tag:blogger.com,1999:blog-10781944.post987677494542716994..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Overselling the microbiome award - many - for stories about placental vs. oral microbiomesJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-10781944.post-56025037600698889412016-07-02T15:17:18.549-07:002016-07-02T15:17:18.549-07:00Read the actual journal review articles cited in t...Read the actual journal review articles cited in the Wikipedia article about the topic Placental microbiome. You don't even have to read the article, just read the references and form your own conclusions. The popular press always seem to throw in their own speculation. I just wrote this article, check out the references, they answer all your questions.<br /><br />https://en.wikipedia.org/wiki/Placental_microbiomeBarbara Pagehttps://www.blogger.com/profile/11503277698599253440noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-16128450618888911282014-08-28T14:04:48.712-07:002014-08-28T14:04:48.712-07:00Dear Jonathan,
Thank you for this really relevant ...Dear Jonathan,<br />Thank you for this really relevant post and discussion. I’m an associate professor at the Academic Centre for Dentistry Amsterdam (ACTA) in Amsterdam, the Netherlands, focusing on the oral microbial ecology. I happened to hear dr. Aagaard presenting this work during International Human Microbiome Conference in China in September 2013, and started brainstorming with my colleagues about the potential role of the ‘placental microbiome’ harboring oral microbes. This resulted in a hypothesis quite different from that of dr Aagaard, which we have proposed in an open access publication at Frontiers in Microbiology: http://journal.frontiersin.org/Journal/10.3389/fcimb.2014.00085/full . In a nutshell, we propose that development of fetal tolerance toward the microbiome of the mother during pregnancy is the major factor for a successful acquisition of a normal microbiome, where the fetal immune system is ‘trained’ by placental microbes to recognize a ‘friend’ from a ‘foe’. Of course, all of this is still a speculation, in research papers called in a much nicer term - a hypothesis, which we are eager to test.<br />Egja Zaurahttps://www.blogger.com/profile/18065721917244448407noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-58025625138876349692014-06-16T08:54:36.376-07:002014-06-16T08:54:36.376-07:00Thank you Jonathan. How do you believe this variat...Thank you Jonathan. How do you believe this variation is missed? Just because these analyses ultimately depend on having good annotation sets, and functional annotations are likely to be missing?<br /><br />I guess a counter-argument to my point is that the broadly similar pathways across different body sites could be viewed as suggesting these are functionally important conserved pathways. Nonetheless, it's hard to see how the microbiome can contribute to tissue-specific functionality through species diversification alone if the types of genes and pathways present remain the same in different body sites.Anonymoushttps://www.blogger.com/profile/04373774015121144603noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-5070456966970995752014-06-16T07:24:48.508-07:002014-06-16T07:24:48.508-07:00Personally, I think the way most metabolic analyse...Personally, I think the way most metabolic analyses are done leads to much of the variation between sites being missed and this might be an example of that. That being said, I agree with you that this is an important point that should be addressed by those that keep saying the microbiome does everything for everyone all the time. Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8447874495425620672014-06-16T02:27:48.449-07:002014-06-16T02:27:48.449-07:00Thank you Jonathan for this dissection of the arti...Thank you Jonathan for this dissection of the article and surrounding media hype, but despite the overselling, I do feel the article is interesting scientifically.<br /><br />One thing that interests me is that although the microbiome splits quite neatly across the different body sites by taxonomic profile, this is not so for the metabolic profile (using KEGG pathways), which appears quite consistent across all the sites. Although the placenta does look a little different in this respect, it appears simply more noisy than the other sites (Fig 2C). If the microbiome is important functionally in a location-specific manner, would you not expect different gene sets to be involved in the different body regions?Anonymoushttps://www.blogger.com/profile/04373774015121144603noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-67848440279050858152014-05-27T17:37:48.081-07:002014-05-27T17:37:48.081-07:00Marnie;
You raised the issue of informed consent. ...Marnie;<br />You raised the issue of informed consent. I'm not sure what you have in mind. Of course, for all research on human subjects, informed consent is required. BenKhttps://www.blogger.com/profile/16784998250207335412noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-39562062791619396052014-05-27T17:33:45.403-07:002014-05-27T17:33:45.403-07:00Marnie;
