How to Eat Right for a Healthy Microbiome
Written By Microbiome Plus+

How to Eat Right for a Healthy Microbiome

The first question that needs to be answered is “what exactly is the microbiome”? The Microbiome is all of the microbes that live on and in your body. The portion of the Microbiome that you can affect significantly with nutrition is that of the digestive tract and mouth which is called the gut microbiota. With that answered we can turn our attention to figuring out what “eat right”, “fix” or “proper nutrition” mean? What does a healthy Microbiota look like anyway?
There is what the organ should look like “anatomy”, how the organ should work “physiology”, what it looks like in disease “pathology” and how it is working for you? In laypersons terms, I would answer them like this…

What should the organ look like? – Very generally, the higher diversity of organisms, and genes of those organisms, the more balanced/stable/healthy your gut ecosystem is. An accurate and interesting comparison is that our gut is simply another ecosystem like the Earth and diversity of organisms and genes ensures a healthy ecosystem, gut and Earth. But one starved of diversity, where species are extinct becomes unbalanced and can spiral out of control to catastrophe.

How should the organ work? – The microbiome/microbiota plays a major role in: immune function, metabolism, digestion, regulating cholesterol levels, absorption of important vitamins, minerals and nutrients like calcium and vitamin D, maintaining the mucosal barrier of your intestinal tract (which helps regulate immune response), harvesting energy from dietary fiber, providing essential enzymes for digestion, resisting pathogens, synthesizing vitamins, etc..

How is it working for you? Is it contributing to your good or poor health? – Most of the Western Diseases are a result of western food, lifestyle and medical practices. While diet, exercise, and human genetics are essential components one thing that seems to have been overlooked is that between the ages 0-4 we each assemble our own Microbiome/Microbiota, and that Western food and medicine we have created a “Western Gut” which is playing a role is disease. Is there a new component to diet, exercise, and human genetics? The gut seems to be essential and an independent contributor.

Finally, before we start on our quest for a dietary path to a healthy microbiota we should ask the question, is it even possible to change my microbiome and how long will it take? Scientists and studies seem to agree that it is possible to change your microbiome; however, it requires a permanent and significant change in your diet and/or supplementation, and that these changes can take as little as 24 hours. This is not surprising since most gut bacteria divide within 24 hours.

Because the above healthy mirobiome question is such a large one I have broken it into two basic pieces bleow. I hope to be able to revisit some parts of the answer with more detail in the near future because it is such a dynamic, rich and exciting area/topic of discussion and research.

SO HERE IS HOW I would divide it up 1) overall guidance and 2) specific important life stages, drugs and disease.

Overall general nutrition guidance for the microbiome


  • 30-50 servings of vegetables a week
  • 40-50 grams of fiber per day – try from veggie source
  • whole food, complete fiber
  • Keep it whole -whole foods contain complete nourishment for your gut
  • Normal fat and protein levels – too much fat and protein can drastically change your gut within 24 hours
  • Probiotics – try adding Microbiome Plus+ to your diet
  • FODMAP diet (FODMAPs are osmotic; they are not digested or absorbed well and fermented heavily in the intestine and this contributes to the symptoms of IBS. Thus while combating IBS symptoms low FODMAP is sometimes used however this does not mean it is optimal for the long-term health of your microbiome and does not ultimately solve your IBS issue)
  • Avoid overuse of antacids
  • Avoid overuse of oral antibiotics

NOTE: this will help maintain normal bile and cholesterol metabolism, promote the production of appropriate SCFAs which will help with absorption of Calcium and nourishing the lining of the gut and maintain normal gut pH which will help with absorption of Calcium and vitamin D.

Specific nutrition guidance for the microbiome

Pregnant and birthing

Why and how should an expecting mother eat for a healthy Microbiota for her baby?
There is some evidence that there is some transfer of the microbiota during pregnancy and thus it is important for Mom to eat right for her gut during pregnancy. There is also evidence that the mothers microbiome, fecal and vaginal flora are preparing to inoculate the baby optimally for immune system generation and digestion of breast milk. Despite the possibility of this early microbial transfer there is indisputable evidence that… – During natural birth the mothers vaginal and fecal microbiome are transferred to the baby during the birthing process to inoculate the baby and develop a healthy microbiome much like that of the mother – During caesarean section the bacteria present on mothers/doctors/nurses/fathers skin colonizes the newborn baby’s gut, resulting in a microbiome that more closely represents that of the skin. There is also evidence that obesity during pregnancy affects the long-term health of offspring via the microbiome.


SPECIFIC GUIDANCE: Always follow your doctor’s advice and speak to a doctor before making any changes; however, maintaining a diet high in vegetables and fiber and avoiding overuse of antacids and oral antibiotics are generally healthy.



How should a toddler +1 year eat 0-4?
The years 0-4 are so important for every child’s health because these are years when their gut microbiome is forming. This “forgotten” but essential “organ” of the body is developing and will eventually significantly affect immune function, digestion, hormone signaling, vitamin production, and micro/macro nutrient absorption. In the same way that we ensure adequate nutrients for the early development of our child’s brain and heart, the same is true for their microbiome/microbiota. Otherwise there is a risk of permanent damage.

Key points in baby/toddler years…
  1. Expose your children to lots of different foods
  2. Let them get dirty
  3. Breast feed as long as you can – breast feeding is better than bottled milk as it provides more diversity of prebiotic “full spectrum prebiotic”
  4. Plan to have a natural birth, if possible, and if not consider inoculation of mothers vaginal microbiome – Cesarean section and formula feeding increase clostridium in children when compared to natural; clostridium bacteria are potentially pathogenic when not kept in check.
  5. Eat a balanced and healthy diet including vegetables, fiber, whole foods – A healthy nutritional intake in early life is most likely to help reduce the risk of allergies and other noncommunicable diseases.


