Promoting A Healthy Microbiome with Food and Probiotics

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PROMOTING A HEALTHY MICROBIOME WITH

FOOD AND PROBIOTICS

DEFINITIONS

 Prebiotic: The food that probiotics need to sustain themselves (e.g.,

fructooligosaccharides)

 Probiotic: A living organism that benefits the health of the host (e.g., bacteria and

yeast)

 Synbiotic: A supplement that contains both a prebiotic and a probiotic

 Postbiotic: A metabolic byproduct of probiotics (e.g., n-butyrate from fermentation

of fiber and bacteria)

NUTRITION: THE ULTIMATE PREBIOTIC

Although a person’s population of bacteria originates at the time of birth, most of the

microbiome is established in the human gut with the introduction of food. Breast milk

includes milk oligosaccharides (MOS) that provide bacteria with nutrients to grow,

particularly Bifidobacteria. Diets that contain the most fiber, fruit, and vegetables are

known to engender the most diversity and richness of bacteria growth in the gut. Healthy

bacteria produce short-chain fatty acids, such as n-butyrate, that support the health of the

intestinal lining.[1]

Foods rich in choline and carnitine (e.g., red meat and eggs) are metabolized by the

intestinal microbiota to form the gas trimethylamine (TMA). TMA is converted by the liver

to trimethylamine oxide (TMAO). This substance (an unhealthy postbiotic) has been

strongly linked to the development of atherosclerosis and coronary artery disease.[2]

Eating a diet low in red meat and animal fat and rich in fibrous plants has been found to

support bacteria in the gut that can reduce how much energy the body stores; our gut’s

microbiome can influence one’s risk of obesity.[3] When humans were hunters and

gatherers, it was harder to kill wild game, so eating meat and animal fat was less common.

It may have been advantageous in the past to have a gut that contained bacteria able to

maximize energy storage when such foods were available. Unfortunately, in modern times,

when animal-based foods are easy to obtain, it may be that our gut bacteria increase our

risk of obesity.

The number of studies investigating associations between our gut microbiome and various

health conditions continues to grow exponentially. Positive changes in our gut flora have

now been associated with improvements in conditions ranging from acne, nonalcoholic

fatty liver disease, and chronic kidney disease,[4-6] to the conditions listed in Table 1,

below.

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Unfortunately, only 5% of Americans consume recommended amounts of daily fiber (21-38

gm per day depending on sex and age), as the average daily American intake is only 16.2

gm. “Whole grains” are often considered by consumers to be a surrogate for fiber, though

the fiber content of whole grains various widely by grain and type of processing.[7]

A good rule of thumb to optimize one’s fiber intake is to examine food labels and determine

the “total carbohydrate to fiber ratio.” A ratio of less than 10 is good, and a ratio of less

than 5 is ideal. For example, if a serving of cereal has 20 gm of total carbohydrates and 4

gm of fiber, this ratio would be 20/4=5; this would be an excellent choice.

Nutrition is the main therapeutic tool to positively influence the microbiome. A diet rich in

fiber, vegetables, and fruit helps establish a diverse and rich microbiome that promotes the

health of the host.

Prebiotic foods: Asparagus, artichokes, bananas, oatmeal, leeks, chicory root, red wine,

honey, and beans. Soluble fiber, such as guar gum and psyllium, is also a good prebiotic.

FOOD SOURCES OF PROBIOTICS

Fermentation occurs when a food interacts with a microorganism or enzyme and

undergoes anaerobic biochemical change. This process can prolong the shelf life, promote

the growth of healthy bacteria, enhance taste, and improve digestibility of the food.

Microbes that promote fermentation can produce postbiotics that suppress the growth of

harmful bacteria that could otherwise cause spoilage and disease. An example of this is

Lactobacillus. Lactobacillus species produce lactic acid, which facilitates the digestion of

lactose in milk. Fermentation produces antimicrobial substances such as acids, carbon

dioxide, and alcohol. It is one of the oldest methods for preserving food and an excellent

way to populate the gut with healthy bacteria. The byproducts of probiotic fermentation

maintain a balanced ecosystem while also supporting digestion.

Fermentation is self-limited, based on the amount of bacteria found in a given food. Take

wine, for example. When the sugar in the grape is fermented, alcohol is produced, reducing

the amount of bacteria in the wine.

Red wine is a good prebiotic. A 2012 study of 10 men given 9 oz (270 ml) of red wine daily

found that their fecal microbiome was altered. There was more growth of species of

Bifidobacteria, Bacteroides, and Enterococcus. The increase in Bifidobacteria was linked to

lower levels of cholesterol and changes in C-reactive protein, a marker of inflammation

levels. Benefits were attributed to the polyphenols (e.g., resveratrol) found in wine.[8]

Fermented foods contain a broad spectrum of beneficial bacteria, supporting overall

microbiome health. Eating fermented foods has been showed to enhance immune function,

metabolic health, and improve intestinal permeability. Studies have provided positive

associations with improvements in metabolic syndrome, colon cancer incidence,

depression, stress hormones, anxiety, and even anger.[9]

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COMMON PROBIOTIC FOODS

The following list includes types of probiotics and which foods they can be found in.

