A reader email indicating that he believe that some of my suggestions also produced lactic acid. At present that is no option for filtering, but I am working on that. This appears to be a subset of ME/CFS patients. A 2015 Guest Blog post on Health Rising provided a summary of early studies. The latest study is below.

Examining clinical similarities between myalgic encephalomyelitis/chronic fatigue syndrome and D-lactic acidosis: a systematic review. [2017]

This is associated with neurlogical issues (brain fog etc).

Sleep Consequences

Sleep issues in ME/CFS may be connected to excessive D-Lactic acid (A known characteristic of ME/CFS)

Results and conclusion: Administration of L-lactate does not influence sleep-wake cycle of experimental animals. At the same time, its artificial optical analog D-lactate induces the significant (as compared to the control) decrease in wake (34.8% to 26.5%) and increase in slow wave sleep (57.4% to 69.2%). It has been suggested that D-lactate may be the antagonist of one or several L-lactate receptors.

[D-lactate as a novel somnogenic factor?] [2020]

Root cause: Low Veillonella?

See this post: on what this bacteria does with lactic acid.

I have lactate acid producer estimates on the microbiomeprescription site for uploaded 16s samples (typically ubiome). My own numbers appear to follow the research. With onset it kept increasing, and with the last ubiome started to decrease.

I did not have significant neurological issues BUT these values are all low according to the uploaded samples. Which suggests that while the amount increased, it did not reach impairing levels for neurological issues

The list below are what is in the database as producing the two items above. If you know of additional items, please forward the information (with a link to the study of course!).

