Hand picking bacteria to modify

Many bacteria have no known effect. The default approach is to focus on high and low bacteria with a goal to move them towards the commonly seen values using all of the bacteria.

There are various filters available (i.e. use only bacteria associated with some medical conditions), but some people wish to really focus on certain bacteria only. A recent enhancement provides that ability

Where you can pick bacteria

There are three spots that you can pick bacteria on http://microbiomeprescription.com/ . You can select some from each spot; the ones selected will be aggregated.

Start by going to My Biome View
Put a check besides the ones of concern and click the top button
These hand picked buttons will now appear
Click on View Hand Picked Taxa to see what you have selected and the values
Looking at Symptoms, Click and then pick one of your symptoms
On Bacteria Explorer Plus, the checkboxes are on the left side. Select and click
We have both selections merged
Using data from published medical studies click above
And for published studies, the same pattern
We have a composite selected in three different ways.

Suggestions

A lot of the bacteria filtering options are removed because they are not needed. You have already picked the bacteria.

  • If you have only a few bacteria (< 20) then Include Parent / Children is recommended

The Video Walkthru

ThyrveInside Reports vs MicrobiomePrescription Reports

This post is looking at Thyrve Subject Reports vs MicrobiomePrescription reports. Interpretation depends on which studies you use and methodologies. There is no right or wrong answer.

With that said, having received my first Thryve Report, I am curious on how they compare (when there are tough equivalents).

Gut Score

The first item is that Thryve is building their report on “compared to those of the healthy population from the American Gut Project“. Oops we have an apples to crab apples scenario, different equipment, different processes. I am disappointed that they do not have a reference using only their equipment and samples. uBiome attempted to do that (but some employees submitted their pet’s microbiome into the mix!)

So I am healthier than the average person
I am 11% above a healthy score — what does that mean? How was healthy determined?
Microbiome Prescription gives a percentile score. The numbers are in conceptual agreement

Likelihood Analysis

Reviewing this page, I chuckled because they do not give a single likelihood (a probability measure). They simply give your numbers against the average range.

They cite two bacteria only and it is unclear if high or low will cause the pain.

While on MP we have some 17 bacteria associations with where the peak values are.

We are in agreement for Faecalibacterium but Lactobacillus did not reach statistical significance

And on MP we have the following being statistically very significant for bloating:

  • Butyricicoccus (genus)
  • Faecalibacterium (genus)
  • Ruminococcaceae (family)
  • Subdoligranulum (genus)

On MP, well, we have many bacteria identified. Lactobacillaceae (family) is there, but it’s child Lactobacillus (genus) is not. Bifidobacterium is not.

Likelihood Analysis Bottom Line

It looks like Thryve’s information is very old and very stale. The information may well be coming from studies that did not use 16s to obtain populations.

They have been entrusted with a warehouse of data from their customers and have not been good stewards of it (I am an old fashion person that grew up with a strong understanding of and importance of stewardship).

Your Gut Bacteria

Thryve attempts to give health benefits and associated diseases. Again, they seem to have old stale information.

http://microbiomeprescription.com/library/details?taxon=1239
http://microbiomeprescription.com/library/details?taxon=28890
http://microbiomeprescription.com/library/details?taxon=256845

Probiotics

They do not appear to make recommendation solely off the microbiome. I speculate they take the health information and look up based on that information.

For me, they came up with:

  • Lactobacillus reuteri
  • Lactobacillus rhamnosus
  • Lactobacillus casei 
  • Bifidobacterium lactis

The MicrobiomePrescript site came up with:

And near the top of my avoid list

Lactobacillus rhamnosus did not show up.

We both had the same microbiome data. Microbiome Prescription does provide the studies that the suggestions were based on. Thryve does not.

Bottom Line

ThryveAlive works well for providing reports on your microbiome. Given the demonstrated staleness of the data on their site (it costs a lot of money to keep current unless you have someone willing to donate the many hours for the public good).

Most microbiome providers likely fall into the same staleness trap. They put the effort in to get their website up and looking good, then they coast along without keep current because they do not wish to spend the money to keep current (especially true if there is venture capital backing the firm).

NOTE: The data on MicrobiomePrescription is available for Commercial Licensing, see this post.

Eating for your heritage microbiome

I thought that it would be good to recap my belief of what the real super foods are. The logic is simple and should be seriously considered.

Our microbiome has evolved over thousands of years. It has become tuned to the available diet in a region. Classic Darwinism. Many alternative medicine types will focus on the dangers of new modern foods. I agree with their core model but they really blew it when it comes to what the older food diet should be! We tend to have two schools –“The Paleolithic diet, Paleo diet, caveman diet, or stone-age diet is a modern fad diet requiring the sole or predominant eating of foods presumed to have been available to humans during the Paleolithic era. “[Wikipedia] and food styles/processing that came into existence after the 1960’s. IMHO, both are very wrong.

