Tag: Misc.

Open source software tool for the week: AXIOME: automated exploration of microbial diversity

Just found this paper via Google Scholar Updates:
GigaScience | Abstract | AXIOME: automated exploration of microbial diversity

From Josh Neufeld’s lab this paper describes a series of tools for automation of microbial diversity analyses.

Abstract:
BackgroundAlthough high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.
FindingsAXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows.
ConclusionsAXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.

Workflows like this are what many many people need.  I note – I have not used this yet but it looks promising.  It has some parallels to the WATERS workflow package that came from my lab a few years ago (see more about it here: https://phylogenomics.wordpress.com/software/waters/.)  Alas WATERS is no longer being actively developed.  Anyway – AXIOME has additional features and certainly seems like it would be useful to many people.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Wanted: examples of family friendly policies for tenure review

I am on a committee at UC Davis that is part of an National Science Foundation “ADVANCE” grant that UC Davis’ Chancellor Linda Katehi and others at UC Davis received last year.  The goal of the project is “increasing the participation of women, especially Latinas, in academic science, technology, engineering and mathematics careers.”

More about the UC Davis ADVANCE program

One of the things the committee I am on is charged with is looking into how the policies and practices of tenure review might differentially impact women and minorities.  So – related to that I am writing to ask if people out there have examples of what one might call “family friendly” policies relating to extending the amount of time one is allowed before tenure review occurs.  Some questions I would love answers to for various institutions:

  • What are the policy guidelines for tenure review?
  • Can the tenure clock be extended for family related issues (e.g., birth of a child, adoption of a child, dependent medical care, etc)?
  • What is the specific wording of such policies?
  • How are such policies explained to tenure review committees and letter writers?

For UC Davis here is what I have been able to find (well, with help from the other people on the committee)

I posted a quick request to Twitter earlier.

//platform.twitter.com/widgets.js And got some responses

//platform.twitter.com/widgets.js

Any other information would be great.  I am hoping to make this an “open discussion” of such issues rather than just an internal UC Davis discussion …
//platform.twitter.com/widgets.js

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Digging around in National Science Foundation "news" is mostly a lesson in science by press release

Last week I wrote about how the National Science Foundation was involved in a painful press release about microbial genomics and evolution: Ugg – story about gene transfer/evolution based on NSF press release has a NASA-esque smell.  Today after getting some emails from people about this I decided to look to see if this was unusual or just what NSF press releases tend to look like.

I went to this site: News – US National Science Foundation (NSF) and decided to look at the links for stories I might know something about.  Here are some of them – a mix of NSF Press Releases and Links to outside PRs.

Alas most of these have some issues – some more than others.  Going through them one by one

Untangling Life’s Origins.  Link to an outside PR about work supported by NSF.  Not so bad – some painful stuff in the PR like the following:

  • “They are not the standard trees that people see in phylogenetic analysis,” he said. “In phylogenetic analysis, usually the tips of the trees, the leaves, are organisms or microbes. In these, they are entire biological systems.”
  • But overall reasonably tolerable compared to the others.
Home Toxic Home.  Link to an outside PR.  Filled with really painful stuff. Some examples
  • “Most organisms would die in the volcanic sulfur pools of Yellowstone and Mount Etna. Robust simple algae call it home, and their secrets to survival could advance human medicine and bioremediation. ”  Everything could advance human medicine and just about any other topic if you stretch it.  And it is a big stretch to find any connections here.
  • “Michael Garavito, Michigan State University professor of biochemistry and molecular biology was part of a research team that revealed how primitive red algae use horizontal gene transfer, in essence stealing useful genes from other organisms to evolve and thrive in harsh environments. ”  Ahh.  Back to the same general story that got me riled up to begin with.  This also has the fun “primitive” reference for algae which are not in any obvious way primitive. 
  • “The algae’s membrane proteins are biologically quite interesting because they’re receptors and transporters, the same classes of proteins that play key roles in energy metabolism and human immune response,” said Garavito. “This has applications in human medicine because virtually all of the important pathways that contribute to disease treatment involve membrane proteins.” So let me get this straight.  The algae has membrane transporters and receptors.  And therefore it is relevant to studies of human disease because many diseases are due to problems in transporters and receptors.  So – what organism on the planet then would not be relevant?  Uggh. 
  • They then clarify “What makes the algae’s membrane proteins attractive as a model for humans is their robustness. Other traditional candidates, such as yeast, insect cell cultures and slime mold, are fragile. The algae give researchers extra time to manipulate and examine their membrane proteins.”  Oh.  I see.  So nobody has ever thought of this before.  No work has ever been done on organisms that are “robust” as a model system.  Like – say – thermophiles?  Wouldn’t that be cool (or hot) to work on.  
  • There is more. I will not cover it.
Genetic Study of House Dust Mites Demonstrates Reversible Evolution.  Outside PR that is just completely full of crap.
  • A few days ago I posted about this to Facebook and to Twitter.  
  • And it still riles me up.  Some lines to treasure:
  • In evolutionary biology, there is a deeply rooted supposition that you can’t go home again: Once an organism has evolved specialized traits, it can’t return to the lifestyle of its ancestors. 
How to Thrive in Battery Acid and Among Toxic Metals.  This is the specific PR that got me riled up to begin with.  Awful.
“True Grit” Erodes Assumptions About Evolution.  Actually this one seems OK.