Acidiphilium (genus)
Acidiphilium cryptum (species)
Aerococcus (genus)
Aerococcus christensenii (species)
Aerococcus urinae (species)
Aerococcus urinaeequi (species)
Aerococcus vaginalis (species)
Aerococcus viridans (species)
Allobaculum (genus)
Allobaculum stercoricanis (species)
Anaerostipes (genus)
Anaerostipes butyraticus (species)
Anaerostipes caccae (species)
Anaerostipes hadrus (species)
Anaerostipes sp. 1y-2 (species)
Anaerostipes sp. 3_2_56FAA (species)
Anaerostipes sp. 494a (species)
Anaerostipes sp. 5_1_63FAA (species)
Anaerostipes sp. AIP 183.04 (species)
Anaerostipes sp. IE4 (species)
Atopobium (genus)
Atopobium parvulum (species)
Atopobium rimae (species)
Atopobium sp. BS2 (species)
Atopobium sp. DMCT15023 (species)
Atopobium sp. F0209 (species)
Atopobium sp. HHRM1715 (species)
Atopobium sp. ICM57 (species)
Atopobium sp. ICM58 (species)
Atopobium sp. MVA9 (species)
Atopobium sp. S3MV24 (species)
Atopobium sp. S3PFAA1-4 (species)
Atopobium sp. S4-A11a (species)
Atopobium vaginae (species)
Bacillus coagulans (species)
Bifidobacterium (genus)
Bifidobacterium actinocoloniiforme (species)
Bifidobacterium adolescentis (species)
Bifidobacterium angulatum (species)
Bifidobacterium animalis (species)
Bifidobacterium asteroides (species)
Bifidobacterium biavatii (species)
Bifidobacterium bifidum (species)
Bifidobacterium bohemicum (species)
Bifidobacterium bombi (species)
Bifidobacterium boum (species)
Bifidobacterium breve (species)
Bifidobacterium catenulatum (species)
Bifidobacterium choerinum (species)
Bifidobacterium commune (species)
Bifidobacterium dentium (species)
Bifidobacterium gallicum (species)
Bifidobacterium gallinarum (species)
Bifidobacterium indicum (species)
Bifidobacterium kashiwanohense (species)
Bifidobacterium longum (species)
Bifidobacterium magnum (species)
Bifidobacterium merycicum (species)
Bifidobacterium minimum (species)
Bifidobacterium mongoliense (species)
Bifidobacterium pseudocatenulatum (species)
Bifidobacterium pseudolongum (species)
Bifidobacterium pullorum (species)
Bifidobacterium ruminantium (species)
Bifidobacterium saeculare (species)
Bifidobacterium scardovii (species)
Bifidobacterium sp. (species)
Bifidobacterium sp. 120 (species)
Bifidobacterium sp. 138 (species)
Bifidobacterium sp. 65947 (species)
Bifidobacterium sp. MSX5B (species)
Bifidobacterium stercoris (species)
Bifidobacterium subtile (species)
Bifidobacterium thermacidophilum (species)
Bifidobacterium tsurumiense (species)
Cardiobacterium (genus)
Cardiobacterium hominis (species)
Cardiobacterium valvarum (species)
Carnobacterium (genus)
Carnobacterium divergens (species)
Carnobacterium maltaromaticum (species)
Catenibacterium (genus)
Catenibacterium mitsuokai (species)
Collinsella (genus)
Collinsella aerofaciens (species)
Collinsella intestinalis (species)
Collinsella sp. GD3 (species)
Collinsella stercoris (species)
Collinsella tanakaei (species)
Comamonas (genus)
Comamonas testosteroni (species)
Coprobacillus (genus)
Coprobacillus cateniformis (species)
Coprobacillus sp. D6 (species)
Desulfitobacterium (genus)
Desulfitobacterium aromaticivorans (species)
Desulfitobacterium metallireducens (species)
Desulfobacterium (genus)
Desulfobacterium autotrophicum (species)
Enterococcus (genus)
Enterococcus alcedinis (species)
Enterococcus asini (species)
Enterococcus avium (species)
Enterococcus canis (species)
Enterococcus casseliflavus (species)
Enterococcus cecorum (species)
Enterococcus columbae (species)
Enterococcus durans (species)
Enterococcus faecalis (species)
Enterococcus faecium (species)
Enterococcus gilvus (species)
Enterococcus haemoperoxidus (species)
Enterococcus hermanniensis (species)
Enterococcus hirae (species)
Enterococcus italicus (species)
Enterococcus malodoratus (species)
Enterococcus mundtii (species)
Enterococcus pallens (species)
Enterococcus raffinosus (species)
Enterococcus sp. C6I11 (species)
Enterococcus sp. SI-4 (species)
Enterococcus sulfureus (species)
Enterococcus ureasiticus (species)
Fusobacterium (genus)
Fusobacterium equinum (species)
Fusobacterium gonidiaformans (species)
Fusobacterium mortiferum (species)
Fusobacterium necrogenes (species)
Fusobacterium necrophorum (species)
Fusobacterium nucleatum (species)
Fusobacterium perfoetens (species)
Fusobacterium periodonticum (species)
Fusobacterium sp. ACB2 (species)
Fusobacterium sp. CM21 (species)
Fusobacterium sp. CM22 (species)
Fusobacterium sp. CM55 (species)
