Last Updated on March 23, 2016 by Patricia Carter

SUMMARY:  Surprisingly, only a narrow range of microbes has been researched to date, mainly microbes involving disease or probiotic types.  Little is known regarding what microbes actually exist in our food, their quantities, or even how much they vary for the differing diets (or even meal to meal for that matter!)   This study estimated the total numbers and kinds of microorganisms consumed in a day by an average American adult for three differing diets: Average American Diet, USDA, and Vegan.

Actually, we know more about what microbes are in our feces than the microbes in our food!  This is somewhat surprising given that we know that diet has one of the greatest impacts on our microbiome, where 80 to 85 percent of our immunity resides (see Natasha Campbell-McBride, MD, the “1st International Symposium on the Microbiome in Health and Disease with a Special Focus on Autism,” July 2014: “the microbiome refers to the constellation of enteric bacteria that create an organ system that makes up 80% of our immune system…“ as well as posts, OPTIMAL MICROBIOME DIET FROM AMERICAN GUT DATA and MICROBIOME RULES, WHAT IS IT? for more details).  

Other factors that also influence the gut microbiome include the nature of the initial colonization at birth (e.g., vaginal vs. C-section delivery), host genotype, and age.  See the posts, NEWBORN GUT MICROBIOME BEGINS DURING BIRTH, WHAT DISRUPTS THE MICROBIOME? and DELIVERY & BREASTFEED STUDIES & MICROBIOME MANIPULATION for those details.  Actually many things impact the microbiome as shown on this slide:

How to effectively shift the microbiome and restore balance is a key question for disease prevention and treatment.  Since diet is a readily modifiable factor, it is an obvious target for interventions.

Our diet, which feeds our microbiome, includes food, environmental chemicals, and medications… did you know?

These ingested compounds serve as food substrates (e.g., complex sugars), are metabolized by the microbiota, or affects the metabolism of the microbiota.  Some of these inputs have much research:

• Probiotics.   Just google pubmed and probiotics and see the list.  Alternatively, check out the post, CLA GRASSFED SCD YOGURT & CYTOKINE STUDIES: ERIVAN & WHOLE FOODS 365 in the section titled, “OK… NOW IT’S TIME TO SHARE SOME RECENT STUDIES CONCERNING THE BENEFITS OF PROBIOTIC YOGURT AND IT’S ANTI-INFLAMMATORY IMMUNOMODULATING FACTORS.”)
• Certain sugars such as galactooligosaccharides, fructooligosaccharides, and oligosaccharides are found in milk and other foods.  These are prebiotics that support the establishment and growth of certain commensal microbial species (Brownawell et al., 2012; de Vrese & Schrezenmeir, 2008; Roberfroid, 2007; German et al., 2008; Zivkovic & Barile, 2011).  Actually the FODMAPS diet pulls many of these foods out for those with IBS thereby modulating the microbiome to alleviate symptoms in over seventy percent of patients.  Check out some of the slides below for schematics of what the FODMAPS diet allows and eliminates.  FODMAPS is not a life diet; rather re-introduction of foods allows one to learn the “dosing” tolerance for these fermentable substrate compounds.  For the studies, see Clinical Ramifications of Malabsorption of Fructose and Other Short-chain carbohydrates, Practical Gastroentereolgy, Aug 2007 and The low FODMAP diet improves gastrointestinal symptoms in patients with irritable bowel syndrome: a prospective study, Int J Clin Pract. 2013 Sep;67(9):895-903. doi: 10.1111/ijcp.12128. Epub 2013 May 23.
  

  Slide source: biomeonboardawareness.com

  

  Slide source: biomeonboardawareness.com

  

  Slide source: biomeonboardawareness.com

  

  Slide source: biomeonboardawareness.com
• Antibiotics and pathogens impact the microbiota composition which includes its recovery (or lack of recovery) to the pre-antibiotic microbiome. Much research exists on this; just google antibiotics and microbiome.  You can also check out the YouTube Microbiome Manipulation via Diet and Environment (YouTube), featuring Eric Alm, PhD, MIT:

  

  

  

   

or see Manichanh et al., 2010; Ubeda & Pamer, 2012; Bien, Palagani & Bozko, 2013; Dethlefsen & Relman, 2010.

