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integration of these with systems biology tech-


REVIEW SUMMARY niques, such as next-generation sequencing
and high-sensitivity omics methods, has al-
lowed for the design and potential development
BIOENGINEERING
of millions of chemical production pathways.
The use of genome engineering technologies
Industrial biomanufacturing: The such as clustered regulatory interspaced short
palindromic repeats (CRISPR)associated pro-

future of chemical production tein Cas9 systems and multiplex automated


genomic engineeringand recent advances

in screening and select-
James M. Clomburg, Anna M. Crumbley, Ramon Gonzalez* ON OUR WEBSITE ing for edited organisms
Read the full article using biosensors have re-
at http://dx.doi. duced the time required
BACKGROUND: Environmental, geopolitical, less technologically complex processes. These org/10.1126/ to complete genomic edit-
and economic factors are reshaping our view characteristics enable flexible, smaller-scale, and science.aag0804 ing to a fraction of the
..................................................
of global energy and manufacturing demands. capital expenditureefficient operation that can traditional time require-
Addressing these challenges may require a shift both support and benefit from a large number ments. Automation-based process design im-

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from the current model of industrial chemical of facilities, according to the economies of unit provements of these biotechnology advances
manufacturing, which employs large-scale mega- number model. For example, the capital ex- have also facilitated rapid advances in indus-
facilities that benefit from economies of unit penditure entry-level cost of corn-grain ethanol trial biomanufacturing.
scale. Contrary to the traditional approach, a facilities, the most widely developed current
model based on economies of unit number is example of a bioconversion process, has sub- OUTLOOK: Continued development of indus-
proposed to reduce capital costs per unit ca- stantially decreased as the number of plants trial biomanufacturing in the 21st century will
pacity. Industrial biomanufacturing, which ex- has increased over the past few decades. This require further advances in biocatalyst design
ploits biological processes for manufacturing, has facilitated rapid, small-scale, and wide- and process design engineering. To facilitate a
offers one way to address these changing global spread deployment resulting in a more than future based on industrial biomanufacturing,
factors while using the economies of unit num- 10-fold increase in U.S. ethanol production further development of genomic tools and in-
ber model. This model employs both facility- from 1995 to 2015. dustrial design automations suited to these
level mass production of small-scale, modular Advances in metabolic engineering, syn- purposes is paramount. Furthermore, reduc-
units and improvements to process design re- thetic biology, genomics, and industrial process ing the time required from concept design to
sulting from repetition in a learning-by-doing design have pushed industrial biomanufactur- industrial relevance is essential. Specific de-
approach. The lower investment and financial ing closer to more widespread adoption. Partic- velopments in the area of one-carbon feed-
risk associated with smaller-scale, lowercapital ular emphasis on single-carbon feedstocks, stocks stand to exploit the opportunity presented
cost facilities allow a larger number and more such as methane or CO2, in applications where by currently wasted, distributed methane through
diverse group of technology players to be in- large-scale chemical manufacturing is infea- the increased adoption of an economy of unit
volved, in turn enabling faster innovation and sible or too costly can leverage both econo- numbers approach in industrial biomanufac-
novel technology adoption as well as a faster mies of unit number for mass production of turing. Although much work remains, the fu-
response to market drivers. facilities and the benefits of manufacturing ture of industrial biomanufacturing holds great
automation to reduce capital expenditure per promise in meeting the evolving demands of
ADVANCES: In contrast to current chemical unit scale. Current research efforts focused on chemical production in the current century and
manufacturing methods, characteristics in-
herent to bioconversion processessuch as
the design of carbon- and energy-efficient meta-
bolic pathways have been particularly beneficial.
beyond.

the ability to operate at mild temperatures Advances in tool development for metabolic
and pressures and achieve high carbon- and pathway design have included in silico organism The list of author affiliations is available in the full article online.
*Corresponding author. Email: ramon.gonzalez@rice.edu
energy-conversion efficiencies in single-unit design strategies, genome mining techniques, Cite this article as J. M. Clomburg, A. M. Crumbley, R. Gonzalez,
operationsresult in more streamlined and and computational enzyme design efforts. The Science 355, aag0804 (2017). DOI: 10.1126/science.aag0804

Methane-based industrial biomanufacturing for fuel and chemical production. Exploiting biological processes can enable the conversion of
single-carbon feedstocks, like methane, to the array of chemical products currently produced through industrial chemical manufacturing with con-
siderable economic, environmental, and societal advantages.

Clomburg et al., Science 355, 38 (2017) 6 January 2017 1 of 1


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efficient and economically viable transportation


REVIEW infrastructure (Fig. 1B). For example, the 135
operating U.S. refineries produced more than
19.1 million barrels of oil per calendar day in 2015
BIOENGINEERING (8), with the majority of facilities operating with
a production capacity greater than 75,000 barrels

Industrial biomanufacturing: The per day (Fig. 1C). These large-scale facilities,
spanning upwards of 1375 ha (3500 acres) (Fig. 1A),
are located close to high-volume feedstock sources
future of chemical production (e.g., tight oil/shale gas) or transportation hubs
(e.g., Gulf coast) (Fig. 1B), ensuring high-volume
feedstock availability.
James M. Clomburg,1 Anna M. Crumbley,1 Ramon Gonzalez1,2*
The traditional model of economies of unit
scale described above for industrial chemical
The current model for industrial chemical manufacturing employs large-scale
manufacturing has long held that the only way
megafacilities that benefit from economies of unit scale. However, this strategy faces
to reduce capital costs per unit is by scale
environmental, geographical, political, and economic challenges associated with energy
essentially, bigger is better. Although this model
and manufacturing demands. We review how exploiting biological processes for
has been extremely successful, the inherent high
manufacturing (i.e., industrial biomanufacturing) addresses these concerns while also

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capital expenditure, large scale, and long con-
supporting and benefiting from economies of unit number. Key to this approach is the
struction time result in a high financial risk that
inherent small scale and capital efficiency of bioprocesses and the ability of engineered
very few companies can tolerate, reducing the
biocatalysts to produce designer products at high carbon and energy efficiency with
number of new players able to gain entry. This
adjustable output, at high selectivity, and under mild process conditions. The biological
high financial risk accordingly hinders potential
conversion of single-carbon compounds represents a test bed to establish this paradigm,
transformative innovation by limiting the indus-
enabling rapid, mobile, and widespread deployment, access to remote and distributed
trial diversity and slowing the ability of the in-
resources, and adaptation to new and changing markets.
dustry to adapt to change. These characteristics

