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Metagenomic Analysis of Microbes in Termite Guts May Yield Novel Enzymes for Better Cellulosic Biofuel Production

Termites of the genus Nasutitermes.

Termites digest wood with the help of a large and complex community of intestinal microorganisms. A just-completed metagenomic analysis of this bacterial community in the hindgut paunch of a wood-feeding Costa Rican termite shows the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. This first system-wide gene analysis of a community specialized toward the breakdown of plant cellulose also provides insights into important symbiotic functions, and could lead to the production of novel enzymes for better biofuel production.

The genomic sequencing and analysis of the termite gut microbes by the US Department of Energy Joint Genome Institute (DOE JGI); the California Institute of Technology; Verenium Corporation (formerly Diversa), a biofuels company; INBio, the National Biodiversity Institute of Costa Rica; and the IBM Thomas J. Watson Research Center are highlighted in the 22 November edition of the journal Nature.

The termite is a remarkable machine. Termites can digest a frightening amount of wood in a very short time, as anyone who has had termites in their house is painfully aware. Instead of using harsh chemicals or excess heat to do so, termites employ an array of specialized microbes in their hindguts to break down the cell walls of plant material and catalyze the digestion process. Industrial-scale DNA sequencing by DOE JGI was key to identifying the genetic structures that comprise the tools that termites use. Our task now is to discover the metabolic pathways generated by these structures to figure out how nature digests plant materials. We can then synthesize the novel enzymes discovered through this project to accelerate the delivery of the next generation of cellulosic biofuels.

—Dr. Raymond L. Orbach, Under Secretary for Science, DOE

We were all surprised by the enormous diversity that was revealed, and are excited by the possibilities for future research into the role each gene and enzyme might play in degrading the structural polysaccharides of plants. These are important insights into nature’s mechanisms that may provide keys to unlocking more effective, industrial methods for converting cellulose to ethanol. <>

—Dr. Geoff Hazlewood, Ph.D., Verenium’s Senior Vice President of Research

Like cows, termites have a series of stomachs, each harboring a distinct community of microbes under precisely defined conditions. These microbes are tasked with particular steps along the conversion pathway of woody polymers to sugars that can then be fermented into fuels such as ethanol. The mandibles of the insect chomp the wood into bits, but the real work is conducted in the gut where the enzymes exuded by microbes attack and deconstruct the cellulose and hemicellulose.

The research was funded through DOE’s Community Sequencing program. The principal investigator was Dr. Jared Leadbetter, Associate Professor of Environmental Microbiology at CalTech. Together, the team sequenced and analyzed more than 80,000 genes encoded by many of the termites’ hindgut bacteria species, including about 1,000 cellulase/xylanase genes.

In partnership with INBio, Verenium created an environmental library of DNA collected from the wood-feeding “higher” termite species, Nasutitermes, found in the rainforest of Costa Rica. The DNA was then sent to JGI for sequencing.

Prior to this study, only one gene had been connected to the termite’s rare ability to digest and nourish itself with wood, a substance that is energy rich but difficult to break down. The scientific community long suspected that the bacterial species found in a “higher” termites’ hindgut might be involved in this process and results of this study from the gut community of the Nasutitermes termite demonstrated that these suspicions are correct.

Based on these results, Verenium plans to utilize its gene technologies and high-throughput screening capabilities to evaluate the activity of novel cellulases and hemicellulases encoded in this large collection of novel genes in order to attempt to identify enzyme combinations that can be exploited for converting biomass feedstocks into biofuels.

Our analysis revealed that the hindgut is dominated by two major bacterial lineages, treponemes and fibrobacters. Treponemes have long been recognized in the termite gut due to their distinctive cork-screw shape, but fibrobacters were an exciting new find, because they have relatives in the cow rumen known to degrade cellulose. We could directly link the termite fibrobacters and treponemes to enzymes capable of breaking down wood. However, fibrobacters are specialists in this regard and don’t appear to participate in sugar fermentation, leaving that to the treponemes. This project has really given me a new appreciation for the lowly termite, a mobile miniature bioreactor.

—Phil Hugenholtz, DOE JGI’s Microbial Ecology Program head

In the termite P3 compartment alone, more than 500 genes related to the enzymatic deconstruction of cellulose and hemicellulose were identified by Hugenholtz and colleagues. The termite gut metagenome dataset will become publicly available in the next version of DOE JGI’s metagenome data management and analysis system, IMG/M (, scheduled for release in January 2008.

