#1GINKGO BIOWORKS Grow with Ginkgo Q2 2022 Update & Business Review August 15, 2022 Ť#2Disclaimer Forward-Looking Statements This presentation, the conference call and webcast may contain certain forward-looking statements within the meaning of the federal securities laws, including statements regarding our plans, strategies, current expectations, operations and anticipated results of operations, both business and financial, all of which are subject to known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievements, market trends, or industry results to differ materially from those expressed or implied by such forward-looking statements. These forward-looking statements generally are identified by the words "believe," "project," "potential," "expect," "anticipate," "estimate," "intend," "strategy," "future," "opportunity," "plan," "may," "should," "will," "would," "will be," "will continue," "will likely result," and similar expressions. Forward-looking statements are predictions, projections and other statements about future events that are based on current expectations and assumptions and, as a result, are subject to risks and uncertainties. Many factors could cause actual future events to differ materially from the forward-looking statements in this presentation, including but not limited to: (i) the effect of the business combination between Ginkgo Bioworks Holdings, Inc. ("Ginkgo") and Soaring Eagle Acquisition Corp. ("Soaring Eagle") on Ginkgo's business relationships, performance, and business generally, (ii) risks that the business combination disrupts current plans of Ginkgo and potential difficulties in Ginkgo's employee retention, (iii) the outcome of any legal proceedings that may be instituted against Ginkgo related to its business combination with Soaring Eagle, (iv) volatility in the price of Ginkgo's securities now that it is a public company due to a variety of factors, including changes in the competitive and highly regulated industries in which Ginkgo operates and plans to operate, variations in performance across competitors, changes in laws and regulations affecting Ginkgo's business, changes in the combined capital structure and expectations associated with increases in the number of shares available for sale, (v) the ability to implement business plans, forecasts, and other expectations after the completion of the business combination, and ability to identify and realize additional opportunities, (vi) the risk of downturns in demand for products using synthetic biology, (vii) the unpredictability of the duration of the COVID-19 pandemic and the demand for COVID-19 testing and the commercial viability of our COVID-19 testing business, (viii) changes to the biosecurity industry, including due to advancements in technology, emerging competition and evolution in industry demands, standards and regulations, and (ix) our ability to close and realize the expected benefits of pending merger and acquisition transactions. The foregoing list of factors is not exhaustive. You should carefully consider the foregoing factors and the other risks and uncertainties described in the "Risk Factors" section of Ginkgo's most recent quarterly report on Form 10-Q filed with the U.S. Securities and Exchange Commission (the "SEC"), and other documents filed by Ginkgo from time to time with the SEC. These filings identify and address other important risks and uncertainties that could cause actual events and results to differ materially from those contained in the forward-looking statements. Any forward-looking statement made by us in this presentation, the conference call during which this presentation is reviewed and any discussions that follow speaks only as of the date on which it is made. You are cautioned not to put undue reliance on forward-looking statements, and Ginkgo assumes no obligation and does not intend to update or revise these forward-looking statements, whether as a result of new information, future events, or otherwise. Ginkgo does not give any assurance that it will achieve its expectations. Industry and Market Data In this presentation, Ginkgo relies on and refers to certain information and statistics regarding the markets and industries in which Ginkgo competes. Such information and statistics are based on Ginkgo management's estimates and/or obtained from third-party sources, including reports by market research firms and company filings. While Ginkgo believes such third-party information is reliable, there can be no assurance as to the accuracy or completeness of the indicated information, and Ginkgo has not independently verified the accuracy or completeness of the information provided by the third-party sources. Use of Non-GAAP Financial Measures Certain of the financial measures included in this presentation, including Adjusted EBITDA, have not been prepared in accordance with generally accepted accounting principles ("GAAP"), and constitute "non-GAAP financial measures" as defined by the SEC. Ginkgo has included these non-GAAP financial measures because it believes they provide an additional tool for investors to use in evaluating Ginkgo's financial performance and prospects. Due to the nature and/or size of the items being excluded, such items do not reflect future gains, losses, expenses or benefits and are not indicative of our future operating performance. These non-GAAP financial measures are supplemental to, should not be considered in isolation from, or as an alternative to, financial measures determined in accordance with GAAP. In addition, these non-GAAP financial measures may differ from non-GAAP financial measures with comparable names used by other companies. See the reconciliation below for additional information regarding certain of the non-GAAP financial measures included in this presentation, including a description of these non-GAAP financial measures and a reconciliation of the historic measures to Ginkgo's most comparable GAAP financial measures.