C
may also restrain the suitability of the current
hemical manufacturing firms currently pro- for the commercial-scale production of both med- model to address the many interconnected eco-
duce more than 70,000 products as part of ical and industrial compounds (7). Despite these nomic, environmental, geographical, and political
a worldwide industry projected to grow advancements, the earlier adoption, better un- factors that are shifting the way we view global
beyond US$5 trillion by 2020 (1, 2). The derstanding, and suitability of chemical tech- energy and manufacturing demands in the 21st
roots of chemical manufacturing are inher- niques for large-scale manufacturing of industrial century. For example, the requirement of direct
ently tied to the Industrial Revolution, a time chemicals have made this industry essential for access to high-volume feedstocks inherently ties
period in which a predominantly agrarian society our current way of life. However, the recent spot- industrial chemical manufacturing to large-scale
was transformed into one reliant on manufactur- light on sustainability challenges inherent to in- petroleum resources and limits feedstock diver-
ing for domestic and worldwide markets. The dustrial chemical manufacturing, coupled with sification. This not only limits access to fossil
development and use of chemical processes was rapid advances in biotechnology, have brought resources such as remote natural gas but also
a major part of this shift, as chemical techniques a renewed interest in industrial biomanufac- restricts the ability to shift to more sustainable
for the large-scale production of compounds such turing. Here, we review recent advances related resources such as biomass, which are distributed
as sulfuric acid, bleaching powder, and soda ash to harnessing the power of biology for industrial and smaller volume by nature (9). The large-scale
in the 18th century helped transform and shape manufacturing, with a focus on applications pres- and energy-intensive nature of these facilities also
the production of glass, textiles, soaps, and paper enting major challenges for traditional chemical greatly contributes to their environmental impact
(35). These chemical processes laid the ground- techniques. through wasted fossil resources during feedstock
work for continued expansion in the 19th and extraction and chemical processing (10).
early 20th centuries, which would see the devel- What are the limits to industrial The cost, size, and scale characteristic of chem-
opment of manufactured fertilizers and petro- chemical manufacturing? ical processing facilities mandated by the econo-
chemicals that continue to be central to industrial Current chemical manufacturing techniques, mies of unit scale model impose substantial
chemical manufacturing. which dominate fuel and chemical production, barriers to diversifying the players in chemical
Advancing knowledge and understanding in employ processes incurring numerous heat and manufacturing. This represents a concern for the
the field of biology in the 20th century enabled pressure changes, with multiple unit operations globalization of resources and the progression
the use of biological processes for the production and heat integration schemes. Given that capital of developing countries toward self-reliance for
of important industrial compounds, such as ace- infrastructure expenditures (CapEx) are largely chemical production. For example, the cost of
tone and ethanol, in addition to many important correlated to process complexity (i.e., amount building a large-scale ammonia production plant,
compounds in medicine, including penicillin and of energy and material transferred), the chem- oil refinery, or GTL facility (Fig. 1A) is on par with
other antibiotics. However, it was not until the ical manufacturing industry has leveraged an the gross domestic product of countries like
1970s, with the development of recombinant DNA economies of unit scale model to reduce CapEx Equatorial Guinea, Congo, and Gabon (US$8 to
technologies, that the true potential of biological per unit scale. This is reflected in both the large 15 billion) (11), countries that possess large oil
processes for the industrial production of an array CapEx and the immense scale and size of faci- and natural gas reserves. This places an econo-
of compounds was envisioned (6). From there, lities such as oil refineries, ethylene crackers, mic barrier on access to chemical manufacturing
developments in discovery, use, optimization, and ammonia plants, and gas-to-liquid (GTL) plants facilities needed to use local resources for do-
engineering of biological techniques, organisms, (Fig. 1A). The economies of unit scale enabling mestic fertilizer or energy production, products
and processes have led to a quickly evolving field these megafacilities require large amounts of ag- essential for progressive development. As such,
gregated feedstock(s)typically fossil-based, such the characteristics of the economies of unit scale
1
as petroleum and natural gasto support large- model not only impose an access barrier to both
Department of Chemical and Biomolecular Engineering, Rice
University, Houston, TX, USA. 2Department of Bioengineering,
scale production. These factors have led to a mod- countries and companies but also limit the poten-
Rice University, Houston, TX, USA. el in which a small number of large-scale facilities tial for rapid and innovative solutions to tackle
*Corresponding author. Email: ramon.gonzalez@rice.edu rely on access to high-volume feedstocks and/or these challenges.

Clomburg et al., Science 355, eaag0804 (2017) 6 January 2017 1 of 10


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Fig. 1. Comparison of industrial


chemical manufacturing to indus-
trial biomanufacturing. (A) Capital
expenses (CapEx) versus capacity
for industrial chemical manufacturing
(oil refineries, steam crackers,
ammonia, and gas-to-liquids plants)
and industrial biomanufacturing
(corn-ethanol facilities and first-of-
their-kind 1,3-propanediol, cellulosic
ethanol, and 1,4-butanediol facilities)
on an equivalent energy basis
(BOE/day). Insets show satellite
images that illustrate differences in
footprint between a corn-ethanol
plant and an oil refinery. Inset values
highlight aerial productivity
(BOE/ha/hour), an aerial efficiency

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calculation considering capacity and
facility footprint estimated from
Google Map Imagery. [Imagery
copyright 2016 Google; map data
copyright 2016 Google] (B)
Distribution of oil refineries (blue
flame) and corn-ethanol plants (green
leaf) in the United States. Production
capacity is in BOE/day. [Data from
references (90103); Mapping
and georeferencing copyright
OpenStreetMap and copyright Carto,
respectively] (C) Frequency
distribution of corn-ethanol plants
(green) and oil refineries (blue) in the
United States as a function of their
capacity on an equivalent energy
basis (thousand BOE/day).