While most of what I looked at that seemed painful was from outside groups – I wonder whether NSF does any screening of outside press releases before posting them to their News site.  Given how bad some of the NSFs press releases are I am not so sure how they deal with outside PR.  But why aren’t they linking to actual news stories by real journalists?  Instead they simply link to PRs from groups supported by NSF.  Yuck.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Updates about the Undergraduate Research Conference

Hello Everyone,

I have a few updates with regard to the Undergraduate Research Conference.

The abstract that I turned in originally had a few mistakes, so I made sure to contact the Undergraduate Research office at the Student Community Center. Initially, they said that they wouldn’t allow any corrections upon submission of the abstract, but I was slightly insistent, so they agreed.

The updated abstract has been developed after considering everyone’s inputs and modifying the original abstract as necessary. As of now, it reads as below:

Aquarium Biogeography and Succession of Microbial Communities in Aquatic Environments

The biological sciences teaching laboratory for UC Davis maintains a wide variety of large aquaria, including freshwater and marine tanks, designed to mimic both temperate and tropical ecosystems. In this study, we seek to better understand the biogeography of microbial communities associated with these tanks. Using a culture-independent, DNA-based community census approach (i.e., 16S rRNA PCR surveys), we tackle two main questions: 1) how do microbial communities vary with respect to various environmental parameters (temperature, salinity, pH, oxygen and nitrogen concentrations) both within and across tanks; and 2) how does the structure of microbial communities change in response to ecosystem disturbance. To address this second question, we coincided our data collection with the establishment of two new aquarium systems (coral ponds).  We use high-throughput DNA sequencing of the 16S rRNA gene to generate a microbial community profile from hundreds of samples. These microbial community profiles are then compared across tanks (marine vs. fresh water, warm vs. cold) and in response to disturbances introduced during the establishment of the coral ponds.

I hope this acts as an almost accurate summary of what we are doing. The abstract was accepted, reviewed and approved by the URC people, so we are all set as far as that is concerned.

I need to also come up with a poster to represent our lab and the kind of work we do, and I get access to free poster printing services for that, so yay! This work is going to start next quarter, and I’m hoping that some of you will pitch in and help me out to make a good job of it and represent our lab in the way it deserves to be showcased. Also, I don’t know if others are allowed to co-present with me. If you are interested, do contact the URC office, I think it’s a great opportunity.

I attended the mandatory meeting for all participants of the conference. It was hosted by Tammy Hoyer of the Undergraduate Research Office today. It was pretty informative in the sense it gave me information on all the resources that were made available to me and what I could expect at the Undergraduate Research Conference.

Also, Tammy mentioned about the Undergraduate Research Journal, Explorations. They are currently taking papers, and I believe the deadline is 6th June, if I heard correctly. I know we wouldn’t have completed all of our research by then, but just letting you know of the opportunity.

Well, that’s all for now.

Also, starting next quarter, I will try my best to do the 8 hour a week thing, will be coming in on Mondays and Fridays, a 4+4. I hope to work with most of you during that time.

