Thursday, April 04, 2019

My talk on "The Twisted Tree of Life Awards" for #Nelli19

So I gave a lunchtime talk a few days ago for the New Lineages of Life 2019 meeting (aka #Nelli19) in San Francisco.  My talk was on

The Twisted Tree of Life Awards and Why We Should Care About Misrepresentations of the Tree of Life

I will be posting a lot of notes about the talk soon but wanted to get at least some of the main material down here for people to look at if they are interested.

Slides:



Screencapture video with Audio

 


Some Tweets about the Talk
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Saturday, March 23, 2019

Blog post w/ Twitter thread about Twitter threads & blog posts & how to turn a Twitter thread into a blog post

So I am writing a blog post here where I have captured a Twitter thread about blog posts and Twitter threads. I saw a Tweet from Pat Schloss and responded to it:
But that was not the only Tweet I made about this. I made a whole frigging thread. You can see the thread in most Twitter clients by clicking on the Tweet. But I figured I would also capture the thread here in this blog post. Tweet #2 in the thread.
Tweet #3 in the Thread.
Tweet #4 in the Thread.
Tweet #5 in the Thread.
Note - I got the embed codes for these Tweets from Twitter by selected the drop down menu in the upper right of the Tweet which I see in Safari at the Twitter site. I am not sure if this shows up in all Twitter clients but it works on the Twitter web site.



This gets me this menu


I then selected "Embed Tweet" and it gives me this



I then selected customization options because when posting all the Tweets I wanted just the Tweets and not the full conversation of the Tweet. First you get this menu:



I then selected "Hide Conversation"


And clicked update and then it showed me the new Embed code.  I then copied it and inserted it into this blog post.  I did this for each of the five tweets shown above.

And Voila - I have a blog post with a Twitter thread embedded in it where the thread discusses blog posts vs. Twitter threads.

Also - one can also include other Tweets about the same topic here.  So for example I can include responses too ...

Like this one.

If a thread is long, this is a real pain.  A much easier though less controllable approach is to use Wakelet or Twitter moments.  However, since Twitter seems to be abandoning moments as far as I can tell, Wakelet seems a better option


Here is the Wakelet I made --- Anyhow - there you go. A quick guide to turning a Tweet thread about blog posts and Tweet threads into a blog post.
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Playing with iNaturalist Places ..

So - have been experimenting a bit with iNaturalist. Just testing some embedding here. This embed is for a "place" where I do a lot of birding - the rural areas between Davis and Woodland. I love that with iNaturalist I can outline my own places on maps so am going to see how this goes. It should show observations from this area ...

The place is: https://www.inaturalist.org/places/rural-areas-between-davis-and-woodland
 
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Friday, March 15, 2019

The "Ben Franklin Award for Open Access in the Life Sciences" should be renamed as a "#Manward"

Uggh.

So in 2011 I won this award called the "Benjamin Franklin Award for Open Access in the Life Sciences. "  I was happy about it at the time.  I got a book and a plaque and was toasted at a meeting in Boston.  A few years ago I and others noted that the award had been given only to men.  Then Helen Berman won the award in 2014 and it looked like maybe the process was starting to not be so biased.

But I got alerted to the ongoing issues again by an email a few days ago.  And not only have the other winners all been men, all four nominees this year are men too.

Past Winners
  • 2002 – Michael B. Eisen
  • 2003 – James Kent
  • 2004 – Lincoln D. Stein
  • 2005 – Ewan Birney 
  • 2006 – Michael Ashburner 
  • 2007 – Sean Eddy 
  • 2008 – Robert Gentleman 
  • 2009 – Philip E. Bourne 
  • 2010 – Alex Bateman 
  • 2011 – Jonathan A. Eisen 
  • 2012 – Heng Li 
  • 2013 – Steven Salzberg 
  • 2014 – Helen M. Berman 
  • 2015 – Owen White 
  • 2016 – Benjamin Langmead 
  • 2017 – Rafael Irizarry 
  • 2018 – Desmond Higgins
That comes to 16:1 M:F.  

Yuck.  This just is not reflective of the contributions of people to open access in the life sciences. There are many many many women who have made important contributions in this general area.  