Can industrial biological manufacturing cost reductions as total production volume (i.e., available chemical technologies have not been
make the case for economies of number of facilities times facility production able to operate efficiently in such a fashion, the
unit number? rate) increases. development of technologies with lower overall
Contrary to the traditional model of economies To exploit this economic model in the context complexity that operate efficiently at a smaller
of scale used in industrial chemical manufactur- of chemical manufacturing, one can envision the scale can help support mass-produced, modular,
ing, a model based on economies of unit number custom-built, high-CapEx, large-scale operations small-unit-scale design.
uses facility-level mass production and improve- being replaced with a large number of mass- In this context, exploiting the diversity and
ments to process design resulting from repeti- produced, modular, small-unit-scale technology. strengths of biological processes for fuel and chem-
tion, a learning by doing approach, to reduce This can enable an economies of unit number ical production provides the opportunity for CapEx
capital costs per unit capacity (12). Here, eco- approach that can use automation principles, and process-efficient technology development,
nomies of unit number can be defined as a shift advances in engineering, and streamlining of enabling an economies of unit number model.
from a small number of high-capacity units or efficient technologies to reduce capital costs Industrial biomanufacturing employs biological
facilities to a large number of units or facilities per unit capacity. By efficiently scaling down, catalysts for the conversion of various feedstocks
operating at a smaller scale. Through increasing this type of approach can support small-scale, to fuels and chemicals analogous to those cur-
the number of units produced, this model can CapEx- and process-efficient flexible technolo- rently produced via chemical manufacturing means
leverage cost reduction through mass production gies. The smaller-scale and CapEx efficiency (Fig. 2). Biological processes, such as microbial
in which costs decline as cumulative output reduces both the time and cost required for com- fermentation, efficiently operate at mild temper-
increases because of specialization in the pro- mercial facilities, enabling rapid, mobile, and atures (20 to 100C) and pressures (atmospheric)
duction process and improved process and pro- widespread deployment. This model could address and can achieve high carbon- and energy-
duct design (12). Furthermore, by increasing the many of the aforementioned limitations of in- conversion efficiencies in a single unit operation,
number of operating units and facilities, cumu- dustrial chemical manufacturing by enabling a which in turn leads to more streamlined and less
lative experience on the process is gained that greater number of companies to access distributed technologically complex processes (13, 14). Indus-
can uncover a myriad of improvements in design, and sustainable resources and new markets and trial biocatalysts afford the ability to produce a
materials, and production methods (12). These allowing quick adaptation to both local and single product with an easily adjustable output
continuous improvements can offer substantial global market conditions. Although historically, at high selectivity without dramatically altering

Clomburg et al., Science 355, eaag0804 (2017) 6 January 2017 2 of 10


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Fig. 2. Industrial biomanufacturing for fuel and chemical production. Exploiting biological processes can enable the conversion of numerous industrially
relevant feedstocks to the array of chemical products currently produced through industrial chemical manufacturing with considerable economic, environmental,
and societal advantages.

process conditions (15). As such, the process ities comparable to large-scale chemical oper- ing the scale of facilities per se, but rather in-
equipment for the conversion step is largely ations (Fig. 1A). This system-level productivity creasing the number of facilities built (Fig. 3).
similar regardless of the desired output, which comparison further demonstrates how industrial Although modest cost gains have been achieved
can enable mass production of modular units biomanufacturing facilities can effectively oper- by optimizing the scale of the facilities, techno-
as opposed to custom-built equipment, both re- ate at a small scale, with process intensification logical learning has had a dramatic effect on
ducing equipment cost and fabrication time. enabling further size reduction at comparable CapEx reduction by both reducing costs related
These traits are ideally suited for a shift in chem- magnitudes to that of chemical facilities. to production and energy and driving process
ical production to a model based on economies The ability of these biomanufacturing facilities optimization and integration. As a result of learn-
of unit number. for rapid, small-scale, and widespread deploy- ing by doing, the CapEx per unit capacity of corn-
The potential for industrial biomanufacturing ment has supported a more than 10-fold increase ethanol production facilities of the same scale
to support economies of unit number can be in U.S. ethanol production from 1995 to 2015 has dramatically decreased over the past 30 years,
quantitatively established through the analysis (16). Although one cannot overlook the role that affording industrial biomanufacturing processes
of corn-grain ethanol fermentation, which rep- government incentives had in influencing the the ability to operate at a small scale in a CapEx-
resents the most widely developed current ex- ethanol market and demand, the intrinsic char- efficient manner (Fig. 3). This analysis suggests
ample of a bioconversion process adopted for acteristics (small-scale, CapEx efficiency) of these that not only do industrial biomanufacturing pro-
the production of chemicals and fuels at com- bioconversion facilities enabled their rapid and cesses require lower capital investment and oper-
mercial scale. Comparison of bioethanol plants widespread deployment to capitalize on these ate in a CapEx-efficient manner at a smaller scale
(industrial biomanufacturing) to oil refineries, incentives and outpace the deployment of other (Fig. 1A) but also these processes support and
ethylene crackers, ammonia plants, and GTL technologies. Furthermore, while corn-ethanol benefit from an abundance of small-scale facili-
plants (industrial chemical manufacturing) on a represents the only current process with an es- ties according to the economies of unit number
CapEx and barrels of oil equivalents (BOE) basis tablished network of facilities, other demonstrated model rather than the established paradigm of
demonstrates the extent to which industrial bio- commercial-scale bioprocesses have CapEx per economies of unit scale for industrial chemical
manufacturing can support smaller-scale, CapEx- unit capacities comparable to those of chemical manufacturing (Fig. 3).
efficient facilities (Fig. 1A). This has resulted in manufacturing facilities (Fig. 1A). DuPonts first- The lower investment and financial risk asso-
U.S.-based bioethanol production developing as of-their-kind bio-1,3-propanediol and cellulosic eth- ciated with smaller-scale industrial biomanufac-
a network of distributed plants (Fig. 1B) that anol facilities operate at similar CapEx/capacity turing facilities allows a larger number and more
operate on a substantially smaller scale than metrics to that of many recently constructed re- diverse group of technology players to be involved,
chemical manufacturing facilities. The 195 opera- fineries and ethylene crackers, with the Novamont in turn enabling faster innovation and novel tech-
tional bioethanol plants in the United States in 1,4-butanediol plant, using Genomatica engineered nology adoption as well as a faster response to
2016 have a total production capacity of 0.53 million strains for bioconversion, displaying slightly higher market drivers. The ability for rapid and distrib-
BOE/day, with the majority producing between CapEx/capacity than would be expected of a first- uted deployment enables feedstock diversifica-
1000 and 5000 BOE/day (Fig. 1C). In contrast, of-its-kind process. tion by enabling access to remote, smaller-scale
135 operating U.S. refineries produce more than Central to the rapid adoption of these bio- resources. This can not only help reduce envi-
19.1 million barrels of oil per calendar day, about manufacturing technologies is the fact that the ronmental impact by capitalizing on sustain-
35 times the total BOE produced by ethanol CapEx entry-level cost of ethanol production via able feedstocks such as biomass but also help
plants, and operate with a production capacity fermentation has markedly decreased over the reduce greenhouse gas emissions through tar-
greater than 75,000 barrels per day (Fig. 1C), past few decades. Focusing on capital expend- geting smaller-scale methane resources like flared
which is 15 to 75 times the average production iture costs, which are representative of stan- and vented natural gas and biogas. The smaller-
capacity of ethanol plants. Despite differences dard biological production processes, rather than scale, lower-CapEx facilities can also promote
in production capacities, the reduced land usage process-specific operational costs, the decreasing equitable resource globalization by lowering
of bioethanol facilities enables aerial productiv- CapEx cost has been the result not of increas- the economic barrier to chemical manufacturing.