Good luck for finals!

Sign up: SMBE Satellite Mtg. on Eukaryotic-Omics 4/29-5/2 at #UCDavis

Going to be good:

Eukaryotes | SMBE Satellite Meeting on Eukaryotic -Omics – April 29 to May 2, UC Davis Conference Center

No bias here – given that it is organized by Holly Bik in my lab and it is at UC Davis. The lineup of speakers is great and the topic is timely.  So sign up  …

Speakers:

Rachel Adams UC Berkeley Groundtruthing next-gen sequencing for microbial ecology: is beta diversity robust to errors in pyrosequencing?
Nicholas A. Bokulich UC Davis Regional Patterns in Grape Fungal Consortia Define Wine Fermentation Communities
Sara Branco UC Berkeley Fungi at a small-scale: spatial zonation of fungal assemblages around single trees
C. Titus Brown Michigan State University Sequencing and assembly of diverse eukaryotes: like metagenomics, but much harder
Peter Countway Bigelow Laboratory for Ocean Sciences Title TBA
Simon Creer Bangor University, Wales Title TBA
Tom Delmont Marine Biological Laboratory, Woods Hole Phaeocystis antarctica spatiotemporal diversity, activity and its relation to prokaryotes and viruses using physiological and ‘omic approaches
Jonathan Eisen UC Davis The need for a phylogeny driven genomic encyclopedia of eukaryotes
Laura Eme Dalhousie University Large scale phylogenomic analyses of Blastocystis subtype 1 reveals a major role for lateral gene transfer in adaptation to parasitism of the human gut
Jack Gilbert Argonne National Lab Addressing microbial eukaryotic biogeography in home, hospitals and the world
Jean-David Grattepanche Smith College Title TBA
Victor Hanson-Smith UC San Francisco Identifying Loci of Functional Evolution in Ancestral Genes
Ian King University of Guelph Biomonitoring 2.0: A high-throughput genomics approach for comprehensive biological assessment of environmental change
Andrew Krohn Northern Arizona University Rhizosphere microbial community dynamics of drought-stressed pinyon pines (Poster)
Franck Lejzerowicz University of Geneva Exploring the deep-sea foraminiferal diversity by multiplexed RNA and DNA-based ultra-deep sequencing and ultra-fast bioinformatic analyses
Matthew Morgan CSIRO Australia Next-generation sequencing reveals the impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils
Laura Wegener Parfrey University of Colorado, Boulder Incorporating microbial eukaryotes into analyses of the human microbiome
Katherine Pollard UC San Francisco Title TBA
Dorota Porazinska University of Florida Discrimination of microscopic pests of agricultural importance with NGS
Thomas Richards NHM London Title TBA
Surya Saha Cornell University Composition of the Maize Endophytic Microbiome is Correlated with Maize Genotype (Poster)
Søren Sørensen University of Copenhagen Title TBA
Fabian Staubach Stanford University Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment
Sarah Stephenson CSIRO Australia Metagenetic examinations of benthic eukaryl estuarine communities
Joshua Stern Georgia Institute of Technology Searching for the Phylogenetic Place of Eukaryotes, Using Data from STORI
W. Kelley Thomas University of New Hampshire Title TBA
Xianfa Xie Virginia State University Comparative genomic study of the origin and evolution of eukaryotes
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

And the winner of the painful microbiology press release of the day: U. Maryland and Shil Dassarma

Not much to say here but “yuck”.  A new press release is out from University of Maryland: Strategies for possible survival on Mars: Scientists found differences in core proteins from a microorganism that lives in a salty lake in Antarctica

Some pretty painful things in here such as:

“These kinds of adaptations are likely to allow microorganisms like Halorubrum lacusprofundi to survive not only in Antarctica, but elsewhere in the universe,” says Dr. DasSarma.

What?  Does he really think there will be microorganisms like this elsewhere in the universe?  If there is life elsewhere in the universe is it really going to be like this at all?

And then in a shameless attempt to connect to the work being done on Mars:

“For example, there have been recent reports of seasonal flows down the steep sides of craters on Mars suggesting the presence of underground brine pools. Whether microorganisms actually exist in such environments is not yet known, but expeditions like NASA’s Curiosity rover are currently looking for signs of life on Mars.”

