12. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. Effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14.
  13. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014;513(181-186).
*Individual Results May Vary