Many tissues were thought to be sterile. ...Marnie;<br />Many tissues were thought to be sterile. In fact, to a decent approximation, intramuscular and many other tissues are free of bacteria in most people. Breast tissue apparently is not, which is interesting. The upper female reproductive tract is not, also interesting. Simply observing them and getting an initial sounding of the community diversity and composition is a start. BenKhttps://www.blogger.com/profile/16784998250207335412noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-76285005813945780452014-05-24T12:21:10.830-07:002014-05-24T12:21:10.830-07:00I disagree a bit - there are definitely some scien...I disagree a bit - there are definitely some science reporters out there who I do not elicit that kind of response (at least in me)Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-87004801597530580582014-05-24T09:31:47.223-07:002014-05-24T09:31:47.223-07:00I can't remember any journalist's version ...I can't remember any journalist's version of a science topic where my own internal editor was not stopping after each sentence and commenting, "False." "Irrelevant." "Unsupported." "Correct but pointless" In contrast, most actual peer reviewed science literature, even the piece said journalist was writing about, get's editorial comments like, "Hmmm." "Interesting." "Didn't know that." Why is that? I think that journalism's fundamental drivers - attention, subscriptions, exposure, publicity - differ from those of science: Truth, accuracy, reputation, teaching, knowledge building.<br />I really admire Jonathan for trying to stamp out this spot fire of journalistic excess, but I think...there is a lot of dry fuel out there and a lot of careless ignition sources.Kirk Maxeyhttps://www.blogger.com/profile/11864529687578909475noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-27878309042358002652014-05-23T23:41:22.655-07:002014-05-23T23:41:22.655-07:001. I have no idea if the women who participated kn...1. I have no idea if the women who participated know how it is being used.<br /><br />2. As for bigness of the research topic, I think what microbes are in the reproductive system is potentially very interesting. But I guess I am with you on the notion that just having clusters of microbes is not that interesting ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-35321950331140364392014-05-23T23:39:24.162-07:002014-05-23T23:39:24.162-07:00It would be very interesting to see if there are m...It would be very interesting to see if there are microbes that are specific for any site ..Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-2461324648107710792014-05-23T13:06:24.936-07:002014-05-23T13:06:24.936-07:00@BenK: "There are bacterial populations acro...@BenK: "There are bacterial populations across most of these tissues . . ."<br /><br />So what. Why would anyone assume that there was *not* bacterial in the reproductive system of women?<br /><br />@Jonanthan Eisen: Jonathan, why is it such a big research topic that the reproductive system has clusters of bacterial populations? Also, do the women who participated in this research know how it is being used?Marniehttps://www.blogger.com/profile/10850856778953207810noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-87369653920709857852014-05-23T12:25:43.668-07:002014-05-23T12:25:43.668-07:00Jon (and others, but less directly);
Dr. Miles and...Jon (and others, but less directly);<br />Dr. Miles and I have generated 454/16S + some other marker gene data from 10 patients who underwent hysterectomies and were not pregnant. There is sequence from tissue including the lower reproductive tract, various aspects of the uterus, the fallopian tubes and ovaries. There are bacterial populations across most of these tissues in most of the patients; I will not elaborate more at the moment, but the data was generated less than a year ago and we are working on an ms. If there are people with specific interests, I'm open to discussion so that human subjects are not unnecessarily inconvenienced in the conduct of our science. BenKhttps://www.blogger.com/profile/16784998250207335412noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8822499751454263772014-05-23T11:01:59.772-07:002014-05-23T11:01:59.772-07:00"Modulating early host–microbe interaction by..."Modulating early host–microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease."<br /><br />In a society that strongly encourages C-section deliveries, discourages breast feeding (let me count the ways), and demands that women return to work when their children are still in the primary stages of breastfeeding, it is easy to see why it is so much easier to blame pre-mature delivery and poor infant health on ORAL HYGEINE.<br /><br />This, coupled with Nicholas Wade's (chief genetics reporter at the New York Times) recent book, remind me of why I cancelled my subscription to the New York Times years ago.Marniehttps://www.blogger.com/profile/10850856778953207810noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-11766716124877125192014-05-23T09:04:04.786-07:002014-05-23T09:04:04.786-07:00This is wonderful, which means that the public wil...This is wonderful, which means that the public will outright reject it. Meanwhile, the New York Times is doing a bang-up job with the bad science journalism.Anonymoushttps://www.blogger.com/profile/04068844904769160913noreply@blogger.com