A sustainable future will certainly include technologies based on microbes and small organisms. These will be found through bioprospecting.

The previous post described the first two cycles of innovation derived from bioprospecting. It came from fungal and bacterial products applied to medicines: antibiotics (ca. 1930-1970) and immunosuppressive drugs (ca. 1970-2000).

A prior post described how the next cycle of innovation in this area came from algal and fungal products applied to infant nutrition: DHA omega-3 fatty acid and ARA omega-6 fatty acid (ca. 1990-2010).

The next frontier may emerge to serve markets in health, nutrition, agriculture, and new materials. Let’s look at examples of how this can unfold, along with what to expect in-the-field.

Low cost, sustainably sourced omega-3 oil as dietary supplements

Omega-3 fatty acids are presently sourced by extracting oil from fish. There is a market for omega-3 oils used as dietary supplements, and these are popularly referred to as fish oils. This entrepreneurial opportunity in fish oils was captured two decades ago, as described in this post.

However, new opportunities await. Extracting omega-3 oils from fish is a terribly wasteful process. Tons of fish are dragged from their environment, scalded and shredded apart every year, to separate out their oil for industrial uses and for human consumption. What remains is sent to farm feed.

Hence, the problems with this current product are environmental sustainability and high cost.

New ventures are emerging: “cellular agriculture” companies are advancing a vision of developing new, non-animal sources for traditionally sourced products.

A very low cost algal source for omega-3 oils for dietary supplements would disrupt this space. The need is not finding algal strains. These are known. The innovation needed here is in engineering for cost reduction.

Eicosapentaenoic acid (EPA) for cardiovascular health

Description of the unmet need

Fish oils contain two omega-3 fatty acids: docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). These two acids have different pharmacological activities. DHA is needed for neural and retinal development. EPA has cardiovascular benefits by reducing triglyceride levels in blood.

For infant nutrition, DHA is the important ingredient. You do not want the EPA. Excess EPA increases bleeding risk in infants. Separating the DHA from the EPA in fish oil is prohibitively expensive to serve the infant nutrition market.

Martek Biosciences was the company that first identified this need for DHA, free of any EPA, for infant nutrition. Their innovation was finding a species of algae to produce this product and to use large scale fermentation to manufacture the product. From circa 1990-2012, Martek created a global  business in this area, as described earlier.

There is now a new, disruptive need: a sustainably sourced EPA, free of DHA, This is for cardiovascular health.

The first prescription omega-3 fatty acid capsule for treating high triglyceride levels was launched in 2001. This is a high dose fish oil capsule currently sold by GSK. The problem with this product is that (1) most patients find it uncomfortable to consume such high levels of fish oil to get the pharmaceutical benefit, and (2) about half of its composition is DHA, which is not the ingredient responsible for the cardiovascular benefits.

In the late 1990’s, a Norwegian company saw the product opportunity in creating a high dose fish oil capsule, without the DHA, for treating cardiovascular disease. Removing the DHA reduces the amount of fish oil that a patient needs to consume, making the product more appealing. Their manufacturing process was to purify fish oil by using transesterification and molecular distillation to isolate a highly purified form of EPA. The drawback of this process is that it is extremely expensive, and half the oil—the DHA—is wasted. The product was launched in Europe in 2001, but its high cost did not help with sales.

A biopharmaceutical company, Amarin, acquired this product and then took the risk to run comparative clinical studies, betting that it might be better than GSK’s fish oil capsule. It was a highly controversial move to investors, and the premise was unclear to the medical community at the time. This is the nature of risk taking and entrepreneurship.

That gamble paid off this year. Their clinical study demonstrated superior cardiovascular benefits of taking an omega-3 oil containing 98% EPA. A reduced risk of heart attacks was observed. These dramatic results are now being reviewed by FDA.

The stock price of Amarin has experienced huge volatility through the course of its long development path, but these latest clinical results are validating the original investment thesis.

Figure 1: Amarin’s stock price, 2009 to present.

There is a benefit in having a high dose EPA product. However, using fish as its source is not sustainable, and certainly not if this is to be a high volume product. Furthermore, the manufacturing process is very costly and wasteful. This is where an algal source to produce EPA will be of great value.