Fusobacterium sp. DJF_B100 (species)
Fusobacterium sp. OBRC1 (species)
Fusobacterium ulcerans (species)
Fusobacterium varium (species)
Gemella (genus)
Gemella asaccharolytica (species)
Gemella haemolysans (species)
Gemella morbillorum (species)
Gemella palaticanis (species)
Gemella sp. 933-88 (species)
Gemella sp. oral strain A31SC (species)
Haemophilus (genus)
Haemophilus aegyptius (species)
Haemophilus ducreyi (species)
Haemophilus haemoglobinophilus (species)
Haemophilus haemolyticus (species)
Haemophilus influenzae (species)
Haemophilus parahaemolyticus (species)
Haemophilus parainfluenzae (species)
Haemophilus pittmaniae (species)
Haemophilus sputorum (species)
Holdemania (genus)
Holdemania filiformis (species)
Lachnobacterium (genus)
Lachnobacterium bovis (species)
Lactobacillus (genus)
Lactobacillus acetotolerans (species)
Lactobacillus acidophilus (species)
Lactobacillus agilis (species)
Lactobacillus algidus (species)
Lactobacillus amylolyticus (species)
Lactobacillus animalis (species)
Lactobacillus antri (species)
Lactobacillus apis (species)
Lactobacillus bifermentans (species)
Lactobacillus brantae (species)
Lactobacillus brevis (species)
Lactobacillus casei (species)
Lactobacillus ceti (species)
Lactobacillus coleohominis (species)
Lactobacillus composti (species)
Lactobacillus coryniformis (species)
Lactobacillus crispatus (species)
Lactobacillus crustorum (species)
Lactobacillus curvatus (species)
Lactobacillus delbrueckii (species)
Lactobacillus fermentum (species)
Lactobacillus floricola (species)
Lactobacillus fornicalis (species)
Lactobacillus gasseri (species)
Lactobacillus harbinensis (species)
Lactobacillus hayakitensis (species)
Lactobacillus helveticus (species)
Lactobacillus iners (species)
Lactobacillus ingluviei (species)
Lactobacillus intestinalis (species)
Lactobacillus jensenii (species)
Lactobacillus johnsonii (species)
Lactobacillus kefiranofaciens (species)
Lactobacillus kefiri (species)
Lactobacillus kitasatonis (species)
Lactobacillus lindneri (species)
Lactobacillus malefermentans (species)
Lactobacillus mellifer (species)
Lactobacillus mellis (species)
Lactobacillus mucosae (species)
lactobacillus murinus (Species)
Lactobacillus namurensis (species)
Lactobacillus nodensis (species)
Lactobacillus oligofermentans (species)
Lactobacillus oris (species)
Lactobacillus oryzae (species)
Lactobacillus ozensis (species)
Lactobacillus paracasei (species)
Lactobacillus parafarraginis (species)
Lactobacillus paralimentarius (species)
Lactobacillus perolens (species)
Lactobacillus plantarum (species)
Lactobacillus psittaci (species)
Lactobacillus rapi (species)
Lactobacillus reuteri (species)
Lactobacillus rhamnosus (species)
Lactobacillus rodentium (species)
Lactobacillus rogosae (species)
Lactobacillus ruminis (species)
Lactobacillus saerimneri (species)
Lactobacillus sakei (species)
Lactobacillus salivarius (species)
Lactobacillus sanfranciscensis (species)
Lactobacillus saniviri (species)
Lactobacillus selangorensis (species)
Lactobacillus songhuajiangensis (species)
Lactobacillus sp. 66c (species)
Lactobacillus sp. 7_1_47FAA (species)
Lactobacillus sp. Akhmro1 (species)
Lactobacillus sp. BL302 (species)
Lactobacillus sp. C30An8 (species)
Lactobacillus sp. C4I18 (species)
Lactobacillus sp. CR-609S (species)
Lactobacillus sp. NRCT-KU 1 (species)
Lactobacillus sp. S16 (species)
Lactobacillus sp. TAB-22 (species)
Lactobacillus sp. TAB-26 (species)
Lactobacillus sp. TAB-30 (species)
Lactobacillus taiwanensis (species)
Lactobacillus ultunensis (species)
Lactobacillus vaccinostercus (species)
Lactobacillus vaginalis (species)
Lactobacillus vini (species)
Lactococcus (genus)
Lactococcus fujiensis (species)
Lactococcus garvieae (species)
Lactococcus lactis (species)
Lactococcus raffinolactis (species)
Lactococcus sp. D2 (species)
Lactococcus sp. MH5-2 (species)
Lactococcus sp. STM1 (species)
Lactococcus sp. STM31 (species)
Lactococcus sp. TP1MJ (species)
Lactococcus sp. TP2MJ (species)
Leptotrichia (genus)
Leptotrichia genomosp. C1 (species)
Leptotrichia goodfellowii (species)
Leptotrichia hofstadii (species)
Leptotrichia hongkongensis (species)
Leptotrichia shahii (species)
Leptotrichia sp. oral taxon 223 (species)
Leptotrichia sp. oral taxon 225 (species)
Leptotrichia sp. PG10 (species)
Leptotrichia sp. PTE15 (species)
Leptotrichia wadei (species)
Leuconostoc (genus)
Leuconostoc carnosum (species)
