I’m writing a systematic review about non-invasive tests for diagnosing colorectal neoplasia in patients with Lynch Syndrome.
Your article entitled “Structure of the Mucosal and Stool Microbiome in Lynch Syndrome” was identified during our literature search and I read this article with great interest. Your results could be very valuable for our systematic review. However, I have a few questions regarding your study:
You compared stool samples of patients with and without adenomas, and found that in patients having adenomas a subset of clostridiaceae was depleted, whereas Ruminococcaceae and Desulfovibrio were enriched. As we are interested in the feasibility of using the fecal microbiome as marker for detection of neoplasia: are you able to provide us for example sensitivity, specificity, positive predictive value and negative predictive value rates of these 3 abundances shown to be different between adenoma and non-adenoma patients? Could you provide us the exact number of patients in both groups who were included in this analysis?
Thank you for your interests to our study. Hereby I attached de-identified metadata including sampleID, and baseline adenoma/interval adenoma status Dropbox - Lynch_forums_metadata.xlsx - Simplify your life . You can refer to the supplementary table 2 and get the MetaPhlAn table of stool species abundance. I believe with that two information, it’s feasible to use microbiome as markers for detection of neoplasia. Thanks.
Thank you for your response and for sending the dropbox file.
Good to know which SampleID had an adenoma and which not. However, I don’t think the dropbox file and supplementary Table 2 enables me to get the information I’m looking for for my systematic review. To be more specific:
In the manuscript you write that in patients having adenomas a subset of clostridiaceae was depleted, whereas Ruminococcaceae and Desulfovibrio were enriched. In Table S2 I can find the complete stool taxonomy found in each SampleID. However, this data does not allow me to answer the following questions:
- In how many patients with adenomas compared to patients without adenomas was 1) clostridiaceae depleted, 2) Ruminococcaceae enriched and 3) Desulfovibrio enriched? Do you have the mean level of abundance of these three species, in both the adenoma cohort and the non-adenoma cohort?
- Subsequently: if possible, could you provide us sensitivity, specificity, positive predictive value and negative predictive value rates of the 3 abundances shown to be different between adenoma and non-adenoma patients (clostridiaceae, ruminococcaceae, desulfovibrio)? This will enable us to determine the usability of the fecal microbiome to detect neoplasia in Lynch Syndrome patients?
Thank you in advance
Elsa van Liere
I’m currently doing research about the relation between human gut microbiome and CRC, especially in people at higher risk due to their genetic predisposition, e.g. Lynch Syndrome, FAP, etc.
Your research provided valuable insights on how the human gut microbiome were perturbed in Lynch Syndrome carriers that developed adenoma, as well as showing how colectomy may have a greater effect to human gut microbiome composition compared to gene mutations.
Thank you for sharing the table with details of the adenoma status of the samples.
I wonder if it would be possible for you to share colectomy status and mutated MMR genes of the sample, as it would be very valuable for our study.
Thank you in advance