 When I won the award I was happy but I did notice the gender bias of the winners although that was when I was kind of just waking up to the issue of gender bias in STEM.  I tried to get people to nominate more women for the award the next year via FriendFeed, Twitter, email and other means.  For example: 


But that effort went nowhere I guess.  Helen Berman did win in 2014, but for the last four years it has been all men again.  Uggh.  At this point I think the only conclusion is that there is some bias in the system.  It is actually quite hard to figure out on the web just who is behind the whole award thing anyway.  It is given out by the "Bioinformatics.Org" group.   But the web site does not really have any details about what the group actually is.  There is a page for the award: https://www.bioinformatics.org/franklin/. And then there is a link to information about the selection process.

Here is the summary:

The selection process

  1. Nominations may be submitted by members of Bioinformatics.org using this form (you must be a member and logged in).
  2. Any person may be nominated, but the final list of nominees will be determined by Bioinformatics.org, based on the following criteria:
    • All nominations must be submitted by current members of Bioinformatics.org.
    • Self-nominations will not be counted.
    • Nominations of past laureates will not be counted.
    • There must be evidence that the nominee has done something to promote open access in the life sciences.
    • After the above exceptions have been considered, there must remain at least two (2) nominations per nominee (a member must ``second'' each nomination).
  3. The list of nominees will then be presented for a vote, on a ballot, to the members of Bioinformatics.org.
  4. The time given for all votes to be collected will be specified on the ballot.
  5. The nominee with the most votes will be the initial consideration for the Award. There will not be a run-off vote.
  6. The initial consideration for the Award will then be contacted. He or she must be willing and able to accept the Award in person at the time of the ceremony.
  7. If the initial consideration will not accept the Award in person at the time of the ceremony, then the nominee with the next most votes will be considered. And the process will be repeated until a laureate is found or until the list of nominees is exhausted.
  8. An announcement about the identity of the laureate will be made sometime prior to the ceremony.
Well, that sounds, umm, not ideal.  No committee.  No names of members who do any of the reviewing.  So - my guess is that the gender bias in the award is connected to this highly anecdotal review process.  Pretty disconcerting.  I thus think this award should be renamed "The Ben Franklin Award for Men"


UPDATE:
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Sunday, March 10, 2019

Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500

So - I did a thing today.  A new thing for me.  I officially became a bird nut.  For the first time in my life, I went on an outing to see a rare bird that I read about online.

I went to West Sacramento, to a pond there, to see, and hopefully take pictures of, a garganey.  What, you ask, is a garganey?  It is a kind of duck.  According to Wikipedia:
The garganey (Spatula querquedula) is a small dabbling duck. It breeds in much of Europe and western Asia, but is strictly migratory, with the entire population moving to southern Africa, India (in particular Santragachi), Bangladesh (in the natural reservoirs of Sylhet district) and Australasia in winter,[2] where large flocks can occur. This species was first described by Linnaeus in 1758. Like other small ducks such as the common teal, this species rises easily from the water with a fast twisting wader-like flight.

 So - kind of boring in some sense.  Just another duck right?  But the key for my outing today is that it is not a normal resident of Wast Sacramento, or Central California, or California, or North American even.  It is, as my National Geographic bird field guide says in a colonialist phrasing "An old world species" 

 So when one was spotted a few weeks ago in the West Sacramento area, the birders got very excited.  And they started to share information about it on Facebook, and eBird (which is where I heard about it) and Twitter and such.  And it even made the news: Bird Watchers Flock To West Sacramento To Catch A Glimpse Of Rare Bird

 So why, you may ask, did this interest me?  Well, I have been a birder, on and off, since I was a kid.  Birds, and birdwatching, are what got me into nature, which then got me into natural history, which then got me into biology, which then got me to where I am now.  For example, my first science job, doing field in the summer of 1988, involved studying hummingbirds in Colorado at the Rocky Mountain Biological Laboratory with Bill Calder from Arizona.  

