I have created a new set of charts showing the connection of bacteria to various conditions.  These charts allow drill down by taxonomy rank (phylum, order, class, genus, etc).

http://microbiomeprescription.azurewebsites.net/Condition/Graph

NOTE: As you move down the rank, some items may not be available to graph

Phylum

Class

Order

Family

Genus

Species

Often at this level — there may be no studies.

A reader asked how to compensate for some prescription drugs that he takes for other conditions. In an earlier post, I had added the ability to see the Compare Impact on the microbiome of drugs, supplements, etc. for example

The result can be a long list of bacteria taxonomy impacted Changing this information into an actionable plan is a challenge — until now.

You will notice a new button Get Suggestions for reversing impact on Microbiome.

Clicking this button takes you to the classic suggestion page 

That’s it!

Bottom Line

Trying to correct a microbiome while taking various needed prescription drugs is a complex situation. I hope the above tool will assist you,

Quality Assurance:

For each of the above pages, I have them open in new windows so readers that are interested, can verify the logic being used.

• On the first page, click the substance:  Bile http://microbiomeprescription.azurewebsites.net/Library/Modifier?mid2=54.
• This DECREASES Actinobacteria class, which we see on the next page

Looking next at the suggestions:

Clicking on one of the items, Fish Oil, we see that it increases http://localhost:42446/Library/Modifier?mid2=142

Verification can be complex between of multiple impacts of modifiers against multiple items. If you set the filters as shown below:

Then just clicking thru items until you find the above (or another taxonomy). For example, http://localhost:42446/Library/Modifier?mid2=1768

Recently I have seen a number of articles looking at how the diet needs of the seniors (over 60 y.o.) are very different from younger people. One characteristics of many seniors is a decrease of microbiome diversity — the same situation that happens with some medical conditions. 

Changes with Age

“Beyond descriptive connections between microbial composition and host health status, very few studies to date have dissected the causal role of the gut microbiota during ageing. ” [2018]

“Besides microbiota diversity, reduced microbiota-related metabolic capacity, such as lower short-chain fatty acids (SCFAs) levels, in old age may also be associated with aging-related maladies such as irregular bowel transit, reduced appetite, frailty, weight loss, cognitive decline, hypertension, vitamin D deficiency, diabetes, arthritis, sarcopenia, etc. [47–50].”

• “As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians.” [2010]

• “In centenarians, we observed a reduction in the quantity of enterobacteriaceae, bifidobacteria, and bacteroides and an increase in clostridia sensu stricto.  The presence of Bifidobacterium longum in the gut seems to be a particular feature in centenarians. It is interesting to note that only 1 strain of B. longum was isolated from each centenarian subject.” [2012]

Diet Changes Suggested in the literature

• A high proportion of leucine is required for optimal stimulation of the rate of muscle protein synthesis by essential amino acids in the elderly. [2006]
  • “We conclude that increasing the proportion of leucine in a mixture of essential amino acid  can reverse an attenuated response of muscle protein synthesis in elderly”
• Insufficient Protein Intakes is Highly Prevalent among Physically Active Elderly[2018].
• A Distinct Pattern of Circulating Amino Acids Characterizes Older Persons with Physical Frailty and Sarcopenia: Results from the BIOSPHERE Study[2018].
  • “Older adults with Physical frailty and sarcopenia(PF&S) were characterized by higher levels of asparagine, aspartic acid, citrulline, ethanolamine, glutamic acid, sarcosine, and taurine. The profile of non (PF&S) participants was defined by higher concentrations of α-aminobutyric acid and methionine. “
• Effects of Adherence to a Higher Protein Diet on Weight Loss, Markers of Health, and Functional Capacity in Older Women Participating in a Resistance-Based Exercise Program.[2018]
• A meal with mixed soy/whey proteins is as efficient as a whey meal in counteracting the age-related muscle anabolic resistance only if the protein content and leucine levels are increased.[2018]
• “Most published results, based on data from either epidemiological or short-term studies, indicate a potential beneficial effect of increasing protein intake in elderly adults. These data demonstrate that elderly adults, compared with younger adults, are less responsive to low doses of amino acid intake [18]. However, this lack of responsiveness in healthy older adults can usually be overcome with higher levels of essential amino acid (EAA) consumption [18]. This is also reflected in studies comparing varying levels of protein consumption [19], suggesting that the lack of muscle responsiveness to lower doses of protein intake in elderly adults can be overcome with a higher level of protein intake. The requirement for a larger dose of protein to generate responses in elderly adults similar to the responses in younger adults provides the support for a beneficial effect of increased protein in older populations [8].” [2016]

Back to my primary topic of this blog

Old muscle in young body: an aphorism describing the Chronic Fatigue Syndrome [2018]. 

