The headlines called it “incredibly condescending” (Alexandra Petri, ComPost), “unrealistic” (Jia Tolentino, Jezebel), and “bonkers” (Olga Khazan and Julie Beck, The Atlantic.) The post from the aptly named Brandy Zadrozny at The Daily Beast) wasCategory Archives: archaea
Is the government telling women not to drink? How many microbes in the human body?
The headlines called it “incredibly condescending” (Alexandra Petri, ComPost), “unrealistic” (Jia Tolentino, Jezebel), and “bonkers” (Olga Khazan and Julie Beck, The Atlantic.) The post from the aptly named Brandy Zadrozny at The Daily Beast) wasPosted by in alcohol, archaea, Bacteria, brain, CDC, Centers for Disease Control and Prevention, contraception, drinking, FASD, featured, fetal alcohol spectrum disorders, fungi, health care, media criticism, medically unexplained symptoms, microbes, Microbiology, On Science Blogs, Palaeomerycidae, Politics, psychology, Research, united states, women
Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium
I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter) Sure - some people debate the structure of the tree of life. But I am pretty certain the authors here (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are. They just made what seems to be a colossal screw up. And Nature not only let them, but added to it with things like their "Editors Summary":
Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.
And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted "Twisted Tree of Life Award #16".
UPDATE 5/28 7AM
I love the ad that came up while I was writing this post and searching for some information. I think Nature could use the services from this ad:
Guest post from Kimmen Sjölander about FAT-CAT phylogenomics pipeline
Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru.
Announcing the FAT-CAT phylogenomic annotation webserver.
FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea -- and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately).
Announcing the FAT-CAT phylogenomic annotation webserver.
FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea -- and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately).
FAT-CAT is available at http://phylogenomics.berkeley.
Posted by in archaea, Bacteria, Evolution, guest posts, Kimmen Sjölander, Metagenomics, phylogenomics, UC Berkeley
Worth a read: Jim Staley on a "Universal Species Concept" and the history of microbial species concepts
Interesting paper came up in my automated google searches for "phylogenomics": Transitioning Toward a Universal Species Concept for the Classification of all Organisms | InTechOpen. It is by Jim Staley who has been writing a lot about microbial species concepts in the last few years. In addition to trying to bridge the gap between bacteria/archaea and eukaryotes in terms of species concepts. Not sure how I feel about everything in the paper but it has a really nice history of how species have been defined for bacteria. He breaks down this history into four periods
- Discovery of microorganisms,
- Advent of pure cultures and phenotypic features,
- Introduction of molecular analyses and
- Gene sequencing and genomics.
And goes through a bit of detail on each one. He also discusses what he sees as a need for a universal species concept and even makes some suggestions about how it might be implemented. Definitely worth a read.
Some related posts of mine and or links of potential interest:
- Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet
- Worth a look (from arXiv): Robust estimation of microbial diversity in theory and in practice
- Mendeley collection on number of species of bacteria and archaea
Posted by in archaea, Bacteria, James Staley, Microbiology, number of species, phylogenomics, species
RIP Carl Woese: Collecting posts / notes / other information about my main science hero here
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| My tribute to Carl Woese 12/30/12 |
News stories about Woese's passing
- Champaign/Urbana News-Gazette Visionary UI biologist Carl Woese, 84, dies
- U. of I. News: Renowned microbiologist Carl R. Woese dies at age 84
- University professor of microbiology dies at 84 years old
- Chicago Sun Times: Revolutionary U of I biologist Carl R. Woese dies
- NY Times: Carl Woese Dies at 84; Discovered Life's 'Third Domain'
- Wired: Carl Woese, (R)evolutionary Biologist
- Huff Post: Evolution Scientist Carl Woese Dies: 'The Most Important Evolution Scientist of the 20th Century'
- Carl Woese Dies | The Daily Scan | GenomeWeb
- Chicago Tribune: Carl R. Woese, microbiologist and professor at U. of I., 1928-2012
- January 2013 Reading in detail Carl Woese's 1998 "Manifesto on Microbial Genomics" for the first time ...