#3Disclaimer Trademarks This presentation may contain trademarks, service marks, trade names and copyrights of other companies, which are the property of their respective owners, and Ginkgo's use thereof does not imply an affiliation with, or endorsement by, the owners of such trademarks, service marks, trade names and copyrights. Solely for convenience, some of the trademarks, service marks, trade names and copyrights referred to in this presentation may be listed without the TM, © or symbols, but Ginkgo will assert, to the fullest extent under applicable law, the rights of the applicable owners, if any, to these trademarks, service marks, trade names and copyrights. Additional Information and Where to Find It In connection with the proposed transaction involving Ginkgo Bioworks Holdings, Inc. ("Ginkgo") and Zymergen Inc. ("Zymergen"), Ginkgo intends to file with the U.S. Securities and Exchange Commission ("SEC") a registration statement on Form S-4 that will include a proxy statement of Zymergen and that also constitutes a prospectus of Ginkgo. Each of Ginkgo and Zymergen may also file other relevant documents with the SEC regarding the proposed transaction. This document is not a substitute for the proxy statement/prospectus or registration statement or any other document that Ginkgo or Zymergen may file with the SEC. The definitive proxy statement/prospectus (if and when available) will be mailed to stockholders of Zymergen. INVESTORS AND SECURITY HOLDERS ARE URGED TO READ THE REGISTRATION STATEMENT, PROXY STATEMENT/PROSPECTUS AND ANY OTHER RELEVANT DOCUMENTS THAT MAY BE FILED WITH THE SEC, AS WELL AS ANY AMENDMENTS OR SUPPLEMENTS TO THESE DOCUMENTS, CAREFULLY AND IN THEIR ENTIRETY IF AND WHEN THEY BECOME AVAILABLE BECAUSE THEY CONTAIN OR WILL CONTAIN IMPORTANT INFORMATION ABOUT THE PROPOSED TRANSACTION. Investors and security holders will be able to obtain free copies of the registration statement and proxy statement/prospectus (if and when available) and other documents containing important information about Ginkgo, Zymergen and the proposed transaction, once such documents are filed with the SEC through the website maintained by the SEC at http://www.sec.gov. Copies of the documents filed with the SEC by Ginkgo will be available free of charge on Ginkgo's website at https://investors.ginkgobioworks.com or by contacting Ginkgo's Investor Relations department by email at [email protected]. Copies of the documents filed with the SEC by Zymergen will be available free of charge on Zymergen's website at https://investors.zymergen.com or by contacting Zymergen's Investor Relations department by email at [email protected]. Participants in the Solicitation Ginkgo, Zymergen, their respective directors and certain of their executive officers and other employees may be deemed to be participants in the solicitation of proxies from Zymergen's stockholders in connection with the proposed transaction. Information regarding the persons who may, under the rules of the SEC, be deemed participants in the solicitation of Zymergen's stockholders in connection with the proposed transaction, including a description of their direct or indirect interests, by security holdings or otherwise, will be set forth in the proxy statement/prospectus when it is filed with the SEC. Information about the directors and executive officers of Ginkgo, including a description of their direct or indirect interests, by security holdings or otherwise, is set forth in Ginkgo's proxy statement for its 2022 annual meeting of shareholders, which was filed with the SEC on April 26, 2022, and Ginkgo's Annual Report on Form 10-K for the fiscal year ended December 31, 2021, which was filed with the SEC on March 29, 2022. Information about the directors and executive officers of Zymergen, including a description of their direct or indirect interests, by security holdings or otherwise, is set forth in Zymergen's proxy statement for its 2022 annual meeting of shareholders, which was filed with the SEC on April 20, 2022, and Zymergen's Annual Report on Form 10-K for the fiscal year ended December 31, 2021, which was filed with the SEC on March 30, 2022. Other information regarding the participants in the proxy solicitation and a description of their direct and indirect interests, by security holdings or otherwise, will be contained in the proxy statement/prospectus and other relevant materials to be filed with the SEC regarding the proposed transaction when such materials become available. Investors should read the proxy statement/prospectus carefully when it becomes available before making any voting or investment decisions. You may obtain free copies of these documents from Ginkgo or Zymergen using the sources indicated above. No Offer or Solicitation This communication is not intended to and shall not constitute an offer to buy or sell or the solicitation of an offer to buy or sell any securities, or a solicitation of any vote or approval, nor shall there be any sale of securities in any jurisdiction in which such offer, solicitation or sale would be unlawful prior to registration or qualification under the securities laws of any such jurisdiction. No offering of securities shall be made, except by means of a prospectus meeting the requirements of Section 10 of the U.S. Securities Act of 1933, as amended.