Now… A Study Showing What Microbes are in Various Diets (Average Amer. Diet, USDA, & Vegan)

The study,  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, looked at the microbes we eat, and how they vary in terms of total abundance and relative composition in different meals and dietary patterns typical of American dietary intakes.  15 meals were selected that exemplify the typical meals consumed as part of three different American dietary patterns in order to determine the average total amount of daily microbes ingested via food and beverages, and their composition in the average American adult consuming these typical foods:  

1. The Average American (AMERICAN) which focuses on convenience foods,
2. USDA recommended (USDA) which emphasizes fruits and vegetables, lean meat, dairy, and whole grains, and
3. Vegan (VEGAN) which excludes all animal products.
4. Note:  All meals were prepared in a home kitchen or purchased at restaurants using a combination of anti-bacterial and non-antibacterial cleaning products to simulate home and restaurant cooking.  Meal ingredients were purchased at local grocery stores in Saint Helena, CA, and prepared meals were purchased in restaurants in Napa, CA.

Macronutrient breakdowns were:

1. The AMERICAN meal plan totaled 2,268 calories, which consisted of 35% fat, 53% carbohydrates of which 16.6 g was fiber, and 12% protein.
2. The USDA meal plan totaled 2,260 calories, consisting of 25% fat, 49% carbohydrates of which 45 g was fiber, and 27% protein.
3. The VEGAN meal plan totaled 2,264 calories and consisted of 31% fat, 54% carbohydrates of which 52 g was fiber, and 15% protein.

Diet Design

Diets were designed by a nutritional biologist to deliver the average number of calories consumed by an average American, National Health and Nutrition Examination Survey, per day:

• The average American woman is 63 inches in height and weighs 166 pounds, and
• The average American man is 69 inches in height and weighs 195 pounds with an average age of 35, National Health and Nutrition Examination Survey, which translates to a total daily calorie intake range of 2,000–2,600 calories per day respectively to maintain weight, as determined using the USDA MyPlate SuperTracker tool.
• Therefore an intermediate daily calorie intake of about 2,200 calories was chosen as the target.

The AMERICAN meal plan (see below slides) consisted of:

• Breakfast: a large Starbucks Mocha Frapuccino
• Lunch: a McDonald’s Big Mac, French fries, and Coca Cola
• Dinner: Stouffer’s lasagna
• Snacks: Oreo cookies.

The USDA meal plan (see below slides) consisted of:

• Breakfast: cereal with milk and raspberries
• Morning Snack: an apple and yogurt
• Lunch: a turkey sandwich on whole wheat bread with salad (including a hard-boiled egg, grapes, parmesan cheese, and Ceasar dressing),
• Afternoon Snack: carrots, cottage cheese , and chocolate chips
• Dinner: chicken, asparagus, peas and spinach on quinoa.

The VEGAN meal plan (see below slides) consisted of:

• Breakfast: oatmeal with banana, peanut butter, and almond milk
• Morning snack: a protein shake (including vegetable-based protein powder, soy milk, banana and blueberries)
• Lunch: a vegetable and tofu soup (including soba noodles, spinach, carrots, celery and onions in vegetable broth)
• Afternoon snack: an apple and almonds with tea
• Dinner: a Portobello mushroom burger (including Portobello mushroom, avocado, tomato, lettuce, and a whole wheat bun) with steamed broccoli
• Evening snack: popcorn, hazelnuts and fig bars.

Source: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, Table 3, https://peerj.com/articles/659/

Source: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, Table 3, https://peerj.com/articles/659/

The nutrient composition per meal is shown in these slides:

Source: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, Table 3, https://peerj.com/articles/659/

Source: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, Table 3, https://peerj.com/articles/659/

Source: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types, Table 3, https://peerj.com/articles/659/

Meals that likely contained live probiotics as the food was prepared not heat treated  (i.e., fermented foods whose package labeling listed live active cultures) were: USDA meal plan snack #1 (yogurt), lunch (parmesan cheese), and snack #2 (cottage cheese).

Meals that likely contained destroyed probiotics (i.e., fermented foods that were cooked as part of meal preparation) were: VEGAN meal plan lunch (tofu), and AMERICAN meal plan lunch and dinner (cheese).

Summary of Bacterial (Aerobic & Anaerobic), Yeast & Mold Microbial Loads Found:

Excerpted from the study, The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types:

Across all meals, the aerobic and anaerobic plate counts were the highest and the yeast and mold plate counts were the lowest.

The USDA dietary pattern had the highest total microorganisms for the day at CFU mostly due to the higher amounts of anaerobic bacteria in the morning snack (CFU) and higher amounts of aerobic and anaerobic bacteria in the afternoon snack (5.5 × 108 and 6 × 108 CFU respectively). The USDA meal plan included two meals (yogurt and cottage cheese) with non-heat treated fermented foods, which were likely responsible for the 3-fold higher total microbes in this meal plan compared to the AMERICAN and VEGAN diets.