Clomburg et al., Science 355, eaag0804 (2017) 6 January 2017 3 of 10


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stocks; however, the amounts produced are on mass production of facilities and the benefits of
par with ethanol plants on a BOE basis (compare manufacturing automation to reduce CapEx per
Fig. 1C and Fig. 4B). For example, gas-generation unit scale. Additionally, distributed feedstocks
rates from 1233 U.S. Environmental Protection can be coupled to localized markets by tailor-
Agency (EPA)reporting landfill projects range ing product synthesis to regional market needs.
between 2 and 300 BOE/day (Fig. 4B), whereas The aforementioned characteristics of indus-
gas production from 239 EPA-reporting agricul- trial biomanufacturing (e.g., small-scale, flexible,
tural sites operate at a narrower range centered CapEx-efficient processes) supports this approach
around 2 to 20 BOE/day (Fig. 4B). Flaring from and can provide the needed process and econo-
490 petroleum operations visible through the mic characteristics to recover methane resources
National Oceanic and Atmospheric Administra- through rapid, mobile, and widespread technol-
tions Visible Infrared Imaging Radiometer Suite ogy deployment directly at the feedstock source.
(VIIRS) Nightfire (17) indicates the smaller scale Recovering these distributed gas feedstocks al-
of flare-associated gas as well, with the majority lows capitalization on otherwise wasted or in-
of sites generating 2 to 40 BOE/day (Fig. 4B). accessible resources, which if left to current
Despite the small scale of individual-site meth- technologies will continue to result in consider-
ane generation, the large number of sites results able greenhouse gas emissions.
in substantial total resources, with more than Although the demonstrated abilities of bio-
Fig. 3. Reduction in capital costs of U.S. etha-

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250 billion cubic feet/year generated from vent- conversion processes to operate in a small-scale,
nol plants since 1977. Capital costs have been
ing and flaring and nearly 240 billion cubic feet/ CapEx-efficient manner places industrial bio-
reduced by upscaling, but even more by learning
year from landfill, wastewater, and agricultural manufacturing in a unique position to use these
and other nonscale-related development. Feasibil-
associated sites (Fig. 4). This represents a major resources, several important biocatalyst and pro-
ity study markers have hollow center. [Adapted
opportunity for both U.S. and global fuel and cess considerations must first be addressed. On
from (104). Data obtained from (104111).]
chemical production. In fact, the conversion of the process side, despite the success of bioethanol
all carbon associated with the more than 4 tril- facilities, the process equipment (e.g., reactors),
For example, a lower economic entry threshold lion cubic feet of natural gas vented or flared separation methods and unit operation(s), and
removes a substantial burden on developing worldwide in 2014 is enough to meet global waste-stream management needed for gas-intensive
countries desiring to drive economic develop- production of seven essential building-block or- fermentation present different requirements from
ment, such as in the sub-Saharan Africa natural ganic chemicals (methanol, ethylene, propylene, those established for commercial bioconversion
gas reserve region, through capitalization on local butadiene, xylene, benzene, and toluene) that are processes. However, the widespread nature of
resources for domestic fertilizer and energy pro- currently used for the production of hundreds of remote methane resources that are difficult to
duction and minimization of import products. chemicals (2). Despite this potential, the dis- access using chemical techniques can enable
As such, the use of industrial biomanufactur- tributed and small-scale nature of methane re- exploitation of the learning-by-doing approach
ing can enable the democratization of chemical sources remains a major challenge for use via to address these process requirements. By ac-
production. current chemical technologies, as methane is cumulating process knowledge and improving
difficult to chemically process at mild condi- and optimizing technologies, CapEx costs can
How feasible are single-carbon tions and requires complex techniques. The eco- be reduced as the total number of facilities and
feedstocks as a test bed for nomics of natural gas recovery require a given production volume increases in a manner sim-
industrial biomanufacturing? rate of methane production to justify the in- ilar to that demonstrated by bioethanol plants.
Although the aforementioned characteristics of frastructure expenditures necessary to gather, This not only will further advance bioconversion
industrial biomanufacturing are being recognized, process, and transport volumes of gaseous meth- technology specific to methane use but also can
widespread adoption may be facilitated by suc- ane (Fig. 4C) (18). Although complex, large-scale provide continuous knowledge that can be lever-
cessful implementation in a specific sector where techniques are viable for high production rates aged for other bioconversion applications target-
large-scale chemical manufacturing is not feasi- or short distances to market, the remote locations ing different feedstocks or complex products.
ble. This could be due to small volumes, the dis- of many oil and gas production sites strain tra- Although current research on aspects such as
tributed nature of the feedstock, inherently high ditional economic recovery justification, because gas transfer, continuous process operation, and
technological complexity, inefficiency of chemi- no current conversion technology can efficiently product separation in the context of bioconver-
cal processing, or general market isolation. The access the lower-volume production sites located sion processes are facilitating initial process ad-
production of organic chemicals from single- at far distances from market hubs (Fig. 4C). This vancements, improvement in biocatalyst design
carbon (C1) feedstocks, especially methane, offers results in a large amount of stranded (remote) represents another critical factor. Developing
one such opportunity for industrial biomanu- natural gas, a wasted resource due to the unfav- biocatalysts exhibiting high conversion rates and
facturing to overcome these challenges. Natural orable economics of technically complex, large- efficiencies is a central component that must
gas associated with petroleum extraction, as well scale chemical processes. be improved to enable the required small-scale,
as methane from agricultural and landfill waste Given that the traditional industrial chem- CapEx-efficient processes to capitalize on the op-
decomposition and wastewater treatment, are ical manufacturing characteristics of large scale, portunity presented by remote methane resources.
small-scale, highly distributed sources of meth- high CapEx, and long construction time are not
ane (Fig. 4A), which do not represent a feasible amenable to accessing these small-scale, distrib- How can metabolic engineering enable
feedstock for large-scale chemical manufacturing uted resources, this scenario represents an ideal the biomanufacturing of fuels and
facilities. A quantitative analysis of the amounts test case for the application of an economies of chemicals from C1 feedstocks?
of methane generated from flared natural gas, unit number approach. Feedstock availability in Regardless of whether chemical or biological
agricultural sites, and landfill waste demonstrates small amounts at a large number of sites will methods are used, overcoming the high stability
the feedstock limitation challenge for current require a large number of distributed, small-scale and low reactivity of an inert CH bond is a major
large-scale chemical facilities and the oppor- facilities to capitalize on the available resource, challenge for the conversion of methane. Biolog-
tunity for application of small-scale industrial which is currently wasted due to technical and ically, the vast majority of organisms known to
biomanufacturing technologies. On a BOE ba- economic incompatibility with existing methods. use methane have accomplished this through
sis, these resources generate substantially lower This enables a learning-by-doing approach that oxygen-dependent CH bond activation, cata-
amounts than required for oil refinery feed- can leverage both economies of unit number for lyzed by methane monooxygenases (MMOs), in

