Coming today to a cat near you - microbes

Only three years after first imagined ...

Guest post from Rachid Ounit on CLARK: Fast and Accurate Classification of Metagenomic and Genomic Sequences

Recently I received and email from Rachid Ounit pointing me to a new open access paper he had on a metagenomics analysis tool called CLARK.  I asked him if he would be willing to write a guest post about it and, well, he did.  Here is it:

CLARK: Accurate metagenomic analysis of a million reads in 20 seconds or less…

At the University of California, Riverside, we have developed a new lightweight algorithm to classify accurately metagenomic samples while minimizing computational resources better than any other classifiers (e.g., Kraken).  While CLARK and Kraken have comparable accuracy, CLARK is significantly faster (cf. Fig. a) and uses less RAM and disk space (cf. Fig. b-c). In default mode and single-threaded, CLARK’s classification speed is higher than 3 million short reads per minute (cf. Fig. a), and it also scales better in multithreading (cf. Fig. d). Like Kraken, CLARK uses k-mers (short DNA words of length k) to solve the classification problem. However, while Kraken and other k-mers based classifiers consider the whole taxonomy tree and must resolve k-mers that match genomes from different taxa (by using the concept of “lowest common ancestor” from MEGAN), CLARK rather considers taxa defined for a unique taxonomy rank (e.g. species/genus), and, during the preprocessing, discards any k-mers that can be found in any pair of taxon. In other words, CLARK exploits specificities of each taxon (against all others) to populate its light and efficient data structure. It uses a customized dictionary of k-mers, in which each k-mer is associated to at most one taxon and results in fast k-mer queries. Then, the read is assigned to the taxon that has the highest amount of k-mers matches with it. Since these matches are discriminative, CLARK assignments are highly accurate. We also show that the choice of the value of k is critical for the optimal performance, and long k-mers (e.g., 31-mers) are not necessarily the best choice to perform accurate identification.  For example, high confidence assignments using 20-mers from real metagenomes show strong consistency with several published and independent results. 

Finally, CLARK can be used for detecting contamination in draft reference genome or, in genomics, chimera in sequenced BACs. We are currently investigating new techniques for improving the sensitivity and the speed of the tool, and we plan to release a new version later this year. We are also extending the tool for comparative genomics/metagenomics purposes. A “RAM-light” version of CLARK for your 4 GB RAM laptop is also available. CLARK is user-friendly (i.e., easy to use, it does not require strong background in programming/bioinformatics) and self-contained (i.e., does not need depend on any external software tool). The latest version of CLARK (v1.1.2) contains several features to analyze your results and is freely available under the GNU GPL license (for more details, please visit CLARK’s webpage). Experimental results and algorithm details can be found in the BMC genomics manuscript.

Performance of Kraken (v0.10.4-beta) and CLARK (v1.0) for the classification of a metagenome sample of 10,000 reads (average reads length 92bp).  a) The classification speed (in 103 reads per minute) in default mode. b) RAM usage (in GB) for the classification. c) Disk space (in GB) required for the database (bacterial genomes from NCBI/RefSeq). d) Classification speed (in 10^3 reads per minute) using 1, 2, 4 and 8 threads.

Rob Dunn seeking community participation in suveying & analyzing Duke Forest warming chambers

Just got this email from Rob Dunn from NC State.  He said it was OK to post it ... so I am .. (I note - I just completely love this idea).

Hi folks,

As you might (or might not) know, we have for five years now been running a large-scale warming experiment in which we have warmed twelve 5 meter diameter open-top chambers in forest understory at Duke Forest. We have warmed these chambers in a regression design with the warmest chambers as warm as temperatures are predicted to be in the region in 2100 and the coolest chambers at ambient temperatures (We also have no-chamber controls). These are small worlds each of which mimics aspects of futures we might face. This entire set-up is replicated at Harvard Forest. In these chambers we have been studying the response of insects (with a focus on ants) and plants  over the last five years. When we built them these chambers were the biggest warming experiment in a forest understory in the world. I don't know if it is still true, but it probably is, if only because chambers of this size are so hard to keep going (especially in the early we felt like Fitzcarraldo dragging a ship through the rainforest) that most people have decided against repeating them elsewhere. 

Some basics on the chambers... http://robdunnlab.com/projects/warming-chambers/

I'm writing because on May 25th we are taking the chambers down and doing a final inventory of the response of everything--all the life we can possibly evaluate--to this warming. To varying extents we have considered the phenology of plants in the chambers, many things about ants in the chambers, shifts in composition of invertebrates in the chambers and simple responses of bacterial and fungal assemblages in the chambers. But, we have done all of this delicately, always mindful to not overly disturb the future world we are simulating. Now though that the chambers are coming down we can and will consider roots, plant biomass, the abundance of insect pests, fungal pathogens and much, much, more. 