My Note:  If future studies show that the microbes in meals survive and impact the microbiome (we already know some do: cheese, yogurt, some meat compounds…), than meals containing higher microorganisms would likely be important for a healthy microbiome.  This study showed that “About a quarter of us have up to 40% fewer gut bacteria, reduced bacterial diversity, and harbor more bacteria causing a low-grade inflammation of the body which is reflected in blood samples that reveal a state of chronic inflammation, which we know affect metabolism and increase the risk of type 2 diabetes and cardiovascular diseases.”  

The AMERICAN and VEGAN dietary patterns had 3 orders of magnitude fewer total microorganisms than the USDA dietary patterns, with total microorganisms of CFU and CFU respectively. Neither the AMERICAN nor the VEGAN dietary pattern meals contained fermented foods that were not heat treated as part of meal preparation. For example, the AMERICAN lunch and dinner contained cheese that was either cooked on a grill or baked in the oven and the VEGAN lunch contained tofu, which was cooked in the vegetable broth.

Food preparation techniques such as heating or acid treatment can kill bacteria, however, these processes affect different bacteria to different degrees (spore-forming bacteria can survive heat treatment (Stringer, Webb & Peck, 2011). Once inside the gastrointestinal tract, the low pH of the stomach, as well as bile salts also kill some bacteria, but not those that are acid and/or bile salt resistant. It is unknown what proportion of the microbes we eat make it through the hostile environment of the gastrointestinal tract. However, a recent study showed that food microbes consumed as part of fermented foods such as cheese did appear in the stool and were culturable (David et al., 2013).

The USDA lunch also had the highest amounts of yeast and mold (and CFU respectively) of all the meals, and this meal also had relatively high amounts of aerobic bacteria (CFU).

In the VEGAN dietary pattern, the morning snack had the highest amounts of aerobic and anaerobic bacteria (and CFU respectively).

Factors driving the differences in microbial community composition and diversity of individual meals

1. Nutrient density could matter:  The relative abundance of some particular taxonomic groups was significantly correlated with particular nutrient content of the meals. For example, members of the genus Blautia are frequently observed in human fecal samples and they correlate positively with the sugar content of the meals.  This result suggests that there could be interesting relationships between the nutritional content of the foods that we eat, the microbes that associate with those foods, and our gut microbiome, not just because we are “feeding” our gut microbes, but because we are eating them as well (but, see “Caveats” section below.)
2. There was no effect of dietary pattern on the overall community composition within individual meals.
3. There was no obvious clustering based on any potentially distinguishing feature tested, including whether the meals contained fermented foods, dairy, whether they ware raw or cooked, or the calculated nutritional content (see slides above for Table 5 for complete meal metadata).
4. However, different meals clustered together independent of dietary pattern. For example:
   • Meals that were relatively abundant in Prevotellaceae included the USDA dinner, VEGAN dinner, AMERICAN dinner, USDA breakfast, VEGAN snack 2, and VEGAN snack 3. Prevotellaceae includes organisms that tend to be very abundant in the guts of many animals, and have been associated with Inflammatory Bowel Disease in humans (Henderson et al., 2013; Wu, Bushmanc & Lewis, 2013).
   • Meals that were relatively abundant in Streptococcaceae included the AMERICAN snack, AMERICAN lunch, USDA snack 2 and USDA snack. It is difficult to know what specific features of these meals made them similar in this regard. Possible contributing factors may be provenance of ingredients and/or individual meal components such as presence of a certain fruit or vegetable.

Where all this is going…

The long term diet that we eat creates a stable resilient microbiome.  Individual core microbiota has been found to be stable over long time scales (e.g., 5 years), although the community composition is highly dynamic on shorter time scales (e.g., 0–50 weeks).  The study, The Long-Term Stability of the Human Gut Microbiota, Faith¹  evaluated fecal samples from 37 healthy U.S. adults sampled 2 to 13 times up to 296 weeks apart.  They found that the participants harbored 195 ± 48 bacterial strains, representing 101 ± 27 species, and that:

• On average, 60% of bacterial strains remained stable for up to 5 years and many were estimated to remain stable for decades.  Members of Bacteroidetes and Actinobacteria are significantly more stable components than other population averages.
• Four individuals sampled during an 8- to 32-week period during a calorie-restricted dietary study showed that weight stability is a significantly better predictor of microbiota stability than the time interval between samples (figure, panel B).

How to effectively shift the microbiome and restore balance is a key question for disease prevention and treatment, which has no answer as of yet.