Bioprospecting for a species that produces EPA

The reason there are so many new DHA omega-3 start-up companies is that it is now easy to find new algal species after Martek Biosciences showed us where to look: in mangrove leaves and other vegetation along certain types of shorelines.

Prospecting in these spots will reveal new DHA producing species. Startup companies are founded to commercialize such discoveries on the mistaken belief that there is a need for algal DHA, which is not the case.

The real need is to find a microbial species that produces just EPA, and to develop a large scale production process that is low cost.

Here is a technical overview, to provide a first-hand account of how this could be done.

Figure 2 shows the taxonomy of algae, bacteria and fungi that produce omega-3 oils. Species that produce high levels of DHA are highlighted in red. Species that produce high levels of EPA are highlighted in green.

Figure 2: high producers of EPA and DHA, organized by taxa. Click on image to expand.

Look at the red highlighted taxa. The current commercial source for DHA is produced by a dinoflagellate from the genus Crypthecodinium. A next generation of even higher DHA producers has been found in the Thraustochytriaceae family. Thraustochytriaceae species are easy to find in mangroves and other vegetation along shorelines. However, DHA production from Crypthecodinium is locked into the global infant formula supply chain, and it is not likely to be displaced. New DHA companies make the mistaken assumption that they can displace a locked-in supply chain.

Now look at the green highlighted taxa. There are many species of EPA producers.

Figure 3 shows that there are some very high algal producers of EPA that do not produce DHA. This would be ideal. However, these yields are only achieved when the algae are grown in photosynthetic mode, which is not economical.

Figure 3: fatty acid composition of high EPA-producing algae in photosynthetic mode. Click on image to expand.

The economical mode of production is in the fermentation mode. Figure 4 shows the best algal EPA producers in fermentation mode. However, these yields are too low.

Figure 4: fatty acid composition of high EPA-producing algae in fermentation mode. Click on image to expand.

Figure 5 shows a newer discovery: some bacteria from the genus Shewanella are also EPA producers when grown in fermentation mode. Unfortunately, their yields are even lower than the algae.

Figure 5: fatty acid composition of EPA-producing bacteria in fermentation mode. Click on image to expand.

Almost ten years ago, I came across a paper in an obscure journal showing an early discovery from a research group in India: four new species of bacteria, two from the genus Shewanella and two from a new genus, Halomonas. These were isolated from a deep trench in the Pacific Ocean. They appear to be very high EPA producers when in fermentation mode.

Figure 6 compares these to the highest yielding EPA producers, which are recombinant organisms (recombinant organisms are not desirable in this application). This early discovery seemed too good to be true. Halomonas and Shewanella are both in the Gammaproteobacteria class. This taxonomic relationship makes the findings in this paper plausible.

Figure 6: fatty acid composition of EPA-producing bacteria in fermentation mode, compared to two recombinant organisms that are record EPA producers. Click on image to expand.

This is the modern day version of the Indiana Jones adventure. I contacted the lab. They invited me to visit to discuss the results. The gallery below shows that adventure. I flew into a city in India. I stayed overnight in a local hotel that would not look out of place in a James Bond movie. In the morning, I took a cab to a large university and made my way to the biotechnology department. The professor wanted me to give a lecture to the students, which seemed to be part of the “deal” for a meeting. Then came the highly anticipated meeting where it was revealed that the results were recently found to be irreproducible. They suggested that additional research funding might lead to some better results in the future.

I flew out of the local airport dejected and feeling somewhat foolish. Even a modern day Indiana Jones adventure will come with its cast of characters and intrigue. That’s human nature.

Fortunately, I timed the trip to coincide with travel plans anyway. So it was not an expensive detour. The potential opportunity was too great to give up if this was actually real.

Somewhere on this planet, a valuable high EPA-producing species is lurking.

The microbiome: probiotics for human health

Microbiome fields have grown to be of considerable interest to scientific investigators and investors. There are no commercial products yet. What might this first product be? The world already caught a glimpse of this over two years.

The most newsworthy clinical study result of 2017 was published in the prestigious journal Nature. It was so exceptional that mainstream publications like The Atlantic reported on it. Chemical and Engineering News listed it in the top eight research results of that year.

Over 600,000 babies die each year from sepsis, a system wide bacterial infection spread through the blood. This is more prevalent in developing countries.