- April 2010 Most important paper ever in microbiology? Woese & Fox, 1977, discovery of archaea
- October 2010: Here's hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine ...
- September 2012: Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize
- Notes from a talk by Woese in 1993
- Evolution pumpkins - from Darwin to Woese
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| Woese Tree of Life pumpkin (by J. Eisen) |
Storification of Tweets and other posts about his passing
Other posts worth reading about Woese's passing
- So long, and thanks for all the Archaea » Pharyngula
- Prof. Carl Woese – 1928-2012 | C.W. Schadt | Microbial Ecology Lab
- A Sad Post: RIP Carl Woese! - Creatures Great AND Small ...
- T. taxus: Carl Woese 1928-2012
- Carl Woese - NASA Astrobiology: Life in the Universe
- Honoring a scientific revolutionary from Rob Dunn
- In Memoriam Carl Woese from Karl Fogel's blog
- Carl Woese dead at 84 - The Panda's Thumb
- RIP Carl Woese: Evolutionary Pioneer from the DailyKos
- From Larry Smarr
- Reposting of a Woese interview in LaborJournal.De
- El árbol que plantó Carl R. Woese
- Archaea Are More Wonderful Than You Know
- A sad loss for Microbiology
- Curiosidades de la Microbiología: Carl Woese 1928-2012
- The new biology of Carl Woese
Some videos with Woese
Miscellaneous
Miscellaneous
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| My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast. |
More about Carl Woese
- Carl Woese - Wikipedia, the free encyclopedia
- Carl R Woese - The School of Molecular and Cellular Biology ...
- Phenomenal history / discussion of Woese's work: Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
- 2007 Science article by Virginia Morell
Posted by in archaea, Carl Woese, Evolution, microbial diversity, Microbiology, rRNA, tree of life
Welcome to the Microbial Earth Project
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| Map of type strains. |
There are some 10,000 described type strains of bacteria and archaea. Not really a lot given that there are probably millions upon millions of species of bacteria and archaea. But it is what we have available to us in terms of the formally described and accepted species for which there is an available cultured strain.
At this site you can do things like "Adopt a Type Strain" or view a cool "Map of the type strains".
The Steering Committee for the project is
- Jonathan Eisen (University of California, Davis)
- George Garrity (Names for Life, USA)
- Philip Hugenholtz (Australian Centre for Ecogenomics Research, Australia)
- Hans-Peter Klenk (DSMZ, Germany)
- Nikos C. Kyrpides (DOE-Joint Genome Institute, USA)
- William B. Whitman (University of Georgia)
- Tanja Woyke (DOE-Joint Genome Institute, USA)
Much of the real work being done by Nikos Kyrpides, George Garrity, and others though I am very pleased to be a member of the Steering Committee. One of my key jobs will be to get the word out early and often. Hence this post.
Posted by in archaea, Bacteria, genomes, JGI, microbes, microbial earth project, Nikos Kyrpides
Get the genomes of up to 12 type strains of bacteria and/or archaea sequenced, for free
Barny Whitman asked me to post this announcement and, well, I am. I made one edit below (see strikethrough) in honor of Norm Pace.
Genomic Sequencing of
The Community Sequencing Program (CSP) Quarterly Microbial call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species. The type strains may also include proposed species prior to publication. Type strains must be relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity. However, strains of human pathogens and human associated species are not eligible. Proposals for genome sequencing of type strains can be submitted through the CSP Quarterly Microbial call, whose deadline is December 17, 2012, with approval usually being completed within one month. Up to 12 strains can be included in each proposal. Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring. If you cannot make the December call, Quarterly calls are also scheduled for March 25, June 17, and September 23, 2013.
Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals. You will need to register and sign in to this server. Once on the server, follow the links to the “CSP Quarterly Microbial/Metagenome”. All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA.
For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).