More recently, I have rediscovered birding and bird science.  From a birding point of view, I got back into birding when we went on a trip to Costa Rica a few years ago.  For that trip, I got my first good pair of binoculars (Leica Trinovid 8 x 42) I have ever owned.  And I got my first digital SLR camera (a Nikon D80) and a nice lens (a Nikkor 70-200 f/2.8).  This was a great set up to have. although I confess I never fully learned all the ins and outs of using it for photography.  I mean, I used it a lot, but I never learned how to do much other than leave it on auto settings and use some of the "scene" settings to vary things up.  I wrote some blog posts about birding in the area on and off too and also started to spend a lot of time in Yolo Bypass nearby Davis.  See for example:
I even made some collections of my better pics. For example see

From a science point of view, I have been slowly trying to do more bird work in my lab.  And since I study microbes, the easiest thing to do seemed to be to study bird associated microbes.  I tried to get a project going on microbes of Darwin's Finches and to jump start this I even helped sequence one of the finch genomes.  See Nice timing: Our paper on the Darwin's Finch genome is out today on Darwin's birthday.  But we never got funding to work on the finch microbiomes (though am still interested in that).  But I have gotten involved in a few bird microbiome projects recently and am doing a few more now and looking for others.  See for example  The cloacal microbiome of five wild duck species varies by species and influenza A virus infection status and Community-level differences in the microbiome of healthy wild mallards and those infected by influenza A viruses and Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos

And I should note that I also have been going on and on and on about how microbiologists could learn a lot from birders and how I think we need a "Field Guide to the Microbes."

So, yeah, birds and birding were and are bigs parts of my life.

Anyway, back to the garganey.  Why was I checking out eBird reports and following reports of bird sightings?  Well, because I REALLY rediscovered birding in the last two months.  This happened because after about two years of pondering, and about 1 year of serious research, I got a new camera and lens specifically to do more bird photography.  In order to choose what camera to get, basically, I looked and looked and looked and finally found someone online who made recommendations for bird photography that I really trusted.  This person is Mark Smith.  And I found his recommendations via the oracle of Google and then watched a series of his videos on Youtube about comparing and contrasting different set ups for bird photography.  Especially bird in flight photography.  This had been my bane in a way.  I just felt like with my current birding set up I was not able to get close enough to birds or get good pictures of them in flight. And Mark Smith's videos showed me how I could get to the next level.  Based on his videos I finalized my choice to a Nikon D850 w/ a crazy fancy lens (for more than $10,000) or a Nikon D500 with a Nikkor 200-500 mm lens for about $3000.  I decided on the $3000 option both to save money and because I was not sure I would really use the rig enough to justify $10K.  So here is what I got, based on Mark Smith's guidance:
All purchased from B&H photos.

Everything showed up in early January.  And I started to try to learn how to use everything.  And things were slow at first.  I went out for a few weeks taking pictures using auto settings. And, well, it was nice, occasionally.  But the pics just were not as good as I thought they would be. It all came to a head when I went on a local little outing with Jim Koenigsaecker.  And he kept asking me about all the settings I was using.  And I kept saying "blarg" or something like that (actually, I said mostly I was using just the automated settings).  And when I went home from that day, I had some good pics.  And a lot of crummy ones.

So then I decided to consult the oracle again.  Google that is.  And I found Mark Smith had a bunch of videos on how to set up the Nikon D500 for shooting birds in flight



And I watched these. A few times. And then set up my camera with those settings.  And I went out again that afternoon.  And BOOM.  The pics were way way way better.

See for example these.

Anyway - more about my pictures from the past another time.  Back to the garganey.  As part of taking better pictures I started wanting to share them more.  And I started being able to ID birds better and in some cases also wanted help confirming IDs.  So I started using iNaturalist and eBird more.

See my iNaturalist posts here.
See my eBird posts here.

And I signed up for notifications about bird sightings via eBird.

And this is FINALLY where the garganey comes in.  A few weeks ago I saw that some people had reported a rare bird on eBird - a garganey.  I also saw these were reported in the West Sacramento area, near the deep water channel and near where UC Davis students do crew and sailing.  So this stuck in my head somewhere for a few weeks.  And I talked about possibly going to check it out with some birding friends like Mei Yamaguchi. And then, a few days ago my friend from TIGR Karla Heidelberg contacted me and told me she was going to be in the Davis area this weekend since her daughter would be racing in two crew regattas.  So yesterday we met up to see Captain Marvel with my wife, daughter, mom and step dad.  And Karla came with her son, who it turns out, is getting interested in bird photography.  And while chatting before or after the movie I asked where her daughter was going to be racing Sunday and she said "somewhere near West Sacramento".