As we do this intensive survey, we are hoping to train as many different eyes, lenses and perspectives on the chambers as possible. If you are potentially interested in studying some aspect of the response of understory forest life to warming, let us know. If you are interested in studying something that can be extracted from soil or litter samples, we may be able to send you material you can work on. If you have something grander in mind (and we love grand things), then we may need more help from you. If interested, send an email to me, copied to MJ Epps (Mj Epps <mycota@gmail.com>).  This collaboration might be in the form of bringing a new method to the chambers (looking at microbial processes, for instance) or considering a group of organisms we've somewhat ignored (e.g., fly larvae) or it might be something totally off the wall. Feel free to share this email with likable folks that might be interested. 

I'm also delighted to hear creative ideas about visualizing the differences that have emerged over the years of this experiment (hence the inclusion of several artists of various sorts on this email list, if you were wondering why you were copied). 

I hope this email finds you well. 

Best,

Rob

Today's Spammy journal Editorial Board Offer #1

Just got this - pretty lame given that, well, I do not do anything related to this journal.

Dear Dr.Jonathan A Eisen,   

Hope this mail brings you good health and prosperity 

Fisheries and Aquaculture Journal is successfully publishing quality open access journals with the support from scientists like you. We are aware of your reputation for quality of research and trustworthiness in the field of science and thereby we request you to be an Editorial Board Member of our Fisheries and Aqua culture Journal. It would be our immense pleasure to have you as one of our editorial board member. 

Please follow the below link for more information http://omicsonline.com/open-access/editorialboard-fisheries-and-aquaculture-journal-open-access.phpIf you are interested, you are requested to send 

• A recent passport size photo (to display at our website) 
• C.V
• Biography
• Research Interests for our records 

Kindly submit your details at editor.faj@omicsonline.net, editor.faj@omicsgroup.biz We look forward to a close and long lasting scientific relationship for the benefit of scientific community.Waiting for a positive response.

With Kind Regards,XXXEditorial Assistant 

Fisheries and aqua culture Journal7 

31 Gull Ave, 

Foster City CA 94404, USA

More microbe-themed art - the Eden Project's "Human Biome"

Just got pointed to this Wired article by Katie Collins -- Eden Project's 'Human Biome' is a gross, musical microbe showcase (Wired UK)



Fascinating project that I actually don't think is gross in any way.  From the article

Invisible You: The Human Biome will explore the community of microbes that live in and on each and every one of us. Artistic and interactive displays will show bacteria, fungi and viruses, with 11 artists commissioned to create works for the exhibition.

I want to just quote the entire story but I think that is not allowed so let's just say you really should read the whole thing and look at the gallery.

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature

For many reasons I have been interested for the last few years in how agricultural practices affect microbiomes.  For example in regard to crops, how do farming practices affect the microbiomes of the plants, the microbiomes of the soil and area around the plants, and the microbiomes of organisms (including humans) who make use of the plants?

I won't go into all the detail right now for why I am interested in this topic but for some examples of my work in this area see The microbes we eat abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types and Structure, variation, and assembly of the root-associated microbiomes of rice.

Anyway, the reason I am writing this now is that tomorrow I am "testifying" to a NRC Committee about this topic and some related topics.  The presentation will be shown live online (register here).  And I thought, in the interest of openness, I would post some of what I am thinking about here before hand.

One of the key topics for tomorrow is something I have been snooping around at for a few years - how does glyphosate (the key ingredient of RoundUp and a widely used herbicide) affect microbiomes?  I am interested in this from both a scientific point of view (I think it is an interesting topic) and also from a "public policy / education" point of view.  I think this is a really good topic to have a public discussion of "microbiomes" and both the importance of microbial communities and the challenges with studying them.  So a few years ago I started thinking about working on this and developing a "Citizen Science" project around it.  And, well, I am still working on that idea and probably will be trying to launch something in the near future.  As a first start I thought it would be good to start to engage the community (researchers, teachers, the public, etc) in a discussion of this topic.  So .. this is the beginning of that I guess.

Some questions I think are interesting:

• Does glyphosate affect plant microbiomes?
• Does glyphosate affect soil microbiomes?
• Does consumption of plants treated with glyphosate affect the microbiomes of the consumer? 
• Directly (e.g., by glyphosate itself being in the food and directly affecting microbomes"
• Indirectly (by glyphosate affecting the microbiome of the food which in turn affects the microbiome of the consumer)
• If glyphosate affects any of these microbiomes above, are these significant affects (e.g., in terms of health)?

Now I am not the only person who is interested in this topic.  In fact, there have been many people looking into these and related topics for years.  Some of the things I have seen on this topic in the popular press and the scientific literature are, well, not good science.  And some of the things I have seen are fascinating and well done. 