Clomburg et al., Science 355, eaag0804 (2017) 6 January 2017 4 of 10


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Fig. 4. Methane resources are


highly distributed, small-scale
feedstocks that are challenging
for use by large-scale chemical
facilities. (A) Generation of meth-
ane at natural gas (red flame),
agricultural biogas (light blue
grass), and landfill (yellow trash
bag) facilities in the United States.
Relative size of icon correlates with
production (in BOE) at each site.
[Data from references (90103);
mapping and georeferencing
copyright OpenStreetMap and
copyright Carto, respectively] (B) Gas
production rate and BOE equivalency
distribution from 1233 EIA-reporting
landfills with capture/flaring capabil-

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ities (88,779.25 BOE/day), 239 EIA-
reporting agricultural sites with biogas
generation capabilities (1597.434
BOE/day), and 490 visible VIIRS-
identified petroleum flaring wells
(16,118.20 BOE/day). [Data from
references (90103)] (C) Economics
of natural gas transport. Indicated
technologies for a given area repre-
sent economically favorable technol-
ogies for transports. Although
technologies are available for high
production rates and/or short
distances to market, the combination
of low production rates and large
distances to markets results in an
economically infeasible situation
resulting in stranded gas. Modified
from (18). CNG, compressed natural
gas; LNG, liquefied natural gas; GTL,
gas-to-liquid; NGH, natural gas
hydrates.

which a CH bond in methane is converted to a Efforts to identify methanotrophic organisms Methanotrophic bacteria have also been used
COH group. Two variations of MMO exist: par- for industrial fermentation have revealed sev- for the production of a number of compounds
ticulate, membrane-bound MMO (pMMO), and eral promising directions, despite historical li- from methane, including BioProtein (2931), poly-
cytoplasmic, soluble MMO (sMMO) and, given mitations due to low organism productivity and hydroxybutyrate (32, 33), carotenoids (34), vita-
their role and novel function in methanotrophs, a lack of genetic tools for manipulation. Re- mins (35), and methanol (36) (Table 1). Recently,
these enzymes have been extensively studied cent efforts have focused on Methylomicrobium the identification of an active Embden-Meyerhof-
(19). Obligate methanotrophs metabolize meth- buryatense, a Group I methanotroph with a faster Parnas (EMP) pathway in novel gammaproteo-
ane as their sole carbon and cellular energy doubling time compared with traditional meth- bacterial methanotrophs, notable for resistance
[adenosine triphosphate (ATP)] source, oxidizing anotrophs (24, 25). Genetic tools have recently to the toxic components of natural gas and bio-
methane to CO2 via the intermediates metha- been developed for M. buryatense (26, 27) and gas, has redefined carbon efficiency calculations
nol (CH3OH), formaldehyde (CH2O), and formate the ability for transient gene expression opens and ATP availability in certain methanotrophic
(CHO2 ). Methane-derived carbon is assimilated the door for the development of powerful gen- organisms, most notably indicating the opportu-
at the level of formaldehyde via the ribulose- etic tools such as clustered regulatory interspaced nity for organic acid production via fermentation
monophosphate (RuMP) cycle or serine cycle, short palindromic repeats (CRISPR)/CRISPR- (37, 38). EMP pathway presence provides the po-
formate via the serine cycle, or CO2 via the Calvin- associated protein Cas9based genome editing. tential to couple methanotrophic use with con-
Benson-Bassham (CBB), depending on the specific Recently, application of rational metabolic engi- ventional industrial strain-engineering routes
metabolism (Fig. 5) (20, 21). The majority of neering strategies employing these genetic engi- from sugars to biochemical intermediates and
methanotrophs are organized into two groups, neering tools enabled the development of a strain products due to the conserved downstream meta-
designated Gammaproteobacteria or Group I, which of M. buryatense engineered for the production of bolic machinery (Fig. 5). Continued pathway dis-
use the RuMP pathway for carbon assimilation, lactate from methane. Heterologous overexpres- covery, advancements in genetic tools, and focused
and Alphaproteobacteria or Group II, which use sion of a Lactobacillus helveticus L-lactate de- metabolic engineering efforts in the methano-
the serine cycle (22). More recently, thermoacido- hydrogenase in M. buryatense enabled L-lactate trophic space stand well-placed to further ex-
philic aerobic methanotrophs (Verrucomicrobia) production from methane, with cultivation in a pand the number of chemicals produced and
have been identified, which can assimilate car- continuous bioprocess resulting in the produc- improve carbon conversion efficiency. Improv-
bon through the CBB cycle at the level of CO2 (23). tion of 0.8 g/L L-lactate (28). ing both the range of products and the efficiency

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of this activation mechanism is limited by the


basic electron requirement needed to reduce
O2 to H2O. Limitations of electron flow inherent
to currently available MMO enzymes require
that electrons used in the oxidation of methane
to methanol be recovered in subsequent steps,
limiting the overall energy conversion efficiency.
Although directly coupling electrons generated
from methanol oxidation to methane oxidation
provides the most efficient MMO-based route
(40), exploiting alternative, theoretically more
efficient, activation routes is one way to achieve
improved energy efficiency. Several alternative O2-
dependent activation routes have been proposed
that have the potential to reduce the electron re-
quirement for methane activation (13). However,
these strategies have yet to be demonstrated.
One alternative to maximize energy efficiency

