Before/Donor/After FMT Analysis

A user of my site that is active consulting on autism microbiome manipulation obtained permissions for me to do an analysis of one of his patients going through FMT. All of the microbiome testing was done via Biomesight (including the donor). This is specific type of data that I have been pleading to see if we can make predictive models of what could occur with FMT.

MeasurePriorDonorAfter
Taxonomy374406550
Elusive336
Rare4817
Sparse121533
Infrequent283768
Uncommon6689145

I did analysis at the Species, Genus, Family, Order and Class level trying many many approaches. This summarize my key findings.

The second sample was done one month after the FMT. Patient was very good for a couple of days, then “the war started”. New more severe autism symptoms appeared.

Do NOT expect it to reduce overgrowths!

Looking at the lowest numbers of the recipient prior and the donor, we found that the post-FMT numbers had a clear pattern.

  • At the Class level, 97% was higher than the lowest of the two, 58% was higher than the highest
  • At the Order level, 96% was higher than the lowest of the two, 56% was higher than the highest
  • At the Family level, 95% was higher than the lowest of the two, 61% was higher than the highest
  • At the Genus level, 91% was higher than the lowest of the two, 51% was higher than the highest
  • At the Species level, 94% was higher than the lowest of the two, 47% was higher than the highest

This was shocking — 50% of the bacteria will be higher than either the donor’s or recipient’s levels. Many people will assume that the levels will magically average the two levels. The reality seen here is that only 50% of the time will the new level be between these two levels and 50%of the time it will be higher than either. This is unlikely to be a preferred outcome.

Unexpected Disappearances

There were several items where both the recipient and the donor had bacteria, they were gone in the post-FMT sample! This was not expected, of special interest is that Lactobacillus was wiped out.

  • Order: Puniceicoccales
  • Family: Clostridiales Family XVI. Incertae Sedis
  • Family: Lactobacillaceae
  • Family: Puniceicoccaceae
  • Genus: Alkalibacterium
  • Genus: Butyricimonas
  • Genus: Carboxydocella
  • Genus: Catonella
  • Genus: Lactobacillus
  • Genus: Macrococcus
  • Genus: Pelagicoccus
  • Genus: Turicibacter
  • Species: lingnae
  • Species: Streptococcus oralis
  • Species: Veillonella parvula
  • Species: Streptococcus pseudopneumoniae
  • Species: Carboxydocella ferrireducens
  • Species: Sutterella wadsworthensis
  • Species: Catonella morbi

Many New Kids showed up!

These are bacteria not seen in the recipient prior nor the donor sample

  • Class Level: Acidobacteria, Calditrichae,Chitinophagia,Flavobacteriia,Ktedonobacteria,
  • Order Level: Acidobacteriales, Calditrichales, Caulobacterales, Chitinophagales, Chroococcales, Desulfobacterales, Flavobacteriales, Kiloniellales, Nostocales, Oscillatoriales, Rhodocyclales, Rickettsiales, Streptosporangiales, Synechococcales, Syntrophobacterales, Thermogemmatisporales,
  • Family Level: Acetobacteraceae, Acidobacteriaceae, Anaplasmataceae, Calditrichaceae, Caulobacteraceae, Chitinophagaceae, Chroococcaceae, Clostridiales Family XII. Incertae Sedis, Cyanobacteriaceae, Cytophagaceae, Desulfobacteraceae, Dysgonamonadaceae, Flavobacteriaceae, Fusobacteriaceae, Hymenobacteraceae, Kiloniellaceae, Listeriaceae, Nostocaceae, Oceanospirillaceae, Oscillatoriaceae, Oxalobacteraceae, Prevotellaceae, Pseudanabaenaceae, Rhodanobacteraceae, Rhodocyclaceae, Rickettsiaceae, Rivulariaceae, Streptosporangiaceae, Synechococcaceae, Syntrophobacteraceae, Thermogemmatisporaceae, Thiotrichaceae, Verrucomicrobiaceae,
  • Genus Level: Acholeplasma, Acidaminobacter, Aminobacterium, Ammonifex, Anoxybacillus, Asticcacaulis, Bilophila, Caldithrix, Calothrix, Catenibacterium, Chroococcus, Cyanobacterium, Desulfofrigus, Desulfosporosinus, Dokdonella, Dysgonomonas, Edaphobacter, Ehrlichia, Emticicia, Escherichia, Fusibacter, Fusobacterium, Gillisia, Haemophilus, Insolitispirillum, Kushneria, Listeria, Luteibacter, Lysinibacillus, Marinospirillum, Microbacterium, Neisseria, Niastella, Novispirillum, Oleomonas, Olivibacter, Oscillatoria, Parapedobacter, Paraprevotella, Pelotomaculum, Pontibacter, Ralstonia, Rickettsia, Roseomonas, Sarcina, Sebaldella, Skermanella, Tepidanaerobacter, Tepidimicrobium, Thalassospira, Thermoanaerobacter, Thermogemmatispora, Thiothrix,
  • I will skip the species level…

Bottom line is that the microbiome has become much more diverse

Recent FMT aspects

FMT destabilizes the microbiome, there are “strain riots” in the guts. We can see this with all of the “New Kids” showing up because the existing occupants are busy dealing with each other. This can be seen by the post microbiome having a lot more taxonomical items (550 vs 374 before – a 47% increase), The microbiome, over time, will downsize and stabilize with a new normal. During this period, you want to entrench your desired items by feeding it the right things and avoiding the wrong thing.

Personally, I would suggest a new sample every 6 weeks to monitor the stabilization.

Is FMT Worth the Risk?

FMT is effectively an organ transplant. Like organ transplants, there are significant risks of rejection and no way to undo it once it happens. From correspondence with many people who have tried it for ME/CFS, my feelings are that it is not a magic bullet. It is closer to playing Russian roulette, but with 5 of the 6 bullet chambers having bullets in the chambers.

I just spent 90 minutes zooming to the consultant involved with this autistic child. We both agreed that FMT for autistic children is not a wise course. The consultant is scratching their head on what to help this child recover from this situation.

Some prior posts on FMT

4 thoughts on “Before/Donor/After FMT Analysis

  1. It would be nice to know how they did the FMT.
    Did they follow Doctor Adam’s recommendations?
    How was the pre, post Fmt…etc. that isn’t easy as you can read about.

  2. I suggest adding ammonia oxidizing bacteria, such as are sold by AOBiome. They can colonize the gut. I have gotten them there by spraying the Mother Dirt, AOBiome AO+ mist in my mouth and then drinking a glass of water on an empty stomach, to ‘whoosh’ them through the stomach. When the water is absorbed in the gut, they are filtered out on the gut mucus. After doing this several times a day, they do start to colonize the gut. Not sure if they persist, but they do have effects while they are there.

    They should help to stabilize the gut microbiome by inhibiting the facultative anaerobic bacteria so the obligate anaerobes can dominate (what you want).

    1. More technical details please! Which species — a link to the product to sale.
      The only thing that I could find on their site was ” We propose that restoring this dermal microflora with a purified strain of AOB,Nitrosomonas eutropha (D23), may reduce the overall cutaneous inflammatory state and, thus, be a potential therapeutic option for improving the cosmetic appearance of a skin condition such as KP ”

      This species is not generally considered safe for human consumption. Check https://pubmed.ncbi.nlm.nih.gov/?term=Nitrosomonas+eutropha+&sort=date&size=200 My impression is that it’s intended use is topical (i.e. on the skin only)

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