A prevailing hypothesis of early infection is that pathogenic bacteria in the intestines “leak” into the blood. This would not normally happen when the intestines are healthy and colonized with a large population of beneficial bacteria. This is the gut microbiome: a diverse ecosystem of bacteria, mostly beneficial, which crowds out pathogenic bacteria and also keeps them in check.

However, infants have intestinal tracts that are only starting to colonize after birth. It is at this stage of life that infants, who also have underdeveloped immune systems, are most vulnerable. The hypothesis is: what if you could enhance that colonization with good bacteria sooner?

Thus, a professor from the University of Nebraska did some bioprospecting of stool samples for a beneficial bacteria that has the ability to be retained in the gastrointestinal tract. His assays identified a uniquely beneficial bacterial species, Lactobacillus plantarum, strain ATCC-202195, that had a powerful ability to attach to intestinal cells and proliferate and to keep virulent bacteria at bay.

This bacterium is the probiotic. When combined with a prebiotic (“food” for this beneficial bacteria), a “symbiotic” formulation (prebiotic + probiotic) was developed.

He performed a randomized, double-blind, placebo-controlled trial, the gold standard of clinical studies. One study arm of newborns were fed this symbiotic daily for just one week. Newborns in the other study arm were fed a placebo.

Usually, probiotics need to be taken daily. Dosing daily for just one week is very brief. The premise of this particular bacterial strain was that it was a particularly powerful gut colonizer.

Indeed it was. The results were striking. The study design aimed to enroll 8000 patients in India. It was stopped after 4557 patients, because the beneficial effect was statistically evident. In such cases, the study is deemed unethical to continue the placebo arm when it is clear that the treatment arm has therapeutic efficacy.

They found a 40% reduction in infant deaths due to sepsis in the first two months of life when infants were fed the symbiotic daily for just one week.

The size of this study population was also noteworthy. It is very large, enough to produce statistically clear results.

L. plantarum ATCC-202195 would be the world’s first medically important probiotic. So why, two years later, is there no news of any commercial partner, and no news of any pending product launch?

Here is another question: this study took ten years to complete. Granted that the study subjects were in remote locations, and funding for such work is tight. Still, ten years is an unreasonably long time that begs the question of what extraneous factors stretched this work out for so long?

Finally, it is noteworthy that this work was funded, in part, by the Bill & Melinda Gates Foundation. Now, the Bill & Melinda Gates Foundation is funding their own study in this application, using another strain of L. plantarum, Lp-115, provided to them by Dupont.

Most strains of L. plantarum have limited to no efficacy in this application. DuPont-Danisco has been working in this area for a long time looking for their own strain of L. plantarum. This appears to be an attempt to develop an alternative to the ATCC-202195 strain that has since been unavailable.

I have my own theory for this intrigue. I could be wrong. Usually, when an academic discovery does not progress expeditiously in a commercial direction, the reasons lie with the people, rooted in something such as a financial position, ego drive, or some non-negotiable value. This is purely speculation, but anyone who has worked long enough in tech transfer, venture capital, or as legal counsel to early stage deals has seen enough to develop an experience-based deal sense.

We don’t need to wait for the strain. This application has been validated by a gold standard clinical study. We know where to look: strains of L. plantarum. It’s time to bioprospect. Little infants’ lives are at stake.

Fortunately, the Bill & Melinda Gates Foundation is moving ahead in this direction on their own.

This example is just one probiotic application. There will be others.


Chemical pesticides are reaching a tipping point of undesirability.

Natural approaches are favoured and new companies are already creating value in this space. Most of these comprise bacterial and fungal species.

An earlier post gave one example of a technology from the University of Saskatchewan to improve plant yields by using natural microbial organisms already living symbiotically in plant seeds, no chemical fertilizers or genetic modifications required.

Another technology is not to use bacteria or fungi, but entomopathogenic nematodes. These are microscopic worms that only infect and kill insects.

These nematodes are specific to certain insect species. Bioprospecting and assays are used find nematodes in soil that are specific to the insect(s) that cause plant disease. The chosen nematode species must also have a life cycle that enables its practical use.

Some nematode products are already available to gardeners who prefer a biopesticide to chemical pesticides. They work on only certain insect infestations, and they are expensive.

What is required to develop this field are species identification, a formulation to deliver these nematodes effectively, and technology to reduce the cost of this new technology.