Does this mean in my next PR I should mention Curiosity too?

Actually the most painful part of me is the next paragraph

“Dr. DasSarma and his colleagues are unraveling the basic building blocks of life,” says E. Albert Reece, M.D., Ph.D., M.B.A., Vice President for Medical Affairs at the University of Maryland and John Z. and Akiko K. Bowers Distinguished Professor and Dean of the University of Maryland School of Medicine. “Their research into the fundamentals of microbiology are enhancing our understanding of life throughout the universe, and I look forward to seeing further groundbreaking discoveries from their laboratory.” 

First – do they really need to list that Reece is MD, PHD, MBA, VP, Dean and Distinguished Prof?  Seriously? Uggh.  And then the quotes attributed to said person are not impressive.  The basic building blocks of life?  Dassarma is not really looking at that.  And “life throughout the universe”?  Really?  What life exactly is that?  And finally, “further groundbreaking discoveries.”  Just what exactly makes this groundbreaking?

Uggh.  Can someone just make this PR crap stop?  Please?

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Guest post from Ashley Bateman on "Full contact microbes" – Roller Derby

A special guest post from Ashley Bateman.

 

Roller derby players share their skin microbes during play
Single-celled organisms are intimately associated with multicellular organisms across the tree of life, and human beings are no exception. Making up 90% of our cellular composition, these invisible passengers (our microbiome) contribute to our health and well-being in crucial ways, including aiding our digestion, the education of our immune system, and resistance to pathogens. Despite this importance, we still lack a fundamental understanding of where our host-associated microbes actually come from. We know that infants are born practically sterile; early-life events such as birth mode can contribute to the types of microbial species found on an individual, but these events cannot adequately explain the majority of spatiotemporal variation observed over a host’s lifetime. To be able to accurately describe the processes that drive host-associated microbial community dynamics, we must have an informed understanding of the role of dispersal in structuring host-associated microbial communities.
Where do they come from? How do they get there? Do these changes (if any) last?
The Green Lab at the University of Oregon-Eugene attempted to answer some of these questions in our latest publication “Significant changes in the skin microbiome mediated by the sport of Roller Derby”, released today by PeerJ. We decided to use Roller Derby as a model system to investigate the role of contact in dispersing skin microbial communities between hosts. We have known for a long time that pathogens can be transmitted via direct contact; could not our commensal microbial communities be shared in this way?

We swabbed the upper arms (a frequent contact point between players during a bout) of players belonging to 3 geographically distinct derby teams and characterized the skin microbiome of each player using 16s rRNA gene Illumina sequencing. We found that each team’s upper arm microbiome was significantly different from one another before play, and that this difference decreased after bouts were played. Not only did teams’ skin microbiomes become less different from one another after play, but the differences were driven in part “by the presence of unique indicator taxa that are commonly associated with human skin, gut, mouth, and respiratory tract.” There were also environmental bacteria associated with soil and plants found in the skin samples.

Although we weren’t able to show a direct link between contact and transfer of specific microbial taxa, the best explanation of the data seems to be that contact between these players during a one-hour bout effectively resulted in homogenization of their upper arm skin microbiomes.
So much yet to explore! As a 2nd year graduate student in the Green Lab I hope to address some of the questions that the Roller Derby paper has brought to our attention. My dissertation research is gearing up to understand the role of dispersal on our skin microbiome. Are some skin sites more amenable to changes than others? Can we pick up host-associated microbes not just from other individuals, but from objects that other individuals have touched? Can we pick up non-host-associated microbes? If we can pick them up, how long do they stick around? How do they participate in the functions attributed to the skin microbiome?
Hope to keep up the fantastic momentum that has been launched by this latest publication – if you have any thoughts or comments, feel free to contact me at abateman@uoregon.edu, or via Twitter: @microbesrock
And you can check out a stop-motion video I made on the skin microbiome here:
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Special issue on Women in Science (the field) in Nature (the journal) (articles appear to be freely available too)

Definitely worth a look at this special in Nature on Women in Science: Special: Women in Science.  Articles seem to be freely available – at least for now (they were not initially).

