Update on Parkinson’s and the Microbiome

A reader asked me to update my earlier posts (as well as

Blautia coccoides and Clostridium leptum produced the largest amount of hydrogen. Escherichia coli and Bacteroides fragilis constituted the second group that produced hydrogen 34- to 93-fold lower than B. coccoides. Bifidobacterium pseudocatenulatum and Atopobium parvulum constituted the third group that produced hydrogen 559- to 2164-fold lower than B. coccoides. Lactobacillus casei produced no detectable hydrogen. Assuming that taxonomically neighboring strains have similar hydrogen production, we simulated hydrogen production using intestinal microbiota that we previously reported, and found that PD patients produce a 2.2-fold lower amount of intestinal hydrogen compared to controls. 

Quantification of hydrogen production by intestinal bacteria that are specifically dysregulated in Parkinson’s disease [2018]

For what increases Blautia coccoides see this summary. In short:
arabinoxylan oligosaccharides (prebiotic) with rosemary, bernine, and cholic acid! No more red wine, smoking or walnuts!

Changes of Colonic Bacterial Composition in Parkinson’s Disease and Other Neurodegenerative Diseases. Several studies showed an increase of LactobacillusBifidobacterium, Verrucomicrobiaceae and Akkermansia in PD. A decrease of Faecalibacterium spp., Coprococcusspp., Blautia spp., Prevotella spp. and Prevotellaceae was observed in PD. 

Changes of Colonic Bacterial Composition in Parkinson’s Disease and Other Neurodegenerative Diseases. [2018]

Chronic stress-induced gut dysfunction exacerbates Parkinson’s disease phenotype and pathology in a rotenone-induced mouse model of Parkinson’s disease[2018].

Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson’s disease.[2018]

Although most of these differences were associated with disease duration, lower abundance in Lachnospiraceae was the only difference between de novo PD and HC (remaining lower across almost all PD duration strata). Decreased Lachnospiraceae and increased Lactobacillaceae and Christensenellaceae were associated with a worse clinical profile, including higher frequencies of cognitive impairment, gait disturbances, and postural instability. When compared with HC, MSA and PSP patients shared the changes in PD, with a few exceptions: in MSA, Lachnospiraceae were not lower, and Prevotellaceae were reduced; in PSP, Lactobacillaceae were similar, and Streptococcaceae were reduced.

Unraveling gut microbiota in Parkinson’s disease and atypical parkinsonism.

The following genera were enriched in the blood of PD patients: IsoptericolaCloacibacteriumEnhydrobacter and Microbacterium; whereas genus Limnobacter was enriched in the healthy controls after adjusting for age, gender, body mass index (BMI) and constipation. Additionally, the findings regarding these genera were validated in another independent group of 58 PD patients and 57 healthy controls using real-time PCR targeting genus-specific 16S rRNA genes. Furthermore, not only the genera Cloacibacterium and Isoptericola (which were identified as enriched in PD patients) but also the genera Paludibacter and Saccharofermentans were positively associated with disease duration. Some specific genera in the blood were related to mood disorders. We believe this is the first report to provide direct evidence to support the hypothesis that the identified microbiota in the blood are associated with PD. 

Detection of Microbial 16S rRNA Gene in the Blood of Patients With Parkinson’s Disease. [2018]

 In conclusion, the present meta-analysis revealed a higher prevalence of H. pylori infection in PD patients suggesting that H. pylori may contribute to PD pathophysiology. In addition, the significantly lower UPDRS scores in non-infected PD patients and in patients after H. pylori eradication therapy demonstrate that the infection may deteriorate the clinical severity of the disease.

H. pylori and Parkinson’s disease: Meta-analyses including clinical severity. [2018]

Caution: The treatment for H. pylori will also impact the microbiome and the changes may be due to side-effects on other bacteria.

Side Note on Suggestions from MicrobiomePrescription site vs Literature

However, it is not yet clear whether a specific dietary concept or the effects of the intestinal microbiota on the human metabolism could play a role in the course of the disease. Given the lack of prospective nutrition studies, only general recommendations can be given: a “balanced” seasonal regional diet with emphasis on vegetables, fruits, nuts, fish, low amount of red meat, and non-processed foods with a low level of simple carbohydrates may be helpful. 

[Nutritional aspects in Parkinson’s disease: disease risk, dietary therapy and treatment of digestive tract dysfunction] 2018.

From MicrobiomePrescription, based on bacteria shifts alone, we have very similar results, even on non-processed food:


Adherence to the Mediterranean diet is associated with lower probability of prodromal PD in older people. Further studies are needed to elucidate the potential causality of this association, potential relation of the Mediterranean diet to delayed onset or lower incidence of PD, as well as the underlying neurobiological mechanisms

Mediterranean diet adherence is related to reduced probability of prodromal Parkinson’s disease.

In terms of the analysis site, the Mediterranean diet has many plus and many minus. See Explaining Suggestions post for understanding why this may have occurred.

Bottom Line

Microbiome dysfunction and Parkinson’s is getting better and better established. There is a bit of a chicken and the egg situation between infections such as H. pylori or fungus [2017]. Did those pathogens triggered the microbiome dysfunction that lead to Parkinson’s OR did the Parkinson’s microbiome make it easier for those pathogen to occur?

Blind use of antibiotics or other drugs may make things worst. The following ones adversely impacts at least 50% of the microbiome shifts reported:

With literally dozens of drugs of antibiotics impacting 35% of the microbiome shifts adversely.

At the supplement level, we find that B vitamins adversely impact more microbiome shifts than they help:

  • Vitamin B3: Adverse 9, Helps 6
  • Vitamin B1: Adverse 9, Helps 5
  • Vitamin B7: Adverse 7, helps 4
  • Vitamin B6: Adverse 7, helps 4
  • Vitamin B9: Adverse 7, Helps 4

There was not a single clear “you should take” in the list of vitamins generated. At the amino acid and similar, melatonin had a 11 Adverse to 4 Helps. Proline was the exception: 4 increases and 1 adverse.

In terms of food: Whey, sesame cakemeal, red meat all were clean avoids, having adverse shifts for 25% of the known shifts and nothing known to help. (i.e. in the low protein diet above — exclude red meat)

Harsh bottomline: It seems that most of the things that helps CFS and many other conditions — may actually make Parkinson’s worst. “Cook book recipe for healthy living” may make things worst.