Antibiotics can be taken orally for a number of reasons, including the control of bacterial infections within the gut, sinus/nose, skin, or somewhere else on your body. But along the way to these distant sites, antibiotics kill the bacteria in your gut unintentionally, killing a little piece of the microbiome. Additionally, good and bad bacteria co-exist in a balance at all times in a healthy gut and thus, antibiotics that are taken for bad bacteria that are out of control in the gut indiscriminately kill the good bacteria as well and regaining this balance is an important to ending the infection and eliminating reoccurrence. Appropriate nutrition and probiotic therapy are always an important part of this. Medical treatments for cancer such as radiation and chemotherapy are can cause different types of damage to the gut; however, both result in a similar indiscriminate eradication of the microbiome. Patients prescribed chemotherapy and radiation therapy should always consult a doctor before making changes to their diet or using supplements.


SPECIFIC GUIDANCE: heart health patients should replace their BSH active lactobacillus species with Microbiome Plus+ Heart, those with osteoporosis should do the same with Microbiome Plus+ Bone and during and post antibiotics patients should take Microbiome Plus+ GI. Patients should always take their antibiotics as directed by physicians however try not to misuse or over use antibiotics. They should also focus on staying hydrated and note that the chance for malnourishment and lower calories is increased. There should also be a focus on feeding the good bacteria which requires full spectrum prebiotics largely derived from plants.


Better Health/Prevention/Disease

How should you eat with disease or treating disease?
Microbiome Plus+ products were all developed to deliver the most clinically researched, highest quality nutritional supplements available. Our research and development team used the new science of the microbiome to understand a gene deficit that appears to be contributing to heart, bone and gastrointestinal disease and deliver the gene in a probiotic to supplement it. If you use them with your patients they will all work!

  • May reduce coronary heart disease risk**
  • Supports healthy cholesterol and triglycerides*
  • Supports normal inflammatory response*
  • Supports healthy blood pressure*
  • Supports healthy bile metabolism*
Microbiome Plus+ Heart is a more complete heart health dietary supplement that provides the full American Heart Association daily dietary recommendation of omega-3 which may reduce the risk of coronary heart disease plus the probiotic L. reuteri NCIMB 30242, which supports normal cholesterol levels and inflammatory response.* The probiotic in Microbiome Plus+ Heart is the only probiotic shown in clinical trials to support healthy bile metabolism and maintain normal cholesterol levels and inflammatory response.* Microbiome Plus+ Heart also provides the full American Heart Association daily dietary recommendation of DHA and EPA omega-3 fatty acids which may reduce the risk of coronary heart disease.✝ Omega-3 polyunsaturated fatty acids have also been shown to maintain healthy triglyceride levels.*

  • May reduce risk of osteoporosis**
  • Complete source of vitamin D and calcium*
  • Supports healthy levels of 25-Hydroxyvitamin D*
  • Supports healthy bones, joints and muscles
  • Supports healthy bile metabolism*
Microbiome Plus+ Bone is a more complete bone health dietary supplement that provides full daily dietary recommended intake of calcium, and vitamin D3 and the probiotic L. reuteri NCIMB 30242, which helps maintain healthy levels of vitamin D in the body.* The probiotic in Microbiome Plus+ Bone is the only probiotic shown in clinical trials to maintain healthy levels of vitamin D.* Microbiome Plus+ Bone helps replenish the natural bacteria in your body vital for regulating levels of vitamin D and calcium in your blood and also provides the daily requirement of dietary calcium and vitamin D3.* Calcium serves as the key building block for the formation and remodeling of bone. Microbiome Plus+ Bone also contains vitamin D, which is essential to the proper absorption of calcium.* Adequate calcium and vitamin D throughout life, as part of a well-balanced diet, may reduce the risk of osteoporosis.

  • Supports gastrointestinal and immune health*
  • Maintains balance of healthy bacteria*
  • Supports normal inflammatory response*
  • Supports healthy bile metabolism*
  • Synbiotic formulation with pre and probiotic*
Microbiome Plus+ Gastrointestinal is a more complete gastrointestinal health dietary supplement that provides natural prebiotic fiber (scFOS) and the probiotic L. reuteri NCIMB 30242 which work together to maintain the balance of healthy bacteria in your gut and support normal digestive function.* The probiotic in Microbiome Plus+ Gastrointestinal has been shown in clinical trials to help support normal inflammatory response in addition to supporting digestive health.* scFOS is a natural prebiotic fiber that supports a healthy gastrointestinal tract by promoting digestive function, immune health, the growth of healthy bacteria, natural intestinal mechanical barriers, and gut integrity.* Microbiome Plus+ Gastrointestinal combines these two ingredients to provide more complete gastrointestinal health support.* Not only does scFOS support digestive function but as a prebiotic helps L. reuteri NCIMB 30242 to support normal gastrointestinal function.*
Back to blog

Statements made on this website have not been evaluated by the U.S. Food and Drug Administration. Information provided by this website or this company is not a substitute for direct, individual medical treatment or advice. It is the responsibility of you and your healthcare providers to make all decisions regarding your health. Microbiome Plus recommends that you consult with your healthcare providers regarding the diagnosis and treatment of any disease or condition. Products sold on this website are not intended to diagnose, treat, cure, or prevent any disease.

Leave a comment

Please note, comments need to be approved before they are published.