...... READ MORE .......
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Thursday, March 07, 2019

Kisaco Research - sponsoring YAMMMM - yet another mostly male microbiome meeting - again - not their first biased rodeo

Well, sadly, I am not shocked by this. Disappointed, yes.  But not shocked.  Just got an announcement sent to me for this meeting: Animal Microbiome USA 2019 | Kisaco Research

Happening next week in Kansas City.  Run by Kisaco Research.  I have written about their propensity to have meetings where most of the speakers were white men previously.  See
People from the company claimed they were going to do better in the future.  And maybe they have for some meetings.  But alas not for this one.  By my estimate the speakers are ~ 85% male.  15% female.  Grrr.  Not good.  Not representative of the field.  Most  likely some sort of implicit or explicit bias going on.   

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Tuesday, March 05, 2019

If a body wash falls in the forest, is it gentle on the microbiome?

Well, I guess I am happy Dove is interested in the microbiome. My exposure to Dove's thinking on the microbiome started with an ad that was shared with me by Christine Parks.




The ad claims that Dove is gentle on the microbiome.  OK.  I am not sure I get what that means completely.  But I think they are saying "Our product does not mess up your microbiome".  I guess this could be good for some people if it were true.  But for others, maybe you want to mess up the microbiome.  Regardless, I would love to see data, if it exists, behind such a claim because my guess is that any body wash affects up the microbiome in many ways.

So, if they were not going to show evidence for this claim, I wondered, what are the ingredients of this Dover product? Fortunately the company provides them readily: https://www.dove.com/us/en/washing-and-bathing/body-wash/deep-moisture-body-wash.html. And here they are:
  • Water (Aqua), 
  • Cocamidopropyl Betaine, 
  • Sodium Hydroxypropyl Starch Phosphate, 
  • Lauric Acid, 
  • Sodium Lauroyl Glycinate, 
  • Sodium Lauroyl Isethionate, 
  • Hydrogenated Soybean Oil, 
  • Glycine Soja (Soybean) Oil, 
  • Sodium Chloride, 
  • Glycerin, 
  • Fragrance (Parfum), 
  • Phenoxyethanol, 
  • Guar Hydroxypropyltrimonium Chloride, 
  • Stearic Acid, 
  • Citric Acid, 
  • Sodium Isethionate, 
  • BHT, 
  • Tetrasodium, 
  • Iodopropynyl Butylcarbamate (IPBC)
This last one, Iodopropynyl Butylcarbamate (IPBC), is interesting since there is a paper discussing its effect on the microbiome. See "Effect of cosmetic chemical preservatives on resident flora isolated from healthy facial skin". They report "MTI and IPBC displayed the strongest effect on all tested strains (MICs ≤0.01%), followed by EHG and MP (MICs ≤0.3%), and finally PE with the weakest effect (MIC ≤1%)."  IPBC apparently is a known antibacterial and anti fungal agent.  Unclear how that being in the product is consistent with being gentle on the microbiome.

BHT is also interesting as it has been known as an antimicrobial for a long time (e.g., see this 1980 paper). It is used widely as a "preservative" but one of the ways it works as a preservative appears to be that it is anti microbial. 

Phenoxyethanol is also an antimicrobial.  See for example this where they report things like:
The study reveals that the six preservatives-Phenoxyethanol, Methyl paraben, Propyl paraben, Sorbic acid, Potassium sorbate and Sodium benzoate shown antimicrobial activity with the three test organisms at various concentrations and time periods.
My guess is many of the other ingredients can also affect the microbiome.  This would not really be surprising as lots of things affect the microbiome.  So, sorry Dove, but just saying your product is "gentle on the microbiome" just does not cut it for me.