#4Agenda Introduction Jason Kelly, Co-Founder and CEO Q2 2022 Financial Update Mark Dmytruk, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Anna Marie Wagner, SVP Corporate Development 4 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#5engineer easier to biology Make Q2 2022 UPDATE & BUSINESS REVIEW Our mission Property of Ginkgo Bioworks 5#6We aim to make biology easier to engineer for our customers by leveraging our platform for programming cells Ginkgo Foundry Input Customer Specs Recursive Learning SOFTWARE HARDWARE ORGANISMS Design, Write, & Debug DNA Code ACTGGATA CCTGAGAT AUTOMATION GENETIC CODE BIOLOGICAL TOOLS Continuous Improvement Output Cell Program Ginkgo Codebase 9 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#7Continuing to execute well on our plans in the second quarter of 2022 Active Programs 46 5 10 13 9 9 Q2 2021 73 2 26 22 13 10 Q2 2022 CRONOS GROUP • Announced the achievement of the third target productivity milestone, THCV, in our partnership to produce eight cultured cannabinoids Progress on Key Metrics Government Pharma & Biotech Food & Agriculture Industrial & Environmental Consumer & Technology +13 Diverse New Programs: 元 VO novo nordisk SUMITOMO CHEMICAL Strong Biosecurity Performance: $247 million Year-to-date Biosecurity Revenue zymergen Ⓡ Announced a definitive agreement under which Ginkgo will acquire Zymergen Recently awarded contract to continue CDC's Traveler-based SARS-CoV-2 Genomic Surveillance Program • The acquisition is expected to accelerate the development of Ginkgo's innovative horizontal synthetic biology platform evo Company Highlights JOYN BIO BAYER E Signed definitive agreement to acquire Bayer's 175,000-square-foot Biologics R&D center • Ginkgo will also enter into a new multi-year platform collaboration with Bayer to advance several agricultural biological programs 3x+ Y-O-Y Revenue Growth $44 $22 Strong Financial Health $22 Q2 2021 bitome better tools, faster science. • Acquired assets from Bitome are expected to support accelerated product development timelines across Ginkgo's portfolio of cell programs through its real-time metabolite monitoring technology $145 $100 $44 Q2 2022 Biosecurity ($M) Foundry ($M) -$1.4 billion in cash provides ample runway • Appointed Dr. Kathy Hopinkah Hannan to Board of Directors. Dr. Hannan brings over thirty years of experience as a senior C-Suite executive, corporate advisor, independent board director and strategist 7 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#8Agenda Introduction Jason Kelly, Co-Founder and CEO Q2 2022 Financial Update Mark Dmytruk, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Anna Marie Wagner, SVP Corporate Development 8 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#9Total Ginkgo Revenue (Unaudited) 10 $44M $22M $22M Q2 2021 231% $145M $100M $44M Q2 2022 $88M $44M $44M 257% Q2 2021 - YTD $313M $247M $66M Q2 2022 - YTD Biosecurity Foundry 6 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#10Cell Programming Highlights (Unaudited) New Programs 7 22 86% Q2 2021 Total Active Customers Q2 2021 13 64% Q2 2022 36 Q2 2022 Total Active Programs 46 $22 59% Q2 2021 Q2 2022 Foundry Revenue ($M) $11 $11 Q2 2021 Third Party Related Party 73 105% $44 $36 $8 Q2 2022 10 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#11Biosecurity Highlights (Unaudited) 0 $ 22 -10% Biosecurity Revenue ($M) Q1 2021 $22 Q1 2021 Q2 2021 Q3 2021 Q4 2021 Q1 2022 $43 22% Q2 2021 Biosecurity Gross Margin $ 114 48% Q3 2021 $147 42% 42% Q4 2021 Q1 2022 $100 Q2 2022 36% Q2 2022 Concentric's pathogen monitoring network has delivered testing across most of the U.S.) Demonstrated ability to deliver testing in diverse jurisdictions States in which Concentric has delivered testing services Airport testing locations *Map shading reflects all states in which Concentric has delivered testing since launching in 2020, not all states currently have active testing programs. Breadth is important given diverse set of state operating models. 10.3 million+ Samples to date 37,000+ Viral samples sequenced to date 5,400+ Organizations supported to date 4 Key US airports Data updated 08/01/22 Continuing to diversify biosecurity business through new initiatives including passive air and wastewater monitoring New contract with CDC for ongoing inbound air travel monitoring supports our belief that biosecurity is here to stay and that Ginkgo has the opportunity to play a leading role 11 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#12Q2 2022 Financial Summary (Unaudited) In millions of USD except new programs and % YoY New programs launched Revenue: Foundry Biosecurity Total revenue Biosecurity cost of sales Research and development (excl. SBC) General and administrative (excl. SBC) Total operating expenses (excl. SBC) (1) Stock-based compensation Loss from operations Net loss Adjusted EBITDA Capital expenditures Three Months Ended June 30, 2022 13 $44 100 145 64 72 48 184 607 (647) (671) (23) 10 2021 7 $22 22 44 17 52 20 89 15 (60) (54) (38) 24 % YOY 86% 105% 355% 231% 274% 38% 143% 107% NM NM NM 38% (60%) (1) For the three months and six months ended June 30, 2022, amounts include $0.8M and $7.0M respectively of employer payroll taxes related to stock-based compensation Six Months Ended June 30, 2022 24 $ 66 247 313 149 128 91 368 1,266 (1,321) (1,263) (23) 13 2021 11 $44 44 88 41 112 38 190 15 (117) (129) (89) 46 % YoY 118% 49% 467% 257% 266% 15% 140% 94% NM NM NM 74% (71%) 12 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#13Increasing our 2022 Full Year Outlook In millions of USD except new programs and % YoY New Programs GAAP Revenue Foundry Biosecurity Total Revenue FY2020 18 $59 $17 $77 Historical FY2021 31 $113 $201 $314 (20-21) 72% 91% NM 309% Original (March 28) 60 $165 - $180 $160+