Leuconostoc fallax (species)
Leuconostoc gelidum (species)
Leuconostoc inhae (species)
Leuconostoc lactis (species)
Leuconostoc mesenteroides (species)
Leuconostoc miyukkimchii (species)
Leuconostoc pseudomesenteroides (species)
Leuconostoc sp. C7I4 (species)
Methylobacterium (genus)
Microbacterium (genus)
Microbacterium arborescens (species)
Microbacterium aurantiacum (species)
Microbacterium halophilum (species)
Microbacterium lacus (species)
Microbacterium profundi (species)
Microbacterium saperdae (species)
Microbacterium trichothecenolyticum (species)
Microbacterium xylanilyticum (species)
Microbacterium yannicii (species)
Moryella (genus)
Moryella indoligenes (species)
Oenococcus (genus)
Pediococcus (genus)
Pediococcus argentinicus (species)
Pediococcus pentosaceus (species)
Pediococcus siamensis (species)
Pediococcus sp. 3107O2 (species)
Pediococcus sp. MFC1 (species)
Rhizobium (genus)
Rhizobium leguminosarum (species)
Roseburia (genus)
Roseburia cecicola (species)
Roseburia faecis (species)
Roseburia hominis (species)
Roseburia intestinalis (species)
Roseburia inulinivorans (species)
Roseburia sp. 11SE38 (species)
Roseburia sp. 11SE39 (species)
Roseburia sp. 499 (species)
Roseburia sp. DJF_RR73 (species)
Rothia (genus)
Rothia aeria (species)
Rothia dentocariosa (species)
Rothia mucilaginosa (species)
Rothia sp. BBH4 (species)
Rothia sp. THG-N7 (species)
Rothia terrae (species)
Ruminococcus (genus)
Ruminococcus albus (species)
Ruminococcus bromii (genus)
Ruminococcus callidus (species)
Ruminococcus champanellensis (species)
Ruminococcus faecis (species)
Ruminococcus flavefaciens (species)
Ruminococcus gauvreauii (species)
Ruminococcus lactaris (genus)
Scardovia (genus)
Scardovia wiggsiae (species)
Selenomonas (genus)
Selenomonas artemidis (species)
Selenomonas bovis (species)
Selenomonas dianae (species)
Selenomonas flueggei (species)
Selenomonas genomosp. P5 (species)
Selenomonas infelix (species)
Selenomonas lacticifex (species)
Selenomonas noxia (species)
selenomonas ruminantium (species)
Selenomonas sp. oral taxon 137 (species)
Selenomonas sputigena (species)
Serratia (genus)
Serratia marcescens (species)
Streptococcus (genus)
Streptococcus agalactiae (species)
Streptococcus australis (species)
Streptococcus constellatus (species)
Streptococcus cristatus (species)
Streptococcus danieliae (species)
Streptococcus dentapri (species)
Streptococcus dentasini (species)
Streptococcus dentirousetti (species)
Streptococcus didelphis (species)
Streptococcus equinus (species)
Streptococcus gallolyticus (species)
Streptococcus gordonii (species)
Streptococcus hyointestinalis (species)
Streptococcus infantarius (species)
Streptococcus infantis (species)
Streptococcus iniae (species)
Streptococcus marimammalium (species)
Streptococcus massiliensis (species)
Streptococcus merionis (species)
Streptococcus mitis (species)
Streptococcus mutans (species)
Streptococcus oralis (species)
Streptococcus orisasini (species)
Streptococcus orisratti (species)
Streptococcus parasanguinis (species)
Streptococcus parauberis (species)
Streptococcus pasteurianus (species)
Streptococcus peroris (species)
Streptococcus pneumoniae (species)
Streptococcus pseudoporcinus (species)
Streptococcus rubneri (species)
Streptococcus rupicaprae (species)
Streptococcus salivarius (species)
Streptococcus sanguinis (species)
Streptococcus seminale (species)
Streptococcus sobrinus (species)
Streptococcus sp. 11aTha1 (species)
Streptococcus sp. 2011_Ileo_MS_A10 (species)
Streptococcus sp. 2011_Oral_MS_A3 (species)
Streptococcus sp. 3244O2 (species)
Streptococcus sp. BS35a (species)
Streptococcus sp. GMD6S (species)
Streptococcus sp. HPH0090 (species)
Streptococcus sp. oral taxon 071 (species)
Streptococcus sp. oral taxon G59 (species)
Streptococcus sp. oral taxon G63 (species)
Streptococcus sp. S16-11 (species)
Streptococcus suis (species)
Streptococcus thermophilus (species)
Streptococcus urinalis (species)
Streptococcus vestibularis (Species)
Subdoligranulum (genus)
Subdoligranulum variabile (species)
Tetragenococcus (genus)
Tetragenococcus koreensis (species)
Tetragenococcus muriaticus (species)
Tetragenococcus solitarius (species)
Turicibacter (genus)
Turicibacter sanguinis (species)
Vagococcus (genus)
Vagococcus entomophilus (species)
Vagococcus fluvialis (species)
Vagococcus lutrae (species)
Vagococcus salmoninarum (species)
Vagococcus teuberi (species)
Weissella (genus)