Paleolithic ended 12,000 years ago or more. Skipping over twelve millenium of microbiome evolution does not seem rational; it assumes that the microbiome ability to adapt is extremely low and slow. On the other hand, those that attack recent food and diet changes, and jumping back just 60 years assumes an imaginary ‘golden era’ for the gut at a time when there was rapid changes of diet and food.

I wrote about this issue in an earlier post, What is the best diet?

I am a huge fan of Time Team and from it acquire some interesting perspectives. For most of the last two thousand years in Europe, water was not safe to drink. Safe drinking was wine or beer. If you are a northern european, wine was a luxury item… so it became beer.

From one time team episode, I learn that toddlers were given beer once they cease nursing (it was the safest thing to do!). It was not beer as we know it today. The barley malt would be used and reused, with each brewing cycle getting weaker and weaker beer (in terms of alcohol). It was this last cycle of beer that was given to toddlers.

The German Purity Law of 1516, defines what was to be used. It requires that ‘nothing other than barley, hops and water be used’ to produce beer.  No wheat. No Corn. Wheat was actually a luxury grain for most of this time in northern Europe.

What does Barley impacts… lots of bacteria, and I mean LOTS. See this page!

So, for a long time a common child would likely get barley or oats porridge for breakfast, served with weak barley beer. That was my father’s breakfast when he lived with his parents. Sugar was also expensive and a luxury.

Lots of root vegetables – swedes, turnips, and very very later, potatoes (not until after 1800!); in other words, high fiber vegetables.

During my recovery, it was interesting to note how often these specific foods show up as strong suggestions produced by the microbiome AI engine for my microbiome. It almost implied that going apostate from the food of my ancestors was the cause of ME/CFS.

We have lost touch with our microbiome heritage. Salad in winter is unnatural for northern Europeans. Season cycles of food is what our microbiome evolved to handle. In today’s world, we eat the same — year in and year out. IMHO, that is also unnatural.

Bottom line — give some serious thought to what your microbiome’s inheritance is going back many generations. All of us have a high percentage of the common worker in us, what did they eat?

ME/CFS Relapse Report #8

My recovery continues — I am doing up to 12,000 steps/day. Lactobacillus and bifidobacterium has returned to my microbiome. I no longer matching the criteria for a ME/CFS diagnosis and the remaining symptoms are minor and only occasionally appear.

If you are interested in taking this approach, suitable testing labs are listed here.

My last uBiome report was being processed when the uBiome site disappeared. I have since done a Thryve Alive report. I must honestly state that it is superior because it reported on more bacteria, as shown below.

Ken Microbiome Results

Earlier reports for those that are interested in the timeline.

  • Report #1
  • Report #2
  • Report #3
  • Report #4
  • Report #5
  • Report #6
  • Report #7

For consistency, I will start by following the pattern in my prior #7 post.

Diversity

The changing of labs makes this difficult. Thryve reports more taxa which will cause an apparent jump to Diversity. This is very visible in the table below. There are two possible solutions: using FASTQ from all sources, uploading my uBiome FASTQ files to Thryve for processing with their analysis engine. Both of these will take some time to do.

End Products and Taxonomy

I have not had time to update the charts to the fine grain percentile that I am showing for individual samples (on my to do list)

Lactobacillus is BACK!

My levels are normal ( 57%ile)

Bifidbacterium is back

I have some, low compare to other (22%ile), but it is there

More interesting bacteria shifts

Remember the relapse started at the end of March, 2019.

This bacteria is strongly associated to ME/CFS, IBS, Sjögren syndrome in published medical studies.
This bacteria seems strongly associated and appears to keep trying to come back.
I suspect this family are friendly to the above
As is this one.
One more of the ME/CFS Cartel
And more still

Bottom Line

This is a first part of my #8 report. The change to Thryve as a microbiome provider means that I do not have a variety of charts that uBiome provided and in some cases, I have start revising some pages to better show what is happening in terms of bacteria (most of the above charts are from a page that I revised today).

What do I owe my recovery to? “Eating my own dog food”. Before the relapse, I advocated the microbiome model and was already building the AI engine to make suggestions to correct the microbiome. It was a matter of getting regular microbiome samples (Thryve is my preferred provider today) and then adjusting supplements and diet from the suggestions made by the AI.