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is through the use of an anaerobic methane
activation mechanism. Anaerobic oxidation of
methane (AOM) is carried out by anaerobic meth-
anotrophic (ANME) archaea capable of coupling
sulfate reduction to methane oxidation to drive
favorable thermodynamics. AOM is a poorly un-
derstood biological process driven by natural
ANME and syntrophic bacteria consortia. De-
spite decades of effort, neither a natural consor-
tia nor pure microbial culture that grows on
methane anaerobically has been successfully iso-
Fig. 5. Metabolic pathways for the conversion of C1 feedstocks to fuels and chemicals. Leveraging lated (13, 41, 42). However, strong evidence sug-
recent developments in synthetic and systems biology enable the exploitation of various activation and gests that the enzyme responsible for the first
utilization pathways along with engineering integrated product synthesis pathways for the conversion of step of AOM is a homolog of the methyl-coenzyme
C1 feedstock to desired products. Continued understanding and development of mechanisms and M reductase (MCR) from anaerobic methanogenic
organisms for C1 use can enable improved bioconversion efficiency. Formaldehyde is assimilated directly microorganisms (42, 43), and reaction intermed-
through the RuMP pathway (blue) and is channeled to cellular metabolism and product formation via the iates and a proposed mechanism have recently
EMP pathway (gray). Formaldehyde and formate can be assimilated via 5,10-methylene-tetrahydrafolate been identified (44). These discoveries can aid in
(5,10-MTHF) through the Serine cycle (red) and are linked to cellular function through generation of acetyl- the development of technologies for novel meth-
CoA and biosynthesis in the cell via the glyoxylate cycle (purple). The Calvin-Benson-Bassham cycle ane activation. This type of approach was re-
(green) is responsible for carbon fixation in photosynthetic organisms and is tied to cellular metabolism cently demonstrated through the cloning of the
through production of pyruvate (PYR) and acetyl-CoA. Additional pathways for activation of methane and MCR from an unculturable organism, anaerobic
methane-derived substrates include the MCR methanogenesis reversal pathway (orange) and the com- methanotrophic archaeal population 1 (ANME-1)
putationally designed FLS enzyme pathway (pink) for the conversion of formaldehyde to dihydroxyacetone from a Black Sea mat, into the archaeal meth-
(DHA). Rationally engineered products are boxed. Dihydroxyacetone phosphate, DHAP; phosphoenolpyr- anogen Methanosarcina acetivorans to effec-
uvate, PEP; ribulose-5-phosphate, Ru5P; ribulose-1,5-phosphate, Ru1,5P2; 3-phosphoglycerate, 3PG; 1,3- tively run methanogenesis in reverse (41). Upon
biphosphoglycerate, 1,3P2G; glyceraldehyde 3-phosphate, G3P; fructose 1,6-biphosphate, F1,6P2; fructose coupling to iron reduction, engineered M. ace-
6-phosphate, F6P; xylose 5-phosphate, X5P; ribose-5-phosphate, R5P; sedoheptulose 7-phosphate, tivorans was able to grow anaerobically on meth-
S7P; sedoheptulose 1,7-biphosphate, S1,7P2; erythrose 4-phosphate, E4P; 5,10-methylene tetrahy- ane as a pure culture and convert methane into
drofolate, 5,10-MTHF; serine, SER; hydroxypyruvate, HPYR; glycerate, GLYC; 2-phosphoglycerate, acetate. ANME cultures have also been shown
2PG; 3-phosphoglycerate, 3PG; oxaloacetate, OAA; malate, MAL; glyoxylate, GLYOX; glycine, GLY; citrate, to decouple from their syntrophic bacterial part-
CITR; cis-aconite, cisA; succinate, SUCC; acyl-acyl carrier protein, Acyl-ACP; free fatty acid, FFA; ners and perform methane oxidation using sol-
fatty acid methyl ester, FAME; farnesyl pyrophosphate, FPP; geranylgeranyl pyrophosphate, GGPP; uble artificial electron acceptors (45), which holds
hydroxymethylglutaryl-CoA, HMG-CoA; (R)-3-hydroxybutyryl-CoA, (R)-3-HB-CoA; poly(3-hydroxybutyrate), great promise for the use of pure cultures in meth-
PHB. Pathways obtained from (41, 112115). ane bioconversion. More recently, the pathway
responsible for the synthesis of coenzyme F430, a
nickel-containing tetrapyrrole required for MCR
activity, was reconstructed in E. coli, opening the
of conversion is central to the development of gineering. However, attempts to transfer methane door for metabolic engineering efforts based on the
biocatalysts able to support the small-scale, oxidation machinery into heterologous hosts have use of MCR (46). These recent advances in meth-
CapEx-efficient processes needed to exploit avail- proven difficult. Only the soluble domain of the ane activation and energy-efficient pathways for C1
able methane resources and further advance the beta subunit of sMMO has been expressed in E. conversion continue to expand the potential for
potential for industrial biomanufacturing. coli (39), and heterologous expression of a com- developing more efficient biocatalysts target-
The use of model industrial microorganisms, plete, functionally active, pMMO has not been ing the production of fuels and chemicals from
such as Escherichia coli and Saccharomyces reported to date. methane.
cerevisiae, for a methane bioconversion process Even as industrial application of organisms Although methane represents the potentially
is of great interest given their rapid growth rates, using MMO-based methane activation offers most transformative C1 case to further enable
modern molecular techniques, and extensive lib- an attainable route for the conversion of meth- industrial biomanufacturing to target distrib-
rary of knowledge enabling rapid metabolic en- ane to chemical products, the energy efficiency uted, small-scale resources, biological processes

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Table 1. Biological conversion of single-carbon feedstocks to fuels and chemicals.

C1 feedstock Chemical product Titer Organism Reference

Methane L-Lactate 0.8 g/L Methylomicrobium buryatense (28)


............................................................................................................................................................................................................................................................................................................................................
Methane Astaxanthin 2.4 mg/g cell dry weight Methylomonas sp. 16A (34)
............................................................................................................................................................................................................................................................................................................................................
Methane Polyhydroxybutyrate 0.6 g PHB/g cell dry weight Methylocystis parvus OBBP (116)
............................................................................................................................................................................................................................................................................................................................................
Methane Methanol 1.1 g/L Methylosinus trichosporium OB3b (117)
............................................................................................................................................................................................................................................................................................................................................
Methanol Vitamin B12 800 ng/g wet biomass Methylobacterium sp. G-10 (35)
............................................................................................................................................................................................................................................................................................................................................
Methanol (R)-3-hydroxybutyrate 2.8 g/L Methylobacterium rhodesianum (118)
............................................................................................................................................................................................................................................................................................................................................
Methanol L-glutamate 60 g/L Bacillus methanolicus MGA3 (119)
............................................................................................................................................................................................................................................................................................................................................
Methanol L-lysine 65 g/L Bacillus methanolicus M168-20 (120)
............................................................................................................................................................................................................................................................................................................................................
Methanol Cadaverine 11.3 g/L Bacillus methanolicus (121)
............................................................................................................................................................................................................................................................................................................................................
Methanol a-humulene 1.65 g/L Methylobacterium extorquens AM1 (122)
............................................................................................................................................................................................................................................................................................................................................
CO 2 + electricity Isobutanol and 3-methyl-1-butanol 0.14 g/L total Ralstonia eutropha H16 (52)
............................................................................................................................................................................................................................................................................................................................................
Syngas n-Butanol 0.148 g/L Clostridium ljungdahlii (58)
............................................................................................................................................................................................................................................................................................................................................

