Byte Size Biology

“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2

“What-ever” –  Me

In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data as “noisy and partial.” Their review specifically addresses the computational requirements presented by metagenomics, rather than a comprehensive review of the current technologies. The review concludes with a “representative studies illustrating different facets of recent scientific discoveries made using metagenomics.”

–   http://www.genomeweb.com/blog/week-plos-75

I participated in writing this article for two reasons: first, Phil Bourne, the Editor in Chief of PLoS Computational Biology is a very persuasive fellow (in a good way). Second, one of the mandates of my position at the CAMERA project at the time was to develop new and innovative bioinformatics methods for metagenomics.  As I was immersed in the field and the latest professional literature anyway, writing a review seems like a good way to communicate the latest and greatest in the field, both to others but also to ourselves (John, Adam and I, all working in CAMERA). So we decided to write this up. While writing it, this article went through a few drastic alterations: Life Happened to me a couple of times, including changing jobs and a 3,500 km move, which caused a few months  of hiatus in the writing. Once we got back to writing, the field changed: new research and new software materialized and at least one software package we were writing about fell off the face of the Earth, so revisions and insertions were necessary. Second, the manuscript started to blow up uncontrollably: there is so much to touch upon in computational metagenomics! Obviously, the field is a moving target but anything we write, especially about software, will be outdated by the time it is published. We therefore decided against the laundry list approach, and focused more on general methods. We also culled a lot of interesting things (sequencing validation, eukaryotic metagenomics)  to keep the article relatively brief and flowing.

I hope you like the final result. There’s the comment section in PLoS, you are welcome to make good use of it.

Wooley, J., Godzik, A., & Friedberg, I. (2010). A Primer on Metagenomics PLoS Computational Biology, 6 (2) DOI: 10.1371/journal.pcbi.1000667

Blog Action Day focuses this year on climate change, which, like everything else on this planet, is also a microbial matter. Howzat? Methane (CH₄) is a greenhouse gas which has heat retention capability 23 times of that of CO₂.  Soil methanogens are the chief global producers of methane. There are an estimated 7.5x 10⁹ tons of methane trapped in a frozen peat bog in West Siberia which constitute 25% of the estimated methane trapped in soil and ice-age permafrost worldwide. Due to global warming, this permafrost is melting, releasing methane, which in turn contributes to global warming in a vicious cycle. The Nature paper, and an article in TerraNature.

Not only there, but trapped methane in the melting Arctic Ocean is also being released.  The ocean floor permafrost is melting,  clouds of gas bubbles are welling up in “methane chimneys”

These “methane chimneys” sometimes contained concentrations of the gas 100 times higher than background levels and were so large that clouds of gas bubbles were detected “rising up through the water column,” Orjan Gustafsson of the Department of Applied Environmental Science at Stockholm University and the co-leader of the expedition, said in an interview. There was no doubt, he said, that the methane was coming from sub-sea permafrost, indicating that the sea bottom might be melting and freeing up this potent greenhouse gas.

Susan Q. Stranahan, environment360

This may be the only permafrost we will have in a few years

The concern is that methane release might lead to a tipping point in global climate change: flipping a switch rather than turning a dial. At some point, global warming might turn into a runaway scenario when a critical concentration of atmospheric methane is reached. Martin Kennedy and colleagues at the University of California, Riverside claim that this is how Snowball Earth has ended 635 million years ago: a rapid warming period following a runaway positive feedback prompted by a methane pulse.

The effects of permafrost thaw in Dawson City, Canada

How big a problem is this? Big.  We have only recently begun to understand the magnitude of the role of methanogens in soil chemistry. It is very large.  Even in arctic climes, cold adapted methanogens are active at below 0C temperature, down to -20C. However, a study conducted by Dirk Wagner and colleagues shows that a 3 degree rise in soil temperature from -6C to -3C  would increase methane production dramatically. This means that not only trapped methane will be released due to soil thawing, but also that methane production itself will increase due to more favorable growth conditions for soil methanogens. So permafrost thawing hits the atmosphere with a double-whammy of methane release, supporting the concern about a runaway positive-feedback cycle that  will cause sudden climate change.

Dr. Permafrost may actually be the hero here, rather than the villain

Kennedy, M., Mrofka, D., & von der Borch, C. (2008). Snowball Earth termination by destabilization of equatorial permafrost methane clathrate Nature, 453 (7195), 642-645 DOI: 10.1038/nature06961

WAGNER, D., GATTINGER, A., EMBACHER, A., PFEIFFER, E., SCHLOTER, M., & LIPSKI, A. (2007). Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget Global Change Biology, 13 (5), 1089-1099 DOI: 10.1111/j.1365-2486.2007.01331.x

(Continued from  part 1)

Why we are islands

In the previous post we have seen how  our bacterial population affects  our weight  and that by changing our dietary habits we can change the species composition in our guts. Also, we saw how a metagenomic analysis can lead to verifiable hypotheses: using a metagenomic analysis, Gordon’s lab discovered that the microbiome in the guts of obese mice have a high level of bacteria from the Firmicutes division; they also found that they contain a high level of carbohydrate-active enzymes or CAzymes.  These CAzymes break down sugars in our foods more efficiently, extracting more calories that contributes to weight gain in a vicious cycle.

Read more…

No man is an island, entire of itself

— John Donne, Meditation XVII

Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine. From: Human Gut Hosts a Dynamically Evolving Microbial Ecosystem Gross L PLoS Biology Vol. 5, No. 7, e199 doi:10.1371/journal.pbio.0050199

Only one out of ten cells in our body is human

In a certain sense, every man is an island; this interesting finding comes from Jeffrey Gordon’s lab in Washington University. To understand why that is so, we need to understand something about the make up of our bodies. Adult human bodies are comprised of 10¹³ cells. These cells are broadly divided into different types that compose the tissues and organs that make us function the way we do. However, those are not all the cells that are in the human body. In addition to our own cells, we have 10¹⁴ bacterial cells that reside in and on us. Think about it: only one out of ten cells in our bodies contain the DNA inherited from our parents. The other nine cells are not human.

Read more…

(Continued from “On Microbial Sequencing“). Well, it’s really been a great meeting. The biology of pathogens, parasites and symbionts is amazing. Historically, the microbes that chiefly interested us were one of those three: those that causes disease in humans, animals (focus on domesticated animals), plants (again, mostly domesticated). However, as we are (alas, too slowly) learning about our planet, the changes that take place, we learn how embedded many microbes are to the ability of Earth to sustain life. A drastic example is the dreaded “methane pulse”. Methane (CH₄) is a greenhouse gas which has heat retention capability 23 times of that of CO₂.  Soil methanogens are the chief producers of methane. There is an estimated 75x 10⁹ tons of methane trapped in a frozen peat bog in West Siberia which constitutes 25% of the estimated methane trapped in soil and ice-age permafrost worldwide. This permafrost is melting, releasing methane, which in turn contributes to global warming in a vicious cycle. The Nature paper, and an article in TerraNature.

Read more…

This is the 9th year the NSF & USDA  hold  a workshop for their microbial sequencing program awardees. (Full disclosure: I am not one of them).  Most of the talks are by the awardees themselves, and there were some great talks. For me an interesting angle was it to see how software is being developed as an integral part of the research. The workshop was organized by Lita Proctor from the NSF and Ann Lichens-Park from the US Department of Agriculture,  and it was well worth getting up for at the ungodly hour of 6:45 am on two sunny San Diego weekend mornings. (Saturday and Sunday, 10-11/ January). Read more…