The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.
Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes. My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology. I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.
To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer. And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes
I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).
I got in pretty late and worked a little on my talk before going to bed. I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did. Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research. I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture. But once he suggested this notion my talk really congealed (in my head and on paper at least). It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...
Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego). I got there in time to hear Francis Collins' talk. I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there. More about this later I hope. Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more. And eventually went to sleep. Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it). And voila - only 30 minutes before the PM session was to begin I finished the prep. I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).
I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome. Anyway, I gave my talk, and recorded the slideshow with Camtasia. Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk. As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...
Here is a slideshow with Audio (which I recorded via Camtasia)
Well, this is not the most egregious example of a mostly male meeting but it still has some issues: The BSPP - The British Society for Plant Pathology 2015 meeting. Nine speakers. Seven male. And this in a field with plenty of excellent female researchers.
Cassava brown streak disease (1) James Legg - IITA Tanzania (2) Stephan Winter - Leibniz Institute DSMZ Germany (3) Maruthi Gowda - Natural Resources Institute, University of Greenwich
Late blight (1) Bill Fry - Cornell University (2) Sophien Kamoun - Sainsbury Lab, Norwich (3) Jonathan Jones - Sainsbury Lab, Norwich
Rice blast (1) Sarah Gurr - University of Exeter (2) Lauren Ryder - University of Exeter (3) Thomas Kroj - INRA, Montpellier, France
But the weirdest part -- it says
"This year, the BSPP President, Prof. Gary Foster, has only chosen a few invited speakers on specific diseases, and wishes the remainder of the talks to be selected from offered papers."
So does this mean Prof. Gary Foster just picked all speakers? If so, perhaps Prof. Gary Foster needs to do a little thinking about his possible biases ...
I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm). As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems: Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research" Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals" Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production" Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?" Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes" MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.
Authors are offered a variety of benefits: – transparent, comprehensive and fast peer review; – language assistance for authors from non-English speaking regions; – convenient, web-based manuscript submission and tracking system; – efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology; – no publication charge in the first two annual volumes.
I look forward to your manuscript! Please forward this invitation to any interested colleagues and associates.
Seemed right up my alley - an open access microbiome journal. Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:
1. License The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.
Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access". The no derivatives part drives me batty. Also they write:
9. Scope of the Commercial License The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows: to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article, to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same. Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.
Well, no thanks. Too many restrictions and not open access in my view. If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
I realize it's been a while since I've posted, but we have some exciting news to share!
For those who haven't heard already...
We sent Deanna a t-shirt for Christmas to announce our news. When she opened the present, De told us that Deanna didn't quite get it at first, but after a few seconds she smiled and started screaming. I was so happy to learn that Deanna was over-the-moon excited to be a big sister. We can't wait for Don, De and Deanna to visit us in this summer and meet Deanna's new little sibling.
Really disappointed in Oxford Nanopores. Perhaps we can get some of the speakers to cancel on them unless they fix things.
Ron Ammar, University of Toronto, Canada
Ewan Birney, European Bioinformatics Institute, UK
Thomas Hoenen, NIH/NIAID, USA
Nick Loman, University of Birmingham, UK
Brook Milligan, New Mexico State University, USA
Justin O’Grady, University of East Anglia, UK
Jared Simpson, Ontario Institute for Cancer Research, Canada
Yutaka Suzuki, University of Tokyo, Japan
Mick Watson, The Roslin Institute, University of Edinburgh, UK
Update 3/8/15
Well, after I posted about the Nanopore meeting there were some responses on Twitter. So I made a Storify
So I decided to check the meeting today to see whether they "fixed" anything.
Right now they list 11 male and two female speakers. So that added two males and two females. Better ratio. Still pretty bad. They really could do better ...
The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.
Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes. My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology. I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.
To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer. And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes
I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).
I got in pretty late and worked a little on my talk before going to bed. I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did. Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research. I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture. But once he suggested this notion my talk really congealed (in my head and on paper at least). It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...
Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego). I got there in time to hear Francis Collins' talk. I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there. More about this later I hope. Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more. And eventually went to sleep. Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it). And voila - only 30 minutes before the PM session was to begin I finished the prep. I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).
I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome. Anyway, I gave my talk, and recorded the slideshow with Camtasia. Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk. As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...
Here is a slideshow with Audio (which I recorded via Camtasia)
Well, this is not the most egregious example of a mostly male meeting but it still has some issues: The BSPP - The British Society for Plant Pathology 2015 meeting. Nine speakers. Seven male. And this in a field with plenty of excellent female researchers.
Cassava brown streak disease (1) James Legg - IITA Tanzania (2) Stephan Winter - Leibniz Institute DSMZ Germany (3) Maruthi Gowda - Natural Resources Institute, University of Greenwich
Late blight (1) Bill Fry - Cornell University (2) Sophien Kamoun - Sainsbury Lab, Norwich (3) Jonathan Jones - Sainsbury Lab, Norwich
Rice blast (1) Sarah Gurr - University of Exeter (2) Lauren Ryder - University of Exeter (3) Thomas Kroj - INRA, Montpellier, France
But the weirdest part -- it says
"This year, the BSPP President, Prof. Gary Foster, has only chosen a few invited speakers on specific diseases, and wishes the remainder of the talks to be selected from offered papers."
So does this mean Prof. Gary Foster just picked all speakers? If so, perhaps Prof. Gary Foster needs to do a little thinking about his possible biases ...
I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm). As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems: Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research" Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals" Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production" Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?" Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes" MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.
Authors are offered a variety of benefits: – transparent, comprehensive and fast peer review; – language assistance for authors from non-English speaking regions; – convenient, web-based manuscript submission and tracking system; – efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology; – no publication charge in the first two annual volumes.
I look forward to your manuscript! Please forward this invitation to any interested colleagues and associates.
Seemed right up my alley - an open access microbiome journal. Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:
1. License The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.
Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access". The no derivatives part drives me batty. Also they write:
9. Scope of the Commercial License The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows: to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article, to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same. Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.
Well, no thanks. Too many restrictions and not open access in my view. If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
I realize it's been a while since I've posted, but we have some exciting news to share!
For those who haven't heard already...
We sent Deanna a t-shirt for Christmas to announce our news. When she opened the present, De told us that Deanna didn't quite get it at first, but after a few seconds she smiled and started screaming. I was so happy to learn that Deanna was over-the-moon excited to be a big sister. We can't wait for Don, De and Deanna to visit us in this summer and meet Deanna's new little sibling.
Really disappointed in Oxford Nanopores. Perhaps we can get some of the speakers to cancel on them unless they fix things.
Ron Ammar, University of Toronto, Canada
Ewan Birney, European Bioinformatics Institute, UK
Thomas Hoenen, NIH/NIAID, USA
Nick Loman, University of Birmingham, UK
Brook Milligan, New Mexico State University, USA
Justin O’Grady, University of East Anglia, UK
Jared Simpson, Ontario Institute for Cancer Research, Canada
Yutaka Suzuki, University of Tokyo, Japan
Mick Watson, The Roslin Institute, University of Edinburgh, UK
Update 3/8/15
Well, after I posted about the Nanopore meeting there were some responses on Twitter. So I made a Storify
So I decided to check the meeting today to see whether they "fixed" anything.
Right now they list 11 male and two female speakers. So that added two males and two females. Better ratio. Still pretty bad. They really could do better ...