The probiotics that the AI currently advises — I am doing Symbioflor-2 (alternative to Mutaflor) and about to reorder from Custom Probiotics.
The ones that are definite avoids according to the AI
Hmmm.. Apple Pie looks like ‘medicine’ now

My remaining symptoms are occasionally exhaustion after a eight hour day of activities (with no apparent payback on the next day), this may include my tell-tale hiccups of becoming overtired. While I can multitask when required, I do active push back when asked to — it’s simply another stressor which it is best that I minimize.

On the other side, I would not dream of returning to my work situation of January 2019 with 90 minutes commute each way, dysfunctional work team, and occasional 12 hr days on site, etc. I am NOT that much recovered, and honestly, do not expect to be able (or want to) to do that again safely.

I am planning to send off another Thryve sample next week, to continue this story and monitoring.

What are common symptoms with ME/CFS?

It is important to note that the ME/CFS diagnosis often requires only 4 of these when other probable causes are excluded. Typically it is 6 months of tests to do a full and proper elimination of all of the probable causes. Some MDs are known to drop patients into this category (unprofessionally) instead of having to do full testing.

On some facebook groups, I have seen new ME/CFS patients ask “is XYZ common with ME/CFS” – this attempts to answer this with sources of information gathered from experienced professionals.

It is important to note that symptoms, severity etc changes over time –for each of the four incidence of ME/CFS that I have had, the dominant symptoms were different and in transition to remission, symptoms changed a lot (including new one appearing for short periods!)!

Life is never dull with ME/CFS Symptoms!

extreme physical and mental tiredness (fatigue)

sleep problems, such as insomnia

muscle or joint pain

headaches

sore throat or sore glands that aren’t swollen

problems thinking, remembering or concentrating

flu-like symptoms

feeling dizzy or sick

fast or irregular heartbeats (heart palpitations)

National Health Service (UK)

Greatly lowered ability to do activities that were usual before the ill Worsening of symptoms while standing or sitting upright. This is called orthostatic intolerance

Muscle pain and aches

Joint pain without swelling or redness

Headaches, either new or worsening

Tender lymph nodes in the neck or armpits

A sore throat that happens often

Digestive issues, like irritable bowel syndrome

Chills and night sweats

Allergies and sensitivities to foods, odors, chemicals, or noise

Center for Disease Control (US)

[ ]  Fatigue, characterized as a profound loss of energy
[   ] Worsening of symptoms after physical or mental exertion (post-exertional malaise, or PEM)
[   ] Cognitive function problems
[   ] Attention deficit disorder (inability to concentrate)
[   ] Feeling “spaced out” or “cloudy,” “brain fog”
[   ] Calculation difficulties
[   ] Memory loss
[   ] Spatial disorientation
[   ] Word searching or saying the wrong word
[   ] Sleep disturbance, unrefreshing sleep
[   ] Flu-like malaise, feeling “sick all over”, or “poisoned”
[   ] Sore throat
[   ] Low-grade fever or feeling hot often
[   ] Low body temperature
[   ] Muscle and joint aches with or without “trigger points”
[   ] Headache
[   ] Changes in vision
[   ] Numbness or tingling sensations
[   ] Loss of balance, dizziness
[   ] Unusually vivid dreams, nightmares, or lack of dreams
[   ] Depression
[   ] Anxiety, panic attacks
[   ] Personality changes
[   ] Mood swings
[   ] Difficulty moving the tongue to speak
[   ] Tinnitus (ringing in the ears)
[   ] Paralysis
[   ] Severe muscle weakness
[   ] Difficulty walking
[   ] Blackouts
[   ] Photophobia (light sensitivity), and increased sensitivity to noise, smells, touch
[   ] Alcohol intolerance
[   ] Changes in taste, smell, hearing
[   ] Decreased libido, impotence
[   ] Muscle twitches
[   ] Severe premenstrual syndrome (PMS) or exacerbation of symptoms before and during period
[   ] Weight changes, usually loss followed by gain
[   ] Painful, swollen lymph nodes, especially on the neck and underarms
[   ] Abdominal pain, diarrhea, nausea, gas, irritable bowel
[   ] New allergic reactions to medicines, food, and other substances
[   ] Night sweats
[   ] Heart palpitations
[   ] Uncomfortable or frequent urination
[   ] Rash of herpes simplex or shingles
[   ] Flushing, rash
[   ] Hair loss
[   ] Chest pain
[   ] Dry eyes and mouth (sicca)
[   ] Cough, dry
[   ] Canker sores
[   ] Cold hands and feet
[   ] Shortness of breath
[   ] Temperature and weather sensitivity
[   ] Symptoms worsen when standing up (orthostatic intolerance)
[   ] Seizures, usually petit mal, but sometimes grand mal