I decided to see if I could find out anything else about Dove's claim of being gentle on the microbiome so I did the usual thing and Googled "Dove microbiome" and found some of their material on the microbiome.  And I guess I could say I was pretty disappointed. For example see this:Introducing your skin’s microbiome – Dove Nothing there providing data on just how gentle Dove really is or is not on the sin microbiome.  And in addition there was a statement I was not so fond of:
"Think of it as an invisible eco-system that lives on the skin that’s working to help keep it healthy and in good condition. "
Umm -- no -- no evidence for this.  The microbes on your skin appear to mostly be working for themselves.  Some of the time they are harmful. Some of the time they are helpful.  Some of the time they are neither.  But they are certainly not "working" to keep skin healthy.

So - it seems like Dove wants to get in on the microbiome hype.  I guess I am glad they are interested in the microbiome.  But they cannot just make claims about things like "being gentle" on the microbiome without evidence.  Especially when their ingredient list contains a collection of known antimicrobial chemicals.
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Interesting and important story on fecal transplants in @nytimes



This is definitely worth a read:

Drug Companies and Doctors Battle Over the Future of Fecal Transplants - The New York Times. By Andrew Jacobs. March 3, 2019.

The lead in is good:
CAMBRIDGE, Mass. — There’s a new war raging in health care, with hundreds of millions of dollars at stake and thousands of lives in the balance. The battle, pitting drug companies against doctors and patient advocates, is being fought over the unlikeliest of substances: human excrement.
The story is both interesting and includes some very important stuff going on behind the scenes that may affect the future of fecal transplants as a treatment in t. It seems that a variety of folks including those from companies who are trying to develop treatments mimicking fecal transplants are trying to get the FDA to crack down on the use of actual feces for carrying out fecal transplants.
“The first principle of medicine is do no harm, and at the moment we don’t have a long-term track record of F.M.T.’s adverse effects,” said Dr. Sahil Khanna, an associate professor of gastroenterology at the Mayo Clinic who has conducted industry-funded clinical trials on fecal transplants. “We also need to move away from transferring poo from one person to another.”
and
Drug companies, which have been struggling to funnel patients into the clinical studies that are required for F.D.A. approval, would like federal officials to restrict the stool bank’s ability to distribute fecal matter in the hope that more patients will enroll in their trials.
On the other side are those from places like OpenBiome as well as many clinicians who think that the regulation may have already gone far enough or even too far.
“It is very frustrating to see hyperregulation again ruining a good thing in health care,” said Dr. Colleen Kelly, a gastroenterologist at the Brown University medical school.
and
“I never imagined the solution to my nightmare could be so simple,” he said. “I just hope Big Pharma doesn’t make it unaffordable for the people like me.”
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Tuesday, February 26, 2019

A conference where all the speakers are women - happening this week #YAMMM #manels #STEMDiversity #GenderBias

It was now six years ago that I wrote here wondering if it would be a good idea to have a conference where all the speakers were women.

See The Tree of Life: A conference where the speakers are all women?

I wrote about this because of the general issue with excessive numbers of conferences where most or all of the speakers were men.  I had come up with a term for such meetings - YAMMM.  Yet Another Mostly Male Meeting.  I even made some little pics / images to represent such YAMMMs.




And I blogged and Tweeted about such meetings a lot (and still do).  See STEM Diversity posts and related links here for example.

When I wrote the post I was wondering if this would be a good counter to the problem of these YAMMMs (also called manels by others).  The feedback (much of it on Twitter) was really useful, mostly.  And over the years I pondered doing such a thing but to be honest, never felt really comfortable with the idea.  I worried about some of the possible negative sides of doing this, such as how the speakers might get unwanted attention and critiqued for being selected solely because of their gender.  And I also worried about whether this would be viewed in some way as a form of "reverse discrimination".

But I did try to do other analogous things where one reversed the normal gender skew (which is almost always towards males).  For example, when I found out, kind of at the last minute, I was speaking at a meeting with a very very skewed gender ratio of speakers, I gave my talk, but changed only referenced the work of women in the field.  See What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?  And in a class I teach I decided to basically replace most of the white male scientists I had been referencing with women and people of color.  Small things I know.  But I was pleased when people noticed these efforts and commented on how it made them think a bit about the examples we use when we give talks and teach.

Mind you, I have organized or helped organize a lot of meetings and seminar series since that post six years ago.  And I have tried to have the speakers at these be representative of diverse backgrounds in terms of gender, ethnicity, career stage, type of institution, and more.  But I myself have never gone to the next level and flipped the standard gender bias on its head.