Unfortunately, the high temperatures involved in pasteurization kills probiotics. Look for

labeling that says, “contains live cultures” or “contains active cultures.”

PLANTS

 Probiotics: Lactobacillus, Leuconostoc, Pediococcus

 Foods: Sauerkraut (cabbage), miso (soy paste), tempeh (soy), pickles (cucumber)

 Notes: Avoid pickling with vinegar as this can reduce the growth of bacteria.

DAIRY

 Probiotics: Lactobacillus, Streptococcus, Saccharomyces (yeast)

 Foods: Yogurt, milk, kefir

 Notes: Yogurt with live cultures is one of the most accepted methods to obtain

probiotics.

TEA

 Probiotics: Lactobacillus, Pediococcus, Acetobacter, Saccharomyces (yeast),

Brettanomyces (yeast)

 Foods: Kombucha

 Notes: Although the tea leaf is a plant, kombucha is mentioned separately because it

is a good source of a variety of probiotics. Also, it is important to be mindful of the

added sugar content (often from adding juice after fermentation) of many

commercially available products.

PROBIOTIC SUPPLEMENTS

Note: Please refer to the Passport to Whole Health, Chapter 15 on Dietary Supplements for

more information about how to determine whether or not a specific supplement is

appropriate for a given individual. Supplements are not regulated with the same degree of

oversight as medications, and it is important that clinicians keep this in mind. Products

vary greatly in terms of accuracy of labeling, presence of adulterants, and the legitimacy of

claims made by the manufacturer.

Prescribing probiotics can be challenging, as there are thousands of products, each

claiming superiority over the other. Many products have a “special recipe,” a patented

strain, or a mixture of multiple different organisms (a sort of microbiologic shotgun

approach). It is difficult to say whether one probiotic type is superior to another. Studies

indicate that certain microorganisms work better for different illnesses, but it may just be a

matter of which probiotics have been studied and which ones have not.

The goal is to populate the gastrointestinal ecosystem with a healthy balance of

microorganisms that optimally supports the host. At this time, it is not clear what that

Promoting a Healthy Microbiome with Food and Probiotics

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balance should be. In fact, it is probably highly individualized, based on geographic

location, food choices, and even the company one keeps.

WHAT TO LOOK FOR IN A PROBIOTIC

First, look at what genus, species, and strain(s) are in the product. Probiotics’ names have

three parts, usually listed in order. The first part is the name of the genus, the second part

is the species, and the third part is the name of the strain. For example, Lactobacillus

rhamnosus GG is from the genus Lactobacillus and has the species name rhamnosus. GG is

the name of the strain. Different companies patent different strains that they develop.

Lactobacillus is usually abbreviated with an L, and Bifidobacterium is usually abbreviated

with a B. Lactobacilli work in the small intestine, and Bifidobacteria work in the large

intestine. Because antibiotics can kill the bacteria along the entire intestinal tract, it is

important to add back both of these types of bacteria for people who have just taken

antibiotics.

A general rule of thumb is to make sure the product you recommend contains species from

both Lactobacilli and Bifidobacteria. The yeast Saccharomyces boulardii has also shown

benefit for a number of conditions.

Some of the most-researched probiotics are:

 Lactobacillus rhamnosus GG (available as the brand Culturelle)

 Bifidobacterium lactis BB12 (abbreviated as B. lactis BB12)

 L. acidophilus NAS (sometimes just called Acidophilus)

 L. bulgaricus LB-51

 L. gasseri

 L. plantarum

 B. bifidum Malyoth strain

 B. longum

 L. acidophilus DDS1

 Saccharomyces boulardii—this is actually a yeast that has been found to have several

benefits

Others, which have been studied less but are often taken, are L. johnsonii, L. reuteri, L.

rhamnosus, B. breve, B. infantis, E. faecalis, and Streptococcus salivarius.

DOSING

Usually 1x10

, or 1 billion, colony-forming units (CFUs) is a good daily dose. For Crohn’s

disease or irritable bowel, 1x10

or 100 billion, CFUs is recommended daily by some

experts. For treating bacterial infections in the vagina, vaginal suppositories with 1 billion

CFUs of lactobacillus organisms are typically used. Many experts recommend taking

probiotics on an empty stomach, when there is less stomach acid present. Children are

Promoting a Healthy Microbiome with Food and Probiotics

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often given doses in the 1x10

range. Many products that are tailored to infants or young

children are available.