• “The data support the hypothesis that patients with CFS are subjected to some of the problems typical for muscle aging, which is probably related to disorders of muscle protein synthesis and biogenesis of mitochondria.

Bottom Line

There is a lot of literature recently published stating the same things:

• Higher protein content than a younger person “The optimum amount for elderly adults (0.24 g/kg/meal) is approximately 70% greater than that for young adults (0.8 g/kg/day) [19], indicating an age-associated anabolic resistance to dietary protein.”
• Leucine content is very important. See this page for the suggested foods and this page also.
  • 2.5 g is 1 serving of Greek Yogurt = 5 eggs, but half the calories
  • Study with an addition of ( 3.2 g L-leucine, 0.9 g L-valine, 0.9 g L-isoleucine) [2018]

Some 15 years ago, I recall many people with CFS/ME had significant improvement with non-denatured whey — an excellent source of protein.

Translation to American

0.24 g/kg/meal – means for a 200 lb person we are talking ~ 3 oz/day of good quality protein that is high in Leucine.

Condition Citations

I have made viewing the citations (sources of information) easier. At present, there is at least one academic research using my site to find the articles of interest and validating my encoding of the information into the database.

This is located here , http://microbiomeprescription.azurewebsites.net/Library/ConditonAdjustments

When you click on one of these, you will be shown the citations:

Easier viewing of Taxonomy Layers to Conditions 

I have enabled changing the condition by just selecting a condition and clicking a button.

I have been asked this often. My answer is extremely logical but not what you will get from most health experts (and unfortunately, may not be easy to determine for some).

The Diet….

Very simple — the type of diet that your ancestors ate 300+ years ago! 

From a post that I did three years ago:

Some nuggets that I found in a Christmas Present…

My wife gave me “Danish Cookbooks” by Carol Gold. This is NOT a cook book, but rather an academic study of cookbooks published in Denmark.  I’m 100% Danish and very interested in history.

I have always been inclined towards going for ancestral diet patterns, and did Paleo for a while. My problem with Paleo is that it is more idealogical based than actual (scientific) archeologically based. It is also trying to jump the diet back thousands of years which effectively ignores how our bacteria evolved to meet our changes of diet.

A diet based on typical diet of your ancestors 400 – 1400 years ago is likely a better choice. You avoid the newly introduced foods, for example, potatoes. You also avoid process foods and modern additives. On the plus side, your gut bacteria is likely closer to the optimized bacteria your ancestors evolved from eating the same food for a thousand years.

In this book, I found two gems from the historical records:

• We have decreased the use of spice considerably — in 1600, the common spices were:
  • cumin, anise, coriander, dill, fennel, lavender, sage, rosemary, mint, bay leaves, cloves, pepper, saffron, thyme, marjoram, nutmeg, cardamon, ginger, cinnamon, hyssop, wormwood, lemon balm, angelica-root.
  • “The issue here is … the use of seasonings in general slackens” p.47
  • Many of these spices (like wormwood and ginger) have strong antibacterial characteristics which would have kept some gut bacteria families in control well.
• “Their most common food was meat” p. 122
• White (wheat) bread was very uncommon, expensive, and typically seen only in upper class homes on special occasions(not as part of the regular menus). It appears that most of the carbohydrates came from Rye Bread.

I am sure that some readers who favor a diet that is vegan or vegetarian on ideological grounds would object to these suggestions.  My response is simple, if your ancestors were vegetarians for centuries or millenniums (as some friends who were born in India can validly claim), then that is the right diet without any doubts.

Evidence shows that gut bacteria is inherited through generations — hence it is good to know what your ancestors ate because your gut bacteria have likely adapted to that diet. Given my heritage (which likely applies to people from the UK, Poland, northern France and Germany etc), this boils down to:

• Rye Bread without any wheat flour
• Meat and Fish (especially since the family seemed to always been within 5 miles of the coast back to 1500..)
• Vegetables:
  • Cauliflower
  • Artichoke
  • Rutabaga
  • Turnip
  • Beets “From the Middle Ages, beetroot was used as a treatment for a variety of conditions, especially illnesses relating to digestion and the blood.”
  • For more, see http://www.oldcook.com/en/medieval-vegetables

No potatoes — they really did not enter my ancestor dies until the early 1800’s – after one of my great-grandfathers was born. Little or no sugar (“Worldwide through the end of the medieval period, sugar was very expensive^[1] and was considered a “fine spice“,^[2] but from about the year 1500, technological improvements and New World sources began turning it into a much cheaper bulk commodity.” – Wikipedia)

This Wikipedia article may be a helpful start for many.