Thus I was intrigued in September last year when I found out that my friend and colleague Dr. Rob Knight was co-organizing (with Dr. Sandrine Miller-Montgomery) a meeting in San Diego on "microbiomes" (my main area of research) where all of the invited speakers were women.  I blogged briefly about this here: 1st annual CMI International Microbiome Meeting (CIMM) w/ a great #STEMDiversity statement & plan.  I include below the material from the conference site that I included in that post:

On behalf of Dr. Rob Knight, the Center for Microbiome Innovation is pleased to host the 1st annual CMI International Microbiome Meeting (CIMM) on February 27–28, 2019 in San Diego. Additionally, we are pleased to announce that the 1st Urobiome Meeting on February 26, 2019, led by Linda Brubaker MD, will occur in conjunction with CIMM to make the most of your visit to San Diego. 
During the first day of this event, leading researchers will present on the emerging science of the Urobiome and its recently discovered implications for human health, including common conditions such as urinary tract infection, urinary incontinence and bladder overactivity. 
The following two days will feature high-impact presentations on the latest discoveries in microbiome sciences, with sessions on topics ranging from the microbiome in human disease and wellness and the metabolome, to primate microbiomes, to environmental and ocean microbiomes. For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakers. Be prepared to hear from fantastic presenters such as Dr. Katie Amato (Northwestern University), Dr. Rita Colwell (University of Maryland), Dr. Merete Eggesbo (Norwegian Institute of Public Health), Dr Susan Prescott (University of Western Australia), Dr. Lita Proctor (NIH), and many more!
In addition, I agreed to serve on a panel at the end of the meeting discussing "Breaking the Glass Ceiling: How do we solve the gender imbalance in STEM?" (I had found out about their plans for the meetings when they invited me to serve on the panel). As someone who has critiqued meetings for egregiously skewed gender ratios of speakers and as someone who has called attention to in particular the many microbiome focused meetings with gender balance issues, the whole idea behind this conference was in essence represented by this statement:
For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakers
This was certainly a bold move by the organizers. So - now zoom to today.

Today I am heading down to San Diego for the meeting.  And yesterday I found out that there was an editorial in the Wall Street Journal apparently critiquing the plan for having only female speakers.  It is entitled "No Men Allowed" by James Freeman. Alas, I do not have access to the editorial as it is behind a paywall.  There is also an editorial by Mark Perry at the American Enterprise Institute web site: Can the University of California bar males from presenting research at a biology conference?

So -- clearly, some people do not like the idea of a conference where all the speakers are women.  I confess I am still torn about the whole concept for the reasons I mentioned above.  However, even though I am torn, I do think it is important to push back against the clear implicit and explicit biases that have occurred against women in relation to speaking at conferences.  There is an extensive literature on this topic and on the topic of implicit and explicit biases that may be involved.  And I think this conference is an important form of push back.  The organizers may in fact get a bunch of grief over not having any male speakers.  But they will also provide an important venue for people to get challenged.  Conferences with only male speakers occurred for many many years without too many people raising any complaints.  And now some still occur but they are generally frowned upon in most places and are becoming rarer at least in my fields.  So in a way this conference can serve a similar function as Ruth Bader Ginsburg's dream of an all female US Supreme Court (this analogy was pointed out to me by Karen James). In reference to this concept Ruth Bader Ginsburg said:
"So now the perception is, yes, women are here to stay. And when I'm sometimes asked when will there be enough [women on the supreme court]? And I say when there are nine, people are shocked. But there'd been nine men, and nobody's ever raised a question about that."
Of course, gender bias is just one of the forms of bias that happens in STEM fields and with STEM conferences.  It is not the only issue we need to worry about or work on.  But it is a big one.  And the organizers of this meeting have done something bold and risky to confront this issue.

I will report more from the meeting. I would also love to hear what other people think about the plan for this conference.


PS. Thanks to multiple colleagues for some private feedback on this conference.  If I get permission I will post details of their comments.




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Saturday, February 09, 2019

Symbiosis paper of interest: Host-Microbe Coevolution and Complex Marine Invertebrate Holobionts | mBio

This looks potentially interesting.



Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts | mBio



O’Brien PA, Webster NS, Miller DJ, Bourne DG. 2019. Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10:e02241-18. https://doi.org/10.1128/mBio.02241-18.

ABSTRACT
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.


Found out about it on Slack, Twitter and via Google Scholar automated searches so .. caught my attention.
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Today's microbial diversity reading: A census-based estimate of Earth's bacterial and archaeal diversity

Looking at this today: A census-based estimate of Earth's bacterial and archaeal diversity

Louca S, Mazel F, Doebeli M, Parfrey LW (2019) A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 17(2): e3000106. https://doi.org/10.1371/journal.pbio.3000106

Definitely worth a look:

Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.

Author summary
The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Tuesday, January 29, 2019

Wakelet of UC Davis "Research Quality and Design Symposium"

Made a mini Wakelet:
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Wednesday, January 09, 2019

And today in the Twisted Tree of Life Award - the only way to study evolution is to try and make fake reconstructions of past events

See Tweets ...
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Monday, December 10, 2018

Twisted Tree of Life Award: University of Nebraska Lincoln Press Release on Archaeal Epigenetics

Well this one is really painful.  So painful I am re-starting my "Twisted Tree of Life" Award posts here.

See Tweets about it below:








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Thursday, November 29, 2018

YAMMMM: Yet Another Mostly Male Microbiome Meeting - Gut Microbiota for Health World Summit 2019

Uggh. In the middle of a faculty retreat and saw a Tweet about this meeting and could not help looking at their speaker list. And am not impressed.  Too many male speakers.

Gut Microbiota for Health World Summit 2019
A Meeting to Hear Men (81%) Not Women (19%) Discussing Microbiota*, **
YAMMMM: Yet Another Mostly Male Microbiome Meeting

Gail A. Hecht, MD, MS, Loyola University Medical Center (U.S.)
Jack A. Gilbert, PhD, University of Chicago (U.S.)
Session Moderator: Giovanni Barbara, MD, University of Bologna (Italy)
Suzanne Devkota, PhD, Cedars-Sinai Medical Center (U.S.)
Magnus Simren, MD, PhD, AGAF, University of Gothenburg (Sweden)
Christoph Thaiss, PhD, University of Pennsylvania (U.S.)
Session Moderator: Purna Kashyap, MBBS, Mayo Clinic
Eric Martens, PhD, University of Michigan (U.S.)
Liping Zhao, PhD, Rutgers, The State University of New Jersey (U.S.)
Paul Cotter, PhD, University College Cork (Ireland)
Robert Britton, PhD, Baylor College of Medicine (U.S.)
Joseph Zackular, PhD, University of Pennsylvania (U.S.)
Premysl Bercik, MD, McMaster University (Canada)
Dirk Haller, PhD, Technical University of Munich (Germany)
Eran Elinav, MD, PhD, Weizmann Institute of Science (Israel)
Karine Clément, MD, PhD, Pitié-Salpêtrière Hospital (France)
Alexander Khoruts, MD, University of Minnesota (U.S.)
Diane Hoffmann, JD, MS, University of Maryland (U.S.)
Francisco Guarner, MD, PhD, University Hospital Vall d’Hebron (Spain)
Dylan Dodd, PhD, Stanford University (U.S.)
Stanley L. Hazen, MD, PhD, Cleveland Clinic (U.S.)
Rohit Loomba, MD, University of California, San Diego (U.S.)
Gary D. Wu, MD, University of Pennsylvania (U.S.)
Session Moderator: Hania Szajewska, MD, Medical University of Warsaw (Poland)
Purna Kashyap, MBBS, Mayo Clinic (U.S.)
Geoffrey Preidis, MD, PhD, Baylor College of Medicine (U.S.)
Pinaki Panigrahi, University of Nebraska (U.S.)

 * Gender inferred by Google Searches, looking at personal websites, and some guessing
** Assuming just M:F genders which is clearly a bad assumption
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Saturday, November 03, 2018

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:






And I have on and off carved pumpkins on sciency themes every once in a while.




So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.





And I posted about it to Twitter.


But something seemed lacking.  So I went and got another pumpkin


And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

 Assembling the long piece pumpkin shotgun was easy.



Linking assembly.

 Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.




We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.


Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

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