GUIDELINES FOR PRESCRIBING PROBIOTICS

 Take on an empty stomach.

 Heat-dried formulations should be kept refrigerated. Lyophilized ones can handle

room temperature.

 Most doses range from 1 to 10 billion (10

-10

) CFUs 1-2 two times daily.

If taking with antibiotics, separate the antibiotic and the probiotic dosing time by 2 hours.

DURATION OF TREATMENT

This is controversial. Some would say that once a healthy gut ecosystem is established,

continued use of probiotics is not necessary and would be similar to seeding an already

seeded garden. But others argue that the therapeutic benefit of the bacteria may be

beneficial after the microbiome is established. The focus should always be on improving

the whole ecosystem so the individual is not dependent on bacteria in pill form.

Various sources recommend taking probiotics daily anywhere from 2 weeks to 2 months to

fully recolonize the bowel’s healthy bacteria. After the initial course, it may be possible to

back off to 2-3 doses per week. In Crohn’s disease or irritable bowel syndrome (IBS),

people often need daily doses for longer time periods. Improvement in symptoms can help

guide this decision. Many of the studies, where probiotics were given to prevent diarrhea

after antibiotic treatment, had subjects take them at the same time as the antibiotic. It is

best to take them 2 hours apart from each other and continue the probiotic for 1-2 weeks

after the antibiotic course is completed.

WHAT TO TREAT?

Table 1 lists conditions that have the strongest evidence in support of using probiotics for

prevention and treatment. For more information, check out the Probiotics Chapter in

Rakel’s Integrative Medicine textbook, which is available through the national VA

Library.[10]

Promoting a Healthy Microbiome with Food and Probiotics

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TABLE 1. CONDITIONS WITH THE STRONGEST EVIDENCE FOR BENEFIT FROM

PROBIOTICS

Indication Bacteria Strains

Used

Comments Key

Study

Prevention of

upper respiratory

infection (URI) in

children

Lactobacillus

acidophilus +/-

Bifidobacteria

animalis

Benefits seen with Lactobacillus

alone or combined with

Bifidobacteria given twice daily

for 6 months.

[11]

Prevention of

colic, reflux, and

constipation in

infants

Lactobacillus reuteri

DSM 17938 during

the first 3 months of

life

Mean duration of crying time

was 38 minutes for the probiotic

group versus 71 minutes in the

placebo group (P < .01).

[12]

Prevention of

diarrhea in

preschoolers

Lactobacillus reuteri

DSM 17938 1 x 10

CFUs given daily for

3 months

Not only reduces the incidence

and duration of diarrhea but also

reduced the incidence of URI.

[13]

Prevention of

atopic dermatitis

in infants

Lactobacillus

rhamnosus strain GG

(Culturelle)

When this was given to mothers

prenatally and then to their

offspring for 6 months, the

benefit persisted after a 4-year

follow-up.

[14]

Ability to store fat Bacteria from

human twins

(overweight and

normal weight)

were transplanted

into sterile mice.

Bacteria from overweight twin

caused mice to gain more

weight. Eating a high-fiber, low-

fat diet negated the effect.

[3]

Irritable bowel

syndrome

Bifidobacteria

infantis 35624

The dose of 1 x 10

CFUs worked

best in this study of women. The

available data supports

bifidobacteria to be more

effective than lactobacillus at

reducing gas and bloating.

[15,16]

Promoting a Healthy Microbiome with Food and Probiotics

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Indication Bacteria Strains

Used

Comments Key

Study

C. difficile colitis Donor stool infusion

Single-strain

probiotic (no clear

recommended

species)

Significant benefits have

resulted in this becoming the

therapy of choice for drug-

resistant cases.

>50% reduction among

hospitalized individuals if

started[17] within 2 days of

antibiotic initiation

[18]

RESOURCE LINKS

 Passport to Whole Health:

https://www.va.gov/WHOLEHEALTHLIBRARY/docs/Passport_to_WholeHealth_FY

2020_508.pdfAuthorS

“Promoting a Healthy Microbiome with Food and Probiotics” was written by David Rakel,

MD and updated by David Lessens, MD, MPH (2014, updated 2020). Sections were adapted

from “Probiotics and Prebiotics: Frequently Asked Questions” by J. Adam Rindfleisch,

MPhil, MD.

This Whole Health tool was made possible through a collaborative effort between the

University of Wisconsin Integrative Health Program, VA Office of Patient Centered Care and

Cultural Transformation, and Pacific Institute for Research and Evaluation.

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promotes cardiovascular disease. Nature. 2011;472(7341):57-63.

3. Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity

modulate metabolism in mice. Science. 2013;341(6150):1241214.

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