The last item needs to be taken with a touch of salt and sung: “A spoonful of soil helps the microbiome recover!” We have become hyper-hygienic. See the Hygiene hypothesis. This comes from a post in 2016:

“The Amish and Hutterites are U.S. agricultural populations whose lifestyles are remarkably similar in many respects but whose farming practices, in particular, are distinct; the former follow traditional farming practices whereas the latter use industrialized farming practices….Despite the similar genetic ancestries and lifestyles of Amish and Hutterite children, the prevalence of asthma and allergic sensitization was 4 and 6 times as low in the Amish” – i.e. industrialized farming practices resulted in six times (600%) the rate of asthma and allergies. See Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children(2016). This is also echoed in their farm products!!! Amish and Hutterite Environmental Farm Products Have Opposite Effects on Experimental Models of Asthma [2016]. Given a choice of buying groceries from a Hutterite farm or a Amish farm, buy the Amish (non industrialized) groceries!!!!

So I advocate not a Paleo diet, but a medieval-food diet (modified for modern nutritional needs). No prepared foods (talk about being extremely unnatural!), so food prepared from scratch — ideally organic with heritage seeds.

A reader asked me to add some more conditions (and nicely supplied some links to pubmed articles for those conditions reporting the microbiome shifts). So if you want additional ones, just do the same — send me the conditions and pubmed articles for those conditions reporting the microbiome shifts

Available Conditions

These are from this page, http://microbiomeprescription.azurewebsites.net/Library/ConditonAdjustments

•  ADHD – View Taxonomy Layers for this condition
•  All Bacteria associated with any conditions – View Taxonomy Layers for this condition
•  Allergies – View Taxonomy Layers for this condition
•  Alzheimer’s disease – View Taxonomy Layers for this condition
•  Amyotrophic lateral sclerosis (ALS) Motor Neuron – View Taxonomy Layers for this condition
•  Asthma – View Taxonomy Layers for this condition
•  Autism – View Taxonomy Layers for this condition
•  Autoimmune Disease – View Taxonomy Layers for this condition
•  Brain Trauma – View Taxonomy Layers for this condition
•  Chronic Fatigue Syndrome – View Taxonomy Layers for this condition
•  Chronic Kidney Disease – View Taxonomy Layers for this condition
•  Crohn’s Disease – View Taxonomy Layers for this condition
•  Depression – View Taxonomy Layers for this condition
•  Gout – View Taxonomy Layers for this condition
•  Graves’ disease – View Taxonomy Layers for this condition
•  Hashimoto’s thyroiditis – View Taxonomy Layers for this condition
•  High Blood Pressure – View Taxonomy Layers for this condition
•  Histamine Issues – View Taxonomy Layers for this condition
•  Histamine Issues From Ubiome – View Taxonomy Layers for this condition
•  Inflammatory Bowel Disease – View Taxonomy Layers for this condition
•  Irritable Bowel Syndrome – View Taxonomy Layers for this condition
•  Liver Cirrhosis – View Taxonomy Layers for this condition
•  Metabolic Syndrome – View Taxonomy Layers for this condition
•  Mood Disorders – View Taxonomy Layers for this condition
•  Multiple Sclerosis – View Taxonomy Layers for this condition
•  Non-alcoholic Fatty Liver Disease – View Taxonomy Layers for this condition
•  Parkinson’s Disease – View Taxonomy Layers for this condition
•  Psoriasis – View Taxonomy Layers for this condition
•  Rheumatoid arthritis – View Taxonomy Layers for this condition
•  Schizophrenia – View Taxonomy Layers for this condition
•  Sclerosis – View Taxonomy Layers for this condition
•  Sjögren syndrome – View Taxonomy Layers for this condition
•  Small Intestinal Bacterial Overgrowth (SIBO) – View Taxonomy Layers for this condition
•  Stress / post-traumatic stress disorder – View Taxonomy Layers for this condition
•  Systemic Lupus Erythematosus – View Taxonomy Layers for this condition
•  Type 2 Diabetes – View Taxonomy Layers for this condition
•  Ulcerative colitis – View Taxonomy Layers for this condition

New Chart types

Above you see “View Taxonomy Layers” which I spent most of today coding and testing. Some examples below. The reason is simple, some data is by species, other by genus, other by family — these charts connect the data better in a visual fashion. (Click on image below to see it better)

Earlier I had created a page for suggestions based on microbiome shifts reported in the literature. A chart of these relationship is shown here.

Today, I have updated the page to allow multiple conditions to be picked and see what the net results are. For example, suppose someone has:

• Allergies
• Asthma
• Depression
• IBS

Then just click the Suggestions button and the usual suggestions screen appears:

Items like L. Reuteri, L.Rhamnosus gg, L.Kefiri and mastic gum are strong recommendations, while L. Gasseri and E.Coli probiotics are to be avoided.

Bottom Line

This enhancement should reduce the complexity of trying to use this page when you have multiple conditions. 

I review the literature about once a month and add new information regularly — so your results may change each month.