American Myalgic Encephalomyelitis and Chronic Fatigue Syndrome Society

. Most Common Symptoms of ME/CFS
Exhaustion, made worse by physical exercise (100%)
Low-grade fever in early stages (60-95%)
Recurrent flu-like illness (75%)
Frequent pharyngitis (sore throats) (50-75%)
Joint and muscle pain (65%)
Severe muscle weakness (40-70%)
Stiffness (50-60%)
Post-exertional fatigue & flu-like symptoms (50-60%)
Multiple sensitivities to medicines,  foods, and chemicals (40-60%)
Severe nasal & other allergies (often with worsening of previous mild allergies) (40-60%)
Frequently recurring, difficult to treat respiratory infections (40-60%)
Dyspnea (labored breathing or hunger for air) on exertion
Painful lymph nodes (especially on neck and under arms) (30-40%)
2. Neurological Symptoms
Sleep disorders & unrefreshing sleep (50-90%)
Headaches (35-85%)
Visual blurring (50-60%)
Intolerance of bright lights
Parasthesias (numbness or tingling feelings) (30-50%)
Dizziness/ Lightheadedness (30-50%)
Ringing in the ears
Impaired cognition (50-85%)
Attentional difficulties
Calculation difficulties
Memory disturbance
Spatial disorientation
Saying the wrong word
3. Other Symptoms
Worsening of premenstrual symptoms (70% of women)
Nocturia (excessive urination during the night) (50-60%)
Tachycardia (abnormal rapid heart action) (40-50%)
Chest pain (25-40%)
Cough (30-40%)
Weight gain (50-70%)
Nausea, especially in earlier stages (50-60%)
Diarrhea, intestinal gas or irritable bowel (50%)
Intolerance of alcohol
Night sweats (30-50%)
Dry eyes (30-40%)
Dry mouth (30-40%)
Rash (30-40%)
Frequent cancer sores (30-40%)
Herpes simplex or shingles (20%)
Symptoms worsened by extremes in temperature
4. Less Common Symptoms
Mitral valve prolapse
Paralysis
Seizures
Blackouts
5. Psychological symptoms
Depression (reactive or secondary depression)
Anxiety (including panic attacks and personality changes)
Emotional lability (mood swings)
Psychosis

 Massachusetts ME/CFS & FM Association.

Cognitive
difficulties processing information
concentration problems
confusion
difficulties with word retrieval
word mix-ups
short-term memory difficulties
slowness in cognitive processes

Motor (movement) and balance
muscle weakness or paralysis
poor balance, ataxia & tandem gait
clumsiness & tendency to drop things
difficulty in tandem gait
atypical numbness or tingling

Sleep disruption
sleep disturbance – hypersomnia or insomnia
non-refreshing sleep

Visual and auditory[edit | edit source]
photophobia
visual changes or eye pain
double, blurred or wavy vision
dry or itchy eyes
tinnitus – buzzing or ringing in ears
hyperacusis & cocktail party phenomena

Neuropsychological
emotional flattening or personality change
loss of adaptability
anxiety &/or panic attacks
reactive depression
worsening of symptoms with stress

Immune system
new sensitivities to medications, chemicals
tender lymph nodes
recurrent sore throat
recurrent flu-like symptoms

Reproductive
dysmenorrhea
PMS or irregular menstrual cycles
loss of sexual libido or impotence

Respiratory (breathing)
exertional dyspnea (short of breath)
sinusitis
persistent cough & wheezing

Urinary
urinary frequencybladder dysfunction

Circulatory
neurally mediated hypotension
postural orthostatic tachycardia syndrome (POTS)
delayed orthostatic hypotension
dizziness/light-headedness
heart palpitations
fluid retention
extreme pallor
bruising

Digestive
lump in throat
nausea
heartburn
abdominal pain
irritable bowel syndrome

Neuroendocrine
loss of thermostatic stability – low body temperature or diurnal fluctuations
hot flushes
excessive sweating or night sweats
feelings of feverishness
feelings of cold extremities
heat/cold intolerance
anorexia or abnormal appetite
marked weight loss or gain
hair loss

Musculoskeletal
pain in muscles (myalgia)
muscle cramps, particularly in legs
chest pain and pressure
pain in multiple joints (arthalgia)
TMJ

Neurological (nervous system)
persistent fatigue
lack of endurance
migraines or new onset headaches
seizure-like phenomena

Sensory
hypersensitivity to pain
hyper-responsiveness to noxious stimuli
perceptual & dimensional distortions
feeling of burning or swelling
overload phenomena
loss of cognitive map

Canadian consensus criteria (CCC) symptom list

Bottom Line

The model that I use for ME/CFS is a microbiome dysfunction. On my citizen science site, we have found extremely strong associations of some symptoms with specific bacteria shifts.

Review those associations here:
http://microbiomeprescription.com/Data/EurekaExplorer1