Adapting these findings for an industrial-scale system is far from easy. Termites can efficiently convert milligrams of lignocellulose into fermentable sugars in their tiny bioreactor hindguts. Scaling up this process so that biomass factories can produce biofuels more efficiently and economically is another story. To get there, we must define the set of genes with key functional attributes for the breakdown of cellulose, and this study represents an essential step along that path.

—Eddy Rubin, JGI Director




I think its great to find more ways to break down biomass into fuels, but I still see a basic problem in the amount of fresh water needed to grow the plants in the first place> we can rapidly add a water shortage to the oil shortage and third world countries are pretty much screwed over. We need to be working on creating some plants that grow in salty or brackish water that can be converted since 98% of the available water supplies are that way. Do termites like kelp?


You process the cellulose from plants that grow now like corn stalks. Corn for food and stalks for cellulose. There is no extra water required.

James White

I still have big concerns about how we keep the manmade cellulose-eating bacteria genie from eating good forms of cellulose. If we successfully create a prolific bacteria with the cellulosic appetite of a Costa Rican termite, what is going to stop it from eating wood studs in walls, forests, wheat straw, or the foundation of an entire ecosystem?

History is full of examples of man importing exotic species to solve one problem, but end up creating far greater problems.

James White

I still have big concerns about how we keep the manmade cellulose-eating bacteria genie from eating good forms of cellulose. If we successfully create a prolific bacteria with the cellulosic appetite of a Costa Rican termite, what is going to stop it from eating wood studs in walls, forests, wheat straw, or the foundation of an entire ecosystem?

History is full of examples of man importing exotic species to solve one problem, but end up creating far greater problems.



Those kinds of risks must always be weighed against doing nothing. The article says that the microbes exist in the termite gut do so under specific conditions. They can be tailored so they do not survive outside of a controlled environment.

Stan Peterson

This technology can't hurt and might help. But it is only a short term answer. Creating biofuels does not asnwer the need to replace hydrocarbon burning as a source of energy. We need cleaner methods that are unlimited in capcity and intrinsically much smaller in the size or effort needed to extract the energy.

Fusion is coming; and that is the true answer. Combined with the Electric substitutes for transportation, we will no longer need to waste prodigious amounts of effort, in burning enormous quantities ofhydrocarbons, irrespective of whether the source is long dead or only recently created hydrocarbons.


These bacteria exist now and are distributed around the world by their vectors (the ants). they are even seeded freely into woord structures (when an ant vomits or dies inside the wood). Nevertheless, we never see wood disintegrating from itself ; we only see the tunnels made by termites. So, the bacteria by themselves are not able to destroy healthy wood ; only when it is already broken down into very little particles and left at the right conditions (like in a termite gut).
Since all these genes are mixed together in termite guts for millions of years, and there is not a single microbe that can spread easily and destroy healthy wood by itsels, it is very, very unlikely that such a bacterium would be made accidentaly by man. If we don't take the great effort to provide the genetics of a very complicated distribution system to the bacteria, they will never be able to escape the reaction containers of a biorefinery. These bacteria just don't survive in free nature, only in the protective environment of the termite gut (or man-made container).

Fred, whether the cellulose comes from salty water (like mangrove trees) or from other cellulos (like from agricultural waste or normal trees), these enzymes digest cellulose. It is very useful to use cellulose, because this is the only biomolecule that is made by plants and is stored for years or even decades. We could plant big (mangrove) forests now for carbon capturing and let them grow for years of decades, and then harvest them whenever we need the cellulose. If we use algae cultures, the efficiency per acre is much higher, but so are the investments, and the algae must be harvested at the time the algae decide, not at the time we decide.
Moreover, the 'energy plantage' could very well be a very rich ecosystem (like mangrove or other forests), while other energy staples mostly are very ecologically unfriendly (or neutral at best). Mangroveforests don't use freshwater, they produce rainfall by evaporating oceanwater.
If there is an economic incentive to plant milions of acres of (mangrove) forests, this is a great thing. If we do carbon capturing and keep crude underground, it's even better.


Anaerobic microorganisms consuming organic matter (cellulose, proteins, fat, alcohols, etc.) are very widespread in nature. It is abundant in swamps, soil, intestinal of cows, elephants, ants, even humans (it makes human fart combustible). Symbiosis of anaerobic microorganism and animals (and insects) is very beneficial to both: animals supply food, microorganisms digest it in steps, and animals consume part of semi-digested cellulose, other vice unusable. For ruminants (cows, sheep, goat, moose, deer) it is just a lifeline. Current human dietary recommendation to eat more fibers makes direct use of anaerobic biota in human guts and colon: part of intermediate products of anaerobic digestion of fibers – propionic, butyric, and acetic acids – are adsorbed into bloodstream and are beneficial to health.