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CO 2 + H 2 Acetone 3.02 g/L Acetobacterium woodii (63)
............................................................................................................................................................................................................................................................................................................................................
CO + H 2 2 Butyrate 1.3 g/L Clostridium ljungdahlii (61)
............................................................................................................................................................................................................................................................................................................................................

can also be exploited to use other single-carbon processes. As the most oxidized C1 feedstock, CO2 of such organisms (5860). Further efforts have
feedstocks, including methanol, formaldehyde, represents a single-carbon substrate that requires enabled the conversion of syngas feedstocks to
formate, and carbon dioxide. C1 feedstocks not very different mechanisms for use. The high level an array of products, including potential fuels,
only hold great promise for a number of appli- of oxidation requires energy input to produce more biopolymers and precursors, specialty plastics,
cations (31) but also demonstrate the flexibility of reduced carbon forms, and as a result the biological nylon precursors, solvents, and pharmaceutical
biocatalysts and bioconversion processes to tar- fixation of CO2 proceeds through a number of precursors, among others (5964). Benefits of
get various feedstocks. As an intermediate of different enzymes independent of those discussed bioconversion syngas fermentation include bio-
aerobic methane activation, the use of methanol above. Pathways for CO2 fixation include the catalyst tolerance to gas impurities and flexibility
as a carbon source requires similar pathways to Calvin-Benson-Bassham cycle, the reductive tri- regarding gas feedstock composition, whereas
that of methane, and many microorganisms carbocylic acid cycle, the Wood-Ljungdahl pathway, challenges include gas-liquid mass transfer li-
capable of using methane are also able to use the 3-hydroxypropionate:4-hydroxybutyrate cycle, mitations and the availability of genetic tools
methanol. Accordingly, organisms have been and the dicarboxylate:4-hydroxybutyrate cycle (55, 56). Despite these challenges, the potential
engineered to produce compounds from meth- (50). Each uses different key CO2 fixation enzymes, for syngas fermentation through combinatorial
anol (Table 1). Furthermore, identification and and these pathways are found across a wide scope metabolic engineering and process development
characterization of enzymes involved in meth- of various microorganisms. Microalgal species and has recently been demonstrated by the large-
anol use have enabled the construction of path- cyanobacteria are candidates for the conversion of scale production of ethanol (64), also demon-
ways for methanol conversion both in vitro (47) CO2 to various products, and the availability of strating that the challenges of gas-intensive
and heterologously in vivo (48). Notably, a unique genetic tools has enabled the metabolic engineer- fermentations can be overcome.
approach for the fixation of general C1 units ing of cyanobacteria, including Synechococcus Unique approaches for providing the required
has recently demonstrated a computationally elongatus PCC 7942 and Synechocystis sp. PCC reducing power for CO2 use have also been ex-
designed enzyme, formolase (FLS), which cat- 6803, to produce a number of compounds di- plored. One such approach is the use of microbial
alyzes the carboligation of three one-carbon rectly from CO2 (51). Despite this success, a major biofilms that directly accept electrons from elec-
formaldehyde molecules into one three-carbon challenge with the use of photosynthetic or- trodes for the reduction of CO2 to organic products
dihydroxyacetone molecule (49). This approach ganisms is providing large light-exposing sur- (65), a process referred to as microbial electro-
enabled the conversion of formate to the central faces, which requires extensive process design synthesis. Clostridium ljungdahlii has been shown
carbon metabolite dihydroxyacetone phosphate and optimization. to be highly effective in electrosynthesis for
in vitro, providing a proof-of-principle demon- An alternative to light-energy, fixation of the acetate production (65), with a newly developed
stration for the potential of a FLS pathway to oxidized carbon in CO2 can also be accom- genetic toolbox making it feasible to expand
convert C1 feedstocks such as formate or for- plished through the input of reducing power in product synthesis from CO2 (66). Another in-
maldehyde into chemical products. In addition the form of electrons from shuttles such as H2 novative method for direct electron input to
to providing routes to product synthesis from and formic acid. Systems in which H2, either the Wood-Ljungdahl pathway of an acetogen
these C1 feedstocks, these reports also represent externally added or produced via electrocata- has recently been reported in which the microbes
important steps in transferring methanotrophic lytic water splitting, or electrochemically pro- are photosensitized (67). Self-photosensitization
ability because these pathways can be combined duced formate, from water and CO2, are coupled of a nonphotosynthetic bacterium, Moorella
with continued efforts for heterologous MMO to the growth of lithoautotrophic organisms, thermoacetica, was demonstrated in which bio-
expression to enable various routes to metabolic have been demonstrated as a means of convert- logically generated cadmium sulfide semicon-
intermediates and product synthesis from methane. ing CO2 to useful chemical products (5254). Sim- ducting nanoparticles absorb light and use the
Developing and improving pathways for the ilarly, anaerobic fermentation of syngas, a fuel energy to carry out photosynthesis for the pro-
use of the above C1 compounds can aid in the gas mixture of CO2, H2, and CO, by acetogenic duction of acetate from CO2.
development of efficient biocatalysts for tar- bacteria via the Wood-Ljungdahl pathway, has Given the challenge of reducing the highly
geting distributed methane feedstocks. In addition, been demonstrated for the production of fuels oxidized carbon in CO2, continued insight into
given the gaseous nature of CO2, bioconversion and chemicals from C1 feedstocks (5557). A num- the characterization and mechanism of enzymes
processes targeting this feedstock offer the po- ber of acetogens have been used for this pur- for CO2 reduction is another critical area of re-
tential to both contribute to and leverage from pose, with the recent development of genetic tools search. Despite being a widely distributed reaction
knowledge gains for gas-intensive fermentation a key step in enabling the metabolic engineering in nature, relatively little is known about enzymes

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catalyzing CO2 reduction activity. Recently, a can potentially target applications challenging scale without the loss of performance. Typical
novel, hydrogen-dependent CO2 reductase, pur- for a single engineered organism (75). These bioprocess development takes 5 to 10 years and
ified from the model acetogenic organism Ace- include engineering naturally occurring micro- can be considerably more expensive than chem-
tobacterium woodii, was identified that fixes CO2 bial consortia while also developing synthetic ical technologies owing to the relative infancy of
to formate via the electron shuttle H2 (68, 69). consortia to improve efficiency, stability, and the process (87). The holistic consideration of
Furthermore, the ability for enzymes such as control. Beyond the traditional single-cell bio- process parameters, including product purity
formate dehydrogenase to catalyze the reduc- catalyst, another approach uses synthetic cell- and waste-stream management, at an early stage
tion of CO2 has also been discovered (70), and free systems, which convert a substrate to a is desirable to develop small-scale testing pro-
further characterization and discovery can be ex- product using a mixture of enzymes and co- tocols mimicking required larger-scale process
ploited to better understand and improve CO2 factors for the cascade of reactions (76, 77). These parameters. Modeling and designing novel bio-
utilization processes. Of special interest is the in vitro systems provide the potential for greater reactors, especially those for gas-intensive fer-
form of the electron donor, which can potentially control and flexibility by uncoupling product mentations, will be critical to improving the
be coupled to other biological reactions to max- synthesis from cellular viability, complexity, and reproducibility and predictability of bioconver-
imize overall efficiency. physiology and enabling high catalyst loading sion processes at the commercial scale. Process
to support high product titer and productivity. intensification can build on initial success in
What is the future of Advancements in material design and three- commercial-scale gas fermentation, with the
industrial biomanufacturing? dimensional printing have the potential to im- flexibility and modularity of biocatalyst devel-
Despite the promise of C1 feedstocks for indus- prove these efforts, with the use of printable opment enabling direct integration within the