Future study will explore the explicit effects of ingesting food microbes on changes in the gut microbiota but this study was limited to only provide preliminary data on the composition and numbers of bacteria in typical American dietary patterns.  However, since diet is a readily modifiable factor, it is an obvious target for interventions.

The best I can say at this time, is that which has been mentioned in the post, OPTIMAL MICROBIOME DIET FROM AMERICAN GUT DATA, which is Dr. Rob Knight’s October 18, 2014 lecture which detailed the current “American Gut” project microbiome research and provided an Eleven Point list of what has been shown thus far, to be most beneficial for the microbiome, cautioning all is preliminary.  See the post for more details beyond that excerpted below:

1. Eat lots of  plants:  5 to 30 different varieties each week preferably.  See MY NOTES below for more explanation.  
2. Aging increases microbiome diversity:  Microbiomes are more diverse at age 50 to 60 then populations in their twenties  (see below slides).
   

   
3. Having an IBD diagnosis means your microbiome is altered.  NOTE:  Many chronic and autoimmune diseases are also following suit.
4. The time of year alters the microbiome with a more diverse microbiome being with sun and outdoor exposure.
5. Antibiotics wipe the microbiome with some folks recovering relatively soon whereas others do not recover the pre-antibiotic microbiome even one year later.
6. Males vs females:  The sex for a  given microbiome can now be accurately predicted.
7. Sleep 8 hours for a more diverse microbiome.  Less than 6 hours yields a less diverse microbiome.
8. BMI but it only subtly affects the microbiome.
9. Plants: eating 6 to 10 each week is good, but eating 30 plus different varieties is best.  (See further discussion below.)
10. Alcohol: one drink is helpful, more than one reduces diversity.
11. Frequent exercisers have a more diverse microbiome and it is best if exercise is outdoors rather than indoors.

Eat lots of  plants: 5 to 30 different varieties each week preferably –  MY NOTES:  

This finding is so profound that “American Gut” will soon change participant food journal requirements to only ask for frequency on consumption of holistic food within the past month, instead of the three week food journal.  This change is warranted since the long term diet, especially meat and fiber consumption, has been shown to have the largest effect on the microbiome.

The benefits of eating many diverse plants is as expected from general guidelines to date and it includes lots of leafy greens and brightly colored vegetables which also contains carotenoids, anthocyanins, lycopenoids, and other beneficial plant compounds.

Lastly, microbiome diversity is increased by eating more variety of plants.  

It is thought that greater diversity means improved immunity since many diseases (including obesity, diabetes, colon cancer and IBD…) are associated with reduced microbiome diversity.  The ratio of plant to animal foods (a.k.a. the ratio of carbohydrates to protein) significantly affects the microbiome and is complex. Researchers are only now beginning to study individual foods and are learning that they vary in metabolites based on where they are grown, how they are stored, and even how they are cooked.

This study links meat to differences in the gut microbiome when compared to diets that heavily rely on plant foods as does this study.

And there are studies showing adverse healthy consequences associated with meat consumption such as this study,  which found that gut microbes metabolize L-carnitine found in red meat into TMAO, and that can lead to hardening of the arteries.   

That said, there are certain diseases that modified plant/meat ratios seem to benefit such as IBS (where FODMAPS help), or gluten and casein free (or GAPS) for autism, SCD for IBD, Wahl’s diet for MS, a temporary ketogenic type diet for Type 2 Diabetes or Metabolic Syndrome, a ketogenic diet for epileptic seizures…).

Lastly, crystal ball future studies that need to be addressed:

• Do the microbes we eat as part of our normal daily diets contribute to the composition and function of our gut microbiota?
• Under what circumstances do microbes consumed as part of meals remain in the gastrointestinal tract transiently versus persistently following a meal?
• Do the microbes we eat affect the function of the resident gut microbiota, even if they do not affect its composition, as has been suggested by some yogurt feeding studies (McNulty et al., 2011)?
• How do different cooking and preparation methods affect the microbial composition of meals and the survival characteristics of individual microbes through the gastrointestinal tract?  This makes me think about the third fiber, resistant starch, that so many chat about in my world and how for some, increasing such by consuming cold potatoes (potato salad anyone?), green bananas, plantains, and the  infamous “potato starch” supplementation which can cause much distress… and yet, the colon bacteria thrive on resistant starch yielding butyrate beneficial by-products…
• How do specific factors such as length of transport or provenance of individual ingredients (e.g., imported vs. domestic), packaging materials, and handling of ingredients in homes alter the microbial composition of foods?

Last updated: March 23, 2016 at 5:31 am for SEO optimization.

In health through awareness,