Industrial use of anaerobic digestion is also widespread: it is used to treat organic sludges/wastes from food industry and to treat activated sludge at sewage treatment plants. Valuable fertilizers and biogas are bonus products of such treatment.

All enzymatic cellulose ethanol and butanol technologies make use of natural anaerobic microorganisms, beginning with pioneering in the field Iogen corp. of Ottawa. Their particular strain of hydrogenasa enzymes is derived from mold eating uniforms and cotton tents of American JI during WW2 in Pacific. Iogen sold same enzymatic products to companies producing jeans, to stonewash them according to the old fashion. It helped Iogen to survive when oil was cheap and nobody seriously invested in cellulosic ethanol.

Anaerobic biota constantly mutates naturally. Some strains are reported to learn consume coal: in US NE in couple of places sewage sludge was pumped into abandoned coal mines, anaerobic microorganism mutated and learned somehow to consume organic molecules found in coal. Extremely robust anaerobic complexes were found in elephant and termites intestinal.

Anaerobic microorganisms are always loose to much more robust aerobic biota, when oxygen (air) is available. Their energy pass to skim small energy available from reduction of long organic molecules into elementary refuse of methane and carbon dioxide yields much less energy than in aerobic pass, where all digestible organic in presence of oxygen is reduced to carbon dioxide and water. There is no danger from releasing of enhanced anaerobic strains into the nature: it is not even remotely competitive to aerobic biota.


You state Fusion is coming. Share what you know.

green menace

Fusion was coming in the 70s;it was just around the corner. It still is. Continued reliance on the elusive magic bullet to solve our problems is part of the recipe for disaster. Even if we had fusion, would be have the wisdom to use it wisely? Of course not. We have already shown our lack of foresight and prudence with respect to the way we have used and abused the resources we have.


When fusion comes stan (someday) sure, but I would love to see you make plastics with fusion. We still need to convert waste into products, fusion could help power that but it will still be a thermalchemical or biochemical driven process.

Harvey D


Alternatively, a few dozen large updated fission nuclear power plants could safely produce all the excess electric power required for 200+ million PHEVs and BEVs for the next 40 to 50 years.

Of course, wind, solar, waves, geothermal, hydro power etc could meet part of the demand.


wasn't there a study that found that we could replace ~80% of the existing cars with EVs powered on off-peak electricity without the need for extra powerplants?


It's marvelous what nature has been up to hese last millenia, While the apes recline in caves or down the beach, wich reminds me, summers here and the world is there already to enjoy.
As we dont have to desighn that one, just respect the one we have. Look at it this way:
We area curious specie with curious brains in a curious world so curious minds in interesting times learn intersting facts in conventional ways.
So what If I prefer termites this week, and get to know them more intimately. And ultimately they may in time get to Know us and our needs - more than just greed.
in this brave new world.


==wasn't there a study that found that we could replace ~80% of the existing cars with EVs powered on off-peak electricity without the need for extra powerplants?==


Followed by a similar study that finds that even if an electric car were powered by coal, it would be as green as a hybrid.

And another program looking to leverage used car batteries as a stay-put grid storage mechanism.


Also, there's plenty of green energy to be had.

I am sick of that Weng guy using these comment areas as a marketing tool to sell diesel parts. Go away. This is not the place man. At least say something about alternative energies, get into the debate, etc. before shovelling your sh?t.


Some wag said "Fusion has been 20 years away for the last 50 years".  Still seems true.


I have heard its been 50 years away since 1950! even so some do claim to be very close:

fred schumacher

Off-peak power is produced primarily by coal, and burning coal puts out nearly twice as much CO2 per unit energy produced as petroleum. Running cars on coal does not solve our global warming problem. Coal fired power plants would like to increase their off-peak output, since it allows them to run more efficiently and profitably, but it means burning much more coal at night.

Perennial cellulosic biomass crops are quite water efficient. They depend on rainfall for their water, not irrigation. Production of cellulose is accomplished at low fertility levels. It is seed,fruit and vegetable production that requires high water and nutrients.

fred schumacher

An additional exciting thing about this research is that termite gut bacteria are able to break down hemicellulose, which is composed of five-carbon sugar chains. Cellulose is composed of a long chain of glucose, a six-carbon sugar. We can't digest five-carbon sugars (they're what give you gas when you eat beans).

Termites using cellulose for food shows us another use of cellulose people haven't thought much about -- it can form the carbohydrate fraction of animal (or human, for that matter) food. Wes Jackson has been working on perennial grain crops, but perennial cellulose crops could conceivably produce much more food, with less input, than annual grain crops.

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