For now, there are only a few academic departments that have this specialty. Cornell University is one. Startup companies will emerge in this area soon.

A mistaken application: biofuel

Wisdom to engage in successful ventures comes from also knowing where concepts have failed in the past.

One spectacular failure of microorganism-based technology was algal biofuels.

The National Renewable Energy Laboratory (NREL) had been studying algae as an alternate source of oil since the late 1970s. This was based on the premise that harvesting algae can produce more oil than any other organism.

Figure 7: NREL presentation, Algae Biomass Summit, San Francisco, November 15, 2007

Algal biofuel companies emerged between 2003 to 2009.

In 2003, Solazyme was founded in San Francisco to develop algae as a source for renewable energy. By June 2009, Solazyme raised $57 million in a Series C financing round. Within six years off its founding, it raised a total of $76 million from investors.

Sapphire Energy was founded in 2007. One year later, it raised $100 million in a Series B financing round.

Synthetic Genomics was founded in 2005 by Craig Venter, Nobel laureate Hamilton Smith, and others as a synthetic biology company. By 2007, it pivoted to renewable energy as a key application area. In 2009, it struck a $600 million deal with Exxon to develop algal-derived biofuels.

2007 to 2009 was the bull market for startup companies working on algal-derived biofuels. Phycologists (algal scientists) became the new rock stars to investors. Scientific American published a story about the possibility of algae being the biofuel of the future. Mainstream media such as CNN talked about algae as the ultimate renewable fuel.

One year later, it all crashed. Greentech Media has since published a “where are they now” story documenting the failures of 24 such companies, and those are just the bigger ones.

The explanation for the failures is the high cost of cultivating and extracting oil from the algae.

The historic price pattern of crude oil price shows how everyone could be so mistaken.

Figure 8: price for a barrel of WTI crude, 1940 to present. Economic recessionary periods highlighted in gray. (source: Macrotrends)

Figure 8 shows the large price spike of the 1973 energy crisis and the more severe price shock of 1979, both due to geopolitical events associated with OPEC. The 1973 crises launched the NREL in the first place.

The collapse of the oil market in 1986 restored prices for about a decade and then oil prices started a relentless climb to its peak in 2008 before other factors drove the price.

The algal biofuel bull market followed the rise of oil prices during this period, to its peak. So did the steady pace of expansion of Alberta’s oil sands projects, which are cost prohibitive until the price of crude oil exceeds about $60/barrel. Everybody believed that crude oil prices would continue to climb and pursued opportunities accordingly.

Rising oil prices makes daily economic news. Extrapolating the price rise from the mid-1990’s to 2008 would lead to a forecasted oil price of $230/barrel by 2040, which was the prediction of the U.S. Energy Information Administration at the time. Oil prices are an emotional topic to economists, business people, investors, environmentalists and anyone who pays for energy. Emotion will drive herd mentality, along with the psychological assumption that trends continue along a single pattern.

From a technological perspective, it is also mistaken to believe that a new technology will displace a commodity that fills global supply chains in tremendous volumes.

Future opportunities for other microbial-derived materials

This three-part series started in response to sad news showing how our economic and engineered systems are straining this world.

There is a need and opportunity to create new, sustainable solutions that will disrupt the terrible long term consequences of our current industrial practices.

These future opportunities will be in producing materials that are not sourced from the current systems that are wasteful and destructive. Biological sources are sustainable and do not leave wastes that persist in the environment.

An example of an opportunity is a palm oil alternative, as suggested by that earlier post.

In part 1, we saw that the oil profile of many algal species is very similar to that of palm oil. Note that the price of palm oil is presently twice as much as crude oil.

A critical next step towards disrupting, for example, the palm oil supply chain is engineering down the cost of making microbial derived products. This is very possible.

Next, the critical innovation is to create a different supply chain for this new, alternative product.

Whether the material we want to disrupt is palm oil, plastics, or specailty chemicals derived from crude oil, we cannot do it through their existing supply chains. This will be a topic for future posts.

For now, the message is that microbial sources do offer an alternative to industrial chemistry and they do offer an alternative to mass harvesting of natural resources in our oceans and forests. To do this requires a resolve and a purposeful intent, driven by vision and a courage to believe in a better world.

Bioprospecting (part 3) – future opportunities
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