Changes in Bacterial Gut Composition in Parkinson’s Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach
, Natalia Arias-RodrÃguez 1, Juan David Caicedo-Narvaez 1,3, Lena Best 2, Cindy V. Mendieta 4,5, Julieth López-Castiblanco 1, Laura Alejandra Gómez-Muñoz 3,6, Janneth Gonzalez-Santos 7, Humberto Arboleda 6, William Fernandez 3,6, Christoph Kaleta 2,*,†and Andrés Pinzón 1,*,†Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsCongratulations, is a lot of work! I included several observations below.
The paper on gut bacterial microbiome analysis in Parkinson's disease patients and controls within a Colombian population makes a valuable contribution to expanding our understanding of this intricate subject. In this pilot study group in South American population, the authors present genetic and metabolic peculiarities, shedding light on previously studied aspects in other populations (European, North American, Asian). The emphasis on integrating data from various omics layers is a noteworthy approach, as it promises a more comprehensive comprehension of the underlying biology and the intricate interactions between the microbiome and the host. By acknowledging the need for a multi-layered analysis, the study paves the way for a more holistic exploration of the subject. The personalized metabolic modeling of the intestinal microbiome identified alterations in the anticipated production of seven metabolites (Indole, fructose, tryptophan, phenylacetic acid, 3-Methyl-2-Oxovaleric Acid, and N-Acetylneuraminic acid). These metabolites are linked to the metabolism of aromatic amino acids and dietary factors, suggesting potential associations with Parkinson's disease. Particularly promising is the potential identification of metabolites linked to Parkinson's disease, suggesting their plausible utility as biological markers. This research stands as a significant step forward in advancing our knowledge of Parkinson's disease and continues the avenues for further investigations.
1. To include in ‘Materials and Methods’ how many participants were male and female
2. At page 9, is mentioned ‘Supplementary table 7’, but the supplem. material has 4 tables
3. At page 10 is mentioned ‘Supplementary table 12’ ..idem
4. At page 10 is mentioned ‘Supplementary table 13’ ...idem
5. At page 12 is mentioned ‘Supplementary table 14 and 15’, Supplem. Table 14, Supplem. Table 15 ..idem
6. At page 13 is mentioned Supplementary table 16 and 17, ..idem
7. At page 11..to explain FBA .. Flux Balance Analysis?
8. In supplementary mat., in Table 2:; Nutritional assessment by groups’ ..to include the measurement units, for example for BMI, Arm circumference, Arm muscle circumference, etc)
9. The measurement units for table 5
10. To replace in Supplementary material ‘Figura 5’ with ‘Figure 5’.
11. Into the manuscript tehre are several places with more 'spaces' between words.
Author Response
Please see the attachment
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript contains important findings related to the alterations in the composition of the gut microbiota in Parkinson’s disease subjects. The study is original and the differences between diseased and control subjects are clearly presented and discussed.
I have the following comments:
Line 43-45: The conclusion should be altered to justify the results.
The citations of the supplementary tables and figures within the manuscript should be revised.
Line 30: , North American cohorts > , and North American cohorts. Authors may change the words “current studies” to “most of the available studies”.
Line 41: seven metabolites, but only six are listed in parentheses.
Line 43: the diet that may be associated with disease. Which type of diet?
Line 46: keywords should be arranged alphabetically.
Line 77,78: [9], …. misfolding, the two commas could be deleted.
Line 81: North America > North American
Line 122: 6 > six
Line 130, 133: collection. > collection,
Line 131: , 5) > , and 5). Also make sure the numbering order is correct.
Line 154: stratifying > stratification.
Line 177: 2.4.16. S rRNA gene amplicon and sequencing > 2.4. 16S rRNA gene amplicon and sequencing
Line 270-274: (software): please revise this part for typing errors.
Line 276: in the studied population > of the studied population.
Line 280: Controls > controls; indicate > indicates.
Line 313: PCA should be written in full.
The numbering of the subtitles used in the discussion section should be revised.
The conclusion section has minor punctuational errors.
Comments on the Quality of English LanguageThe English of the manuscript is of acceptable quality.
Author Response
Please see the attachment
Author Response File: Author Response.pdf