A reader expressed frustration because he could not remember his symptoms when he took his ubiome sample. In response to this, I have added a new page to allow you to record symptoms when you do a sample AND these symptoms will be automatically applied to your next upload.

This is located on the detail upload page ( http://microbiomeprescription.com/upload)_

This will take you over to the new page.

If you log on first, the email should be yours. If you have never done an upload, then enter your email, click Look Up (to clear out any symptom that some one added to the bogus email) and proceed.

You can return later and adjust the symptoms if you wish.

This item has been on my backburner for a while and today I came up with an efficient algorithm to compute a short most probable symptoms. The results on my own samples were actually quite accurate.

The process is simple: Apply analysis (AI techniques) to the uploaded microbiome samples annotated with symptoms. We then flip the results to predict from an individual sample using these results. A lot of computational magic going in and out.

I have MTHFR issues (reported by conventional testing), this is my age range, cold hands and feet, I have been well aware since the 1970’s of eye focus issues (from eye specialist). The disorientation matches up with my being a high functioning autism spectrum person. The last item makes it a slam dunk….

I checked another person who I know the medical history. The person has TMJ, and just about every symptom listed!

Where is this new feature

One thing that I realized that it predicted symptoms that I would NOT associate with my current state– but actually matches the long term medical issues. For example, eye focus issues — that goes back 40 years and which is not on my radar as an active symptom.

I suspect “mouth sores” which showed up on other issues — may include gum disease being active.

Addendum

A reader try it and posted on facebook.

As a result, I added a link to the page to also give extended prediction with an indicator of the prediction confidence (score).

Recap of this Journey

For new readers: I have had Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) three times in my life and recovered each time. As a result of work stress, I am currently in a ‘flare’, because it was sudden onset and I realized what it was on day one and took aggressive action it did not become established. Established usually means six months of tests ruling out all of the possible alternative causes for the symptoms!

The model foe ME/CFS that I use is a microbiome dysfunction. I reached this conclusion long before mainstream research started to investigate and confirm that it does appear to be that, Some recent literature:

• Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? [2018]
• Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome. [2017]
• A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue SyndromeDiffer in Physiological Parameters and Gut Microbiome Composition. [2016]
• Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. [2016]

Instead of the usual 6 months of testing for what is not there, I proceeded to get my ubiome done. I had two earlier ones done from when I was in remission. I have an actual base line to compare to. This makes interpreting data a lot simpler. It also mean that I could quickly confirm ‘my gut feeling’ that is was ME flaring.

My earlier posts on the progression are below

• Sudden Onset ME Flare – uBiome One Week Later
• uBiome progression in ME Flare
• ubiome followup

First, let us review my perceived changes

Following suggestions from my last microbiome results

I had an interesting experience with a morning bowel of barley (β-Glucan) with unpasteurized yogurt with beet sugar. The first two days, felt good, day 3 & 4 sore throat appeared. Missed a day and sore throat disappear. Back on barley and day 2, sore throat re-appear, more mild than before. Disappeared a couple of days later.

