Clarifications on the results of the microbiome analysis

  • posted by vladimiropelliciardi
    on
    permalink

    The analysis of my microbiome has led to interesting results but it was not clear on the meaning of the high value of the Phylum Cyanobacteria equal to 18.2% which is very different from the average of the recorded values (a few percentage points in general). The relative Class is 4C0d-2 and Order is YS2, but family, genus and species not classifiable.
    The other results are 45% of Bacteroidetes, 33% Firmicutes, (Cyanobacteria 18%), others about 4%.
    I also read the article Di Rienzi et al, Di Rienzi et al. eLife 2013;2:e01102. DOI: 10.7554/eLife.01102, regarding Cyanobacteri in the human gut, but I did not find answers to my question. Can anyone give me clarification on this anomaly can it be advantageous or disadvantageous? Or can you tell me some scientific studies to consult? Thank you

  • posted by Russjames
    on
    permalink

    I have very similar profile but even higher. Do you have digestive issues…i do, reacted to antibiotics years ago. Apparently this bacteria is increased by walnuts and a gluten diet. I have around 23 percent.

  • posted by vladimiropelliciardi
    on
    permalink

    Dear Russjames, I had from an authoritative person (Ed Yong) another explanation for the very high values of cyanobacteria. I forwarded this explanation to the analysis laboratory and they told me that there are no other data of that value to subjects who did analysis in the same days but that probably, being a big vegetable eater, a part of them not perfectly digested ended up in the sample of feces that I sent for analysis. So the cyanobacteria cannot be at 18% but below 1%. Therefore I will ignore the results obtained, Regards

    Ed Yong <edyong209@gmail.com>, ven 17/04/2020 23:29

    Hi, sorry, I don’t have a lot of time to go into this but my gut reaction is that this is most likely to be an error. A lot of these personal microbiome testing companies aren’t great, which is why I don’t mention them at all in my book. And a LOT of microbiome studies turn up organisms that cannot possibly be in the samples that they’re analyzing for the reasons described in this piece –> https://www.nationalgeographic.com/science/phenomena/2014/11/11/contaminomics-why-some-microbiome-studies-may-be-wrong/

    I don’t think you have cyanobacteria inside you and I would encourage you to ignore the results of that analysis.
    Ed Yong, Staff science writer at The Atlantic: https://www.theatlantic.com/author/ed-yong/, I Contain Multitudes, my New York Times bestselling book about the amazing partnerships between animals and microbes, is out now.

    My (Vladimiro) letter :
    Dear Ed Yong, I have just finished reading your book “I contain multitudes” (2016) in the Italian version 2019.
    For a couple of years I have been interested in reading books and scientific articles on the Microbiome out of curiosity and not by profession. I also had my microbiome analyzed (August 2019) by the startup Microbioma Italiano (https://microbiomaitaliano.it/) of the project http://progettomicrobiomaitaliano.org/.
    The results surprised me for the part concerning the Phylum Cyanobacteria (Class 4C0d-2, Order YS2, Family genus and Unidentifiable species) for a percentage of 18.2% when in general it is even less than 1%.
    I asked those who did the analyzes if they had an idea of ​​this anomaly but they also had no hypothesis and they referred me to a scientific article (Di Rienzi et al. ELife 2013; 2: e01102. DOI: 10.7554 / eLife.01102, The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria) which I had already independently consulted and in which I had underlined this sentence: “As Cyanobacteria are photosynthetic organisms, it has been assumed that these sequences represent genomic material derived from ingestion of chloroplasts or Cyanobacterial cells (Turnbaugh et al.,2009; Koenig et al., 2011; Consortium HMP, 2012) “.
    Thinking about it, it occurred to me that in November 2016 I had been in Yucatan (Mexico) and immersed myself in one of the rare places in the world where there are stromatolites, the Bacalar Lagoon. Having swam all day in those waters so rich above the expanse of outcropping sromatolites, I may have ingested a certain amount. Dear Ed Yong, my question is: “Can you help me find an international expert to ask if this hypothesis is plausible? Alternatively, how do you justify a percentage of Cyanobacteria of 18.2%?”
    Thanks in advance and I hope you will answer me just to tell me that you don’t know how to help me. Sincerely. Vladimiro Pelliciardi*
    PhD in Sustainable Development (La Sapienza University, Rome, Italy)

  • posted by Russjames
    on
    permalink

    Thankyou so much for replying. I have emailed my microbiome company for feedback. Yes, maybe it is plant fibres. I eat seaweed, juice plants and orange, lemon peel. I read about your trip to Yucaton, i also have lived many months in Egypt, next to the red sea where i swam daily. Cyanobacteria are very high in this region around the coral. I also suffered from gastroenteritis. Currently i have methane dysbiosis (bloat, slow digestion) and cyano thrive in fermentation. I am curious if your digestion is normal. Thanks again. Ps i did discover some koala bears had 30% cyanobacteria in 2015. If we do have such high numbers, i am not sure what would reduce it. Ciao.

  • posted by Russjames
    on
    permalink

    This is from the scientist who performs the tests.

    Now that we have the DNA, we have to make copies of the region that we’re interested in. DNA extraction is not limited to one type of DNA. When you extract the DNA from a fecal sample, you are getting DNA from the microbes. But you may also be getting DNA from the plants the person is eating, or from other cells that are in the fecal material. We don’t care about that DNA, so we have to separate it out. We do that by making lots of copies of the microbial DNA and throwing away all of the other DNA.
    We make copies of the microbial DNA using polymerase chain reaction.
    Polymerase chain reaction, or PCR, mimics how DNA is copied in nature.

    PCR is the usual technique.

Please log in or register to post a reply.