So as a first step in looking into this, I scoured the literature for papers of interest.  And that is really why I am writing this.  I created an open collection of the papers I have found with the Zotero reference collection system.  See this link for the collection.  And if you know of any other papers truly related to this topic, please add them to the collection (learn more about Zotero here).  I do not profess to know everything about this topic.  But I think it is interesting and possibly important.  

Four simple tools to promote gender balance at conferences - guest post from Julie Pfeiffer @jkpfeiff

Guest post from Julie Pfeiffer.

Julie Pfeiffer
Associate Professor of Microbiology
University of Texas Southwestern Medical Center
https://twitter.com/jkpfeiff
http://www4.utsouthwestern.edu/pfeifferlab/Index/Home.html

---

Four simple tools to promote gender balance at conferences 

1. Know that you are biased. Identify your biases.

We all have biases and many of them are unconscious. You can discover your own biases using online social attitude tests developed by Project Implicit, a non-profit organization affiliated with Harvard University. The Gender-Science Implicit Association Test is particularly relevant here. It turns out that I have moderate bias linking science with males, as well as other biases. Knowing this fact has been extremely important. It is very difficult to alter unconscious bias, but it is easy to understand that you are biased and edit your actions accordingly. For example, if I need to make a list of potential speakers or authors quickly, the list will be of senior men from the United States. The key is to spend time EDITING the list to ensure diversity.

2. Keep track of numbers.

Most individuals in leadership positions are not seeking to exclude women or other groups from plenary talks, career opportunities, etc. Instead, they simply forget to count. They forget to keep track of gender ratio and other types of diversity. They forget to edit. When leaders/organizers have diversity in mind, diversity is relatively easy to achieve. Two examples illustrate this point:

1) Vincent Racaniello is President of the American Society for Virology and his goal was to put together an outstanding and diverse group of plenary speakers for the annual meeting in 2015. He asked for speaker suggestions via emails and Twitter (https://twitter.com/profvrr). He made a list and he edited it. The result? The best representation of female scientists at a conference I have ever seen--- 50% of the plenary speakers at ASV this year are female.



2) The Associate Editors at the Journal of Virology choose topics and authors for short reviews called “Gems”. The goal was to have high diversity in several areas including author gender, author career stage, author location, and topic. To keep ourselves on track to achieve this goal, we included several extra columns in our author/topic spreadsheet: Female? Non-USA location? Junior PI? This simple reminder in the spreadsheet has helped us select relatively diverse authors and topics: ~30% are female, ~30% are Assistant Professors, and ~20% are at institutions outside the United States.

3. Create lists and ask people for suggestions. 


Trying to come up with names of female scientists de novo can be a challenge. A few months ago, Carolyn Coyne, Erica Ollmann-Saphire, and Clodagh O’Shea made a list of as many female virologists as they could. Over wine, they devised a list of 70 names. We have circulated this list to many of our colleagues and tweeted a request to send missing names. The list is now at 349 and is publicly available (please tweet missing names to https://twitter.com/jkpfeiff). It is much easier to think of diverse options for speakers and authors by using a pre-existing list. Virologists with this list can no longer claim that they “couldn’t think of a female speaker”. Each field could benefit from a list like this, which could also include other underrepresented groups. Several of these lists exist, as has been highlighted on this and other blogs.

4. Speak up and enlist the help of supportive senior faculty.

Expressing concern to conference organizers about low speaker diversity can go a long way. While it may be difficult to change the speaker list close to the conference date, mentioning the lack of diversity could change the future landscape of the conference. I have an example from my own experience: I created an international shitstorm that had a great outcome. In year three of my faculty position I was considering whether to attend a major conference, so I checked the speaker list to help make my decision. Zero of 18 plenary speakers were female. I decided not to attend. Instead, I emailed the conference organizer to express my disappointment with the complete lack of female plenary speakers. His response, over several emails, was less than supportive:

“…. Finally, the gender, race, religion has never been, to my opinion, valuable ways to select presenters of scientific works. The selection of the Plenary Lectures has been made by the Organizing Committee, that comprises a woman, based on the topic, then the best possible speaker on the topic…. I am aware of the current debate in our societies about "minimum numbers". I do not think they would help the cause of women in science.”

While this organizer was not supportive or responsive to my speaker suggestions, five senior (famous) faculty members in the field were hyper-supportive. Upon hearing this story, they each contacted the organizer and expressed their concern about the lack of diversity. It was too late to change the program for the conference that year. However, in every subsequent year, the plenary speakers at this conference have included women and other underrepresented groups. So, it’s possible that a simple email from a young scientist can make a difference, particularly with the help of senior faculty.