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trial biomanufacturing of fuels and chemicals, particulate methane monooxygenase-embedded process to shift product output. Early-stage as-
much work remains to develop biocatalysts ex- materials for conversion of methane to methanol sessment of fermentation product separation
hibiting the required overall carbon and energy demonstrating the potential to improve not only is also critical to success, because defining the
conversion efficiencies. Biological conversion rates biocatalysts but also bioreactor and process requirements for separation from a product, pro-
are currently lower than chemical conversion design (78). cess, and cost standpoint can help guide biocatalyst
rates, and when considered alongside the chal- Genome engineering technologies for making development efforts and ensure full process in-
lenges of potential product toxicity and a dilute mutations to microbial genes and genomes in a tegration. All of these process elements will ben-
product output due to high water content, ad- targeted, multiplexed manner, such as CRISPR/ efit from technological learning as bioconversion
ditional robust bioprocess development is required Cas9-based systems (7981) and multiplexed auto- processes are continually explored and devel-
to reach metrics amenable for commercial scale mated genome engineering (82), are becoming oped, which will serve to reduce production and
operation. This will require improvement in both standard tools for model industrial organisms. energy costs and drive process optimization and
biocatalyst design and process development and The use of these tools allows in vivo construction integration.
will rely on continued advancement in a number of the millions of potential biosynthetic pathway Targeting distributed methane feedstocks cur-
of fields, including metabolic engineering and variants generated by in silico metabolic meth- rently inaccessible through chemical processes
synthetic and systems biology, among others. ods and design in a fraction of the traditional can help solidify industrial biomanufacturing
These advancements are critical for the devel- time. Furthermore, continued advances in syn- as an alternative to industrial chemical manu-
opment of bioconversion processes that can ex- thetic biology aimed at the development of de- facturing and serve as an enabling factor for con-
ploit the opportunity presented by currently fined and standardized biological parts can be tinued expansion and adoption for targeting a
wasted, distributed methane feedstocks. Although exploited for the construction of minimal syn- range of complex feedstocks and products. Al-
more mature bioconversion technologies target- thetic genomes and organisms with desired though much work remains, the strengths and
ing other feedstocks are currently available, no function (83). This type of modularization using diversity of biology can be leveraged to further
other feedstock is as widespread and currently standard parts can improve the automation of develop bioconversion processes for rapid, mo-
available as methane. This further underscores construction, serving to reduce both the time bile, and widespread deployment outside of those
the ability to benefit from the learning-by-doing and the costs associated with biocatalyst devel- previously demonstrated. This continued expan-
approach to drive down CapEx costs and ad- opment and improve upstream process design sion can further facilitate the ability for bio-
vance industrial biomanufacturing as a whole. efficiency. conversion to quickly adapt to market changes
Given this potential, reducing time required for The increasing throughput of design and con- or the arrival of new markets. Together, this
biocatalyst and process development is essential struction requires increasingly robust methods provides clear advantages for addressing the
for industrial manufacturing to capitalize on this for testing cellular functions that go beyond the emerging environmental, geographical, politi-
current opportunity and advance the future of traditional analytical tools used today. Screening cal, and economic factors for industrial chem-
the industry. and selection tools based on biosensors can help ical manufacturing. In addition to contributing
Strategies and tools within the iterative de- increase throughput and decrease analysis time to solving complex challenges facing our planet,
sign, build, test, and learn cycle of biocatalyst (84). These techniques can be integrated with an the smaller scale and lower process complexity of
development remain a critical factor for unlock- evolutionary approach to strain development, bioconversion processes also represent a promis-
ing the potential of new approaches to biocon- with systems biology approaches enabling the ing and potentially transformative approach to
version. Expanding available metabolic pathways discovery of the genetic and physiological basis meet the demands of deep space exploration.
through the development of novel synthetic en- of evolved phenotypes (85). Systems biology Extraterrestrial in situ resource use, product
zymes and pathways to improve the carbon and tools, such as next-generation sequencing, high- manufacturing, and human health demands,
energy efficiency of conversion is critical to both sensitivity proteomic and metabolomic methods, among others, will require innovative produc-
support and improve native pathways and orga- and developments in fluxomic techniques, can tion of manufacturing necessities using available
nisms engineered for product synthesis. Aiding also be used to analyze and guide additional natural resources on location, such as atmo-
these efforts are the use of in silico organism de- rounds of rational design for further optimiza- spheric gases (88, 89). Addressing the issue of
sign strategies (71), genome mining techniques tion and biocatalyst performance refinement, in situ resource use through biomanufacturing
(72), and computational enzyme design efforts including improving the tolerance of biocata- solutions, given the potential for small-scale,
(73), in addition to exploiting emerging areas lysts to desired designer products (86). CapEx-efficient design, relative product flexi-
such as substrate channeling (74). As opposed to Even with advancements in biocatalyst devel- bility, and mild operating conditions will use
the traditional design of single microorganisms opment, a critical challenge is scaling production an innovative commercial technology in a novel
for desired function, the use of microbial con- from typical laboratory conditions used for strain setting for potentially transformative solutions.
sortia is an additional emerging approach that development to those required on a commercial All told, the future of industrial biomanufacturing

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Clomburg et al., Science 355, eaag0804 (2017) 6 January 2017 10 of 10


Industrial biomanufacturing: The future of chemical
production
James M. Clomburg, Anna M. Crumbley and Ramon Gonzalez
(January 5, 2017)
Science 355 (6320), . [doi: 10.1126/science.aag0804]

Editor's Summary

The next era of chemical manufacturing


Producing mass quantities of chemicals has its roots in the industrial revolution. But industrial
synthesis leads to sizeable sustainability and socioeconomic challenges. The rapid advances in
biotechnology suggest that biological manufacturing may soon be a feasible alternative, but can it
produce chemicals at scale? Clomburg et al. review the progress made in industrial biomanufacturing,
including the tradeoffs between highly tunable biocatalysts and units of scale. The biological

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conversion of single-carbon compounds such as methane, for example, has served as a testbed for more
sustainable, decentralized production of desirable compounds.
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