Series on Ian Lipkin Research Results

I am starting a series, similar to the last two posts, looking at the highs and lows bacteria reported by Ian Lipkin — and what can be done to correct them. As always, I will be using publications on PubMed to list the research followed by my Bottom Line summary for the brain fogged. I will be looking at supplements, probiotics and food only — antibiotics are likely to be more harmful then helpful when we are dealing with this type of fine re-adjustment of the microbiome.

I will do one bacteria at a time. It is important to note that his results were based on the average. In reality, individuals may be all over the place. Once CFS person may be normal for one family and the next one very abnormal. The model is that of a shift of the microbiome. The shifts will not be identical in everyone because every one’s microbiome is unique when healthy (more distinct than a fingerprint!).

His 2017 paper is available here. This chart from the paper show some controls and some cfs with the almost the same values, and some with a major shift.

You cannot apply one size fit all treatment (for example the high Blautia issue in my last post impacted just 3 of 20 CFS uBiome results that I have looked at, 15%). Getting uBiome results (or equivalent) is likely helpful — whatever test you use, should measure hundreds of families.

The Bacteria to be examined

(links to the posts will be added as they are done)

  • Low
    • Pasteurellales [Order]
      • Lachnospiraceae [Family],
      • unclassified Bacillales[Family] and
      • Pasteurellaceae[Family]
    • Faecalibacterium [Genus],
    • Roseburia[Genus],
    • Coprococcus[Genus],
    • Gemella [Genus],
    • Dorea [Genus], and
    • Haemophilus [Genus]
  • High
    • Clostridiaceae [Family]
    • Clostridium [Genus],
    • Pseudoflavonifractor [Genus],
    • Anaerostipes [Genus]
    • Coprobacillus [Genus]

I have taken the liberty of copying the table from the article below (so I may link from their findings over the next month).

LINKS BELOW ARE TO POSTS ON WHAT CAN BE DONE TO CORRECT IT

Diagnostic groups

Selected bacterial species

In-sample

Cross-Validation

AUC

AUC

ER (%)

FP (%)

FN (%)

ME/CFS (50) vs. control (50)

[Firmicutes] Coprococcus catus

0.831

0.684

36.72

40.00

33.43

[Firmicutes] Pseudoflavonifractor capillosus

[Firmicutes] Dorea formicigenerans

[Firmicutes] Faecalibacterium prausnitzii

[Firmicutes] Coprococcus catus

0.893

0.745

29.68

29.71

29.64

[Firmicutes] Pseudoflavonifractor capillosus

[Firmicutes] Dorea formicigenerans

[Firmicutes] Faecalibacterium prausnitzii

[Firmicutes] Clostridium asparagiforme

[Proteobacteria] Sutterella wadsworthensis

[Bacteroidetes] Alistipes putredinis

[Firmicutes] Anaerotruncus colihominis

ME/CFS + IBS (21) vs. control (50)

[Firmicutes] Faecalibacterium cf

0.771

0.571

33.09

18.57

69.38

[Bacteroidetes] Bacteroides vulgatus

[Firmicutes] Faecalibacterium cf

0.923

0.687

25.59

18.43

43.48

[Bacteroidetes] Bacteroides vulgatus

[Firmicutes] Faecalibacterium prausnitzii

[Bacteroidetes] Alistipes putredinis

[Firmicutes] Coprococcus catus 

[Firmicutes] Faecalibacterium cf

1

0.791

24.31

18.28

39.40

[Bacteroidetes] Bacteroides vulgatus

[Firmicutes] Faecalibacterium prausnitzii

[Bacteroidetes] Alistipes putredinis

[Firmicutes] Coprococcus catus

[Firmicutes] Anaerostipes caccae 

[Firmicutes] Dorea formicigenerans

[Firmicutes] Anaerotruncus colihominis

[Firmicutes] Clostridium asparagiforme

ME/CFS w/o IBS (29) vs. control (50)

[Bacteroidetes] Bacteroides caccae

0.775

0.589

40.67

25.29

66.30

[Firmicutes] Pseudoflavonifractor capillosus

[Bacteroidetes] Bacteroides caccae

0.948

0.754

28.41

21.07

40.65

[Firmicutes] Pseudoflavonifractor capillosus

[Bacteroidetes] Parabacteroides distasonis *

[Bacteroidetes] Bacteroides fragilis

[Bacteroidetes] Prevotella buccalis

[Bacteroidetes] Bacteroides xylanisolvens

[Firmicutes] Dorea formicigenerans

ME/CFS w/o IBS (29) vs. ME/CFS + IBS (21)

[Bacteroidetes] Bacteroides vulgatus

0.913

0.604

37.61

29.30

50.08

[Bacteroidetes] Prevotella buccalis

[Firmicutes] Ruminococcus lactaris 

[Firmicutes] Eubacterium hallii

[Firmicutes] Anaerotruncus colihominis

[Firmicutes] Faecalibacterium cf

[Firmicutes] Clostridium methylpentosum

[Bacteroidetes] Bacteroides vulgatus

0.956

0.604

41.51

27.32

62.80

Bottom Line

This is a major research project. I hope by consolidating the PubMed citations that:

  • patients and their care givers can be empowered to “self-service”
  • front line MDs have a reference that they can use with detail microbiome results from uBiome and other providers
  • researchers have a sounding board for their hypothesis and proposals; ideally with trials of items suggested and seeing what the shift in the microbiome (if any) that results.

Special thanks to L.L.Ingram for encouraging me to undertake this epic project.