I am assuming that the barley and beet sugar feeds bacteria that are attacking other bacteria significantly. The wife was surprised when she tasted the beet sugar — it was not as sweet as cane sugar. I must admit to be confused by the sugar industry saying they are identical, and do find some support for them being different, like in this article.

Oats or barley for β-glucan

 This study compares in the same experiment the β-glucan content of nine barley and 10 oat genotypes grown at two locations in each of two years (i.e., four environments) in North Dakota. Averaged across genotypes, total β-glucan content of barley and oat groat was similar.

Comparisons of β-Glucan Content of Barley and Oat , 1999

Symptom Changes

• Night sweats have largely disappeared.
• Longer periods of mild physical activity before warning signs of two much activity (hiccups — a family trait that my kids always have when they are over tired. Sweats (even on a cold morning with no jacket), lisp in speech appears. By longer, I mean has increased from about 11 minutes until just under 20 minutes.
  • I can handle a 20 minute drive fine and keep to that distance bound. When I have gone longer, suddenly a ton of bricks hits, no gradual tiring.
• Longer periods of sleep at night and more sleep. In the past it was short periods only (90-120 minute) then I was awake for a while. Now, I may get up to 6 hrs in a stretch.
• Much more refreshed at waking in the morning.
• Weight loss — some 20 lbs. Little appetite.
• Still experiencing some Multiple Chemical Sensitivity issues, minor — but my work location is toxic with them, so it’s working remotely or leave as the only viable options.

UBiome Results

In my last post I gave the history of my readings for Lactobacillus, Bifidobacterium and Akkermansia. There was a little improvement in two of them,. but they are still magnitudes below my past normals.

Other Good News

Old News – Ubiome Edition

On the image below, the 2018 values are from remission, 2019 are during the flare.

In terms of the rare/elusive bacteria, we see many of them disappear as the flare progresses, and strangers appear. The strangers are disappearing and some old friends, like Caldicoprobacter are returning. The high Bacillus count was likely from taking Bacillus coagulans as a probiotic.

Old News – MicrobiomePrescription Edition

In terms of symptoms associated with bacteria, there was a significant drop in the number of Condition Matches. We must be careful not to read too much into that, because a microbiome in the process of changing (which we see above) will not match the patterns of people who are stable.

Bottom Line

The direction is improving. The improvement can be seen in both the microbiome and the symptoms moving closer to my pre-flare state. Recovery is fragile and in one sense, I am likely in the most dangerous time — significant symptom improvement and one could stop being diligent in keeping to a treatment plan. Over the decades, I have seen too many people make a good solid recovery and then crash because they pushed themselves too far in recovery.

My criteria is simple and objective: Microbiome must return to the older state, especially the levels of lactobacillus and bifidobacteria; but also for other genus that either waxed or waned during the flare. Being disciplined and objective is essential.

I am still “living in a plastic bubble” of restrictions. The bubble is slowly expanding.

I just got my ubiome results today. The sample was taken after one month on Seed Probiotics. I believe that the Seed Probiotics have made a significant positive impact on me, but the impact that I was most hoping for was seeing more lactobacillus AND bifidobacterium being reported.

See this update on the results after 2 months on Seed.

The answer is, it may.

For new readers, a ME/CFS flare was triggered by work stress around the 12 of March, 2019 — dramatic changes seen across my microbiome (separate posts on these). I am still recovering.

Sample readings

From the last sample (where I had stopped things that I should not have – sampled 04-30) until this time, we see a 10 fold increase in Lactobacillus, but not a single bifidobacterium has appeared. Akkermansia is often associated with these two, so I include it.

I will be continuing on with Seed Probiotic and plan to do my next sample in 8 days. I am feeling better and ME/CFS symptoms are reducing — whether that is a natural recovery or impacted by Seed, is a matter for speculation.

Bottom Line

The evidence for Seed persisting is weak. Good evidence would have been both Lactobacillus and Bifidobacterium to make significant improvement.

Personally, I am happy with it for the bacteriocins (natural antibiotics) appears to be in it. I discovered this the hard way. One night I forgot that I had taken 2 capsules an hour before and took a second dose. It was a rough night.

Some Comments from Facebook on this Post

We will see what next month’s numbers are like.