Here are links to some of the articles:

Any many more … 
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Ugg – story about gene transfer/evolution based on NSF press release has a NASA-esque smell

Well, this made me cringe many many times: Extreme Algae Thieves Its Genes From Bacteria – Science News – redOrbit: Science

The article discusses a new paper which itself sounds potentially interesting.  The paper itself sounds somewhat interesting.  But that is besides the point.  The parts that made me cringe are the inaccurate or overhyped statements about the novelty of this work.  Here are some of the statements I find troubling

  • “While the ability to pilfer genes from another microorganism has been seen before, scientists have never observed this ability in a eukaryote – an organism with a nucleus.”  
    • Wow.  Completely ludicrous.  There are hundreds if not thousands of papers on lateral gene transfer to organisms with nuclei.  
  • “The results give us new insights into evolution,” said co-author Gerald Schoenknecht of Oklahoma State University’s Department of Botany. “Before this, there was not much indication that eukaryotes acquire genes from bacteria.”
    • Same complaint as above. 
  • “The age of comparative genome sequencing began only slightly more than a decade ago, and revealed a new mechanism of evolution – horizontal gene transfer – that would not have been discovered any other way,” said co-author Matt Kane, program director in the National Science Foundation’s (NSF) Division of Environmental Biology. “This finding extends our understanding of the role that this mechanism plays in evolution to eukaryotic microorganisms.”
    • This quote is deeply troubling.  Genome sequencing did not reveal a new mechanism of evolution.  And it is thus also inaccurate to say ‘it would not have been discovered any other way“.  Lateral gene transfer was studies for many many many years before the first genome sequence was determined.  Certainly, comparative genome analysis helped reveal the extent of gene transfer but it is seriously inaccurate to say it “revealed a new mechanism of evolution“.  Here for example is a link to a google search for the specific phrase “lateral gene transfer” in papers published prior to 1995.  And here is one for the phrase “horizontal gene transfer“. 
    • I hoped that this was a misquote because the person quoted is Matt Kane – an NSF program officer responsible for many areas related to microbial studies.  But alas I found the press release from NSF with the same quote.  Perhaps NSF PR people misquoted Matt.  I hope they misquoted Matt.  Because if not – the quote grossly oversells genome sequencing and what has been learned from it and rather than standing on the shoulders of giants it makes the giants of the past seem like ants.  
  • “It’s usually assumed that organisms with a nucleus cannot copy genes from different species–that’s why eukaryotes depend on sex to recombine their genomes. “How has Galdieria managed to overcome this limitation? It’s an exciting question. What Galdieria did is “a dream come true for biotechnology,” says Weber.”
    • This is wrong in so so many ways.  Again, as discussed above, eukaryotes have been known to undergo gene transfer for many years.  
    • And to say that the inability to acquire genes by LGT is why eukaryotes depend on sex to recombine their genes?  Really?  Uggh.  As far as I know there are no major theories out there that suggest sex is there because eukaryotes cannot undergo lateral transfer (although certainly some theories on the origin and maintenance of sex do indeed relate to increasing diversity by recombination).
    • And what makes this a dream come true for Biotech exactly? 
    • I note – this too was in the NSF press release.  Has NSF suddenly decided to become like NASA in terms of ludicrous PRs? 
I note – I do worry about the effect of calling out NSF on this in terms of my ability to get grants from them.  But this is just terrible stuff in this PR and story and it needs to be stopped.  I note further that I consider Matt Kane a friend and I hope that he clarifies his quote here and also manages to get NSF to be more rigorous in their PRs.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Lab presentation last Friday

Unfortunately I missed our lab meeting presentation last Friday, due to a doctor appointment taking longer than expected, but I did learn a huge amount of what’s to come in the data analysis portion of our project (basically everything that happens after sequencing). It’s going to be a lot of work, from assigning OTUs to building phylogenetic trees and much more!

 

For now we will be continuing our normal lab work. We have made a few modifications to speed up the process. For example, for PCR A, we are adding a more rough amount of DNA rather than calculating it all out, which takes a good amount of time. Note: this does not make our end results less accurate.

 

I’m excited to finish our first set of time intervals for Coral Pond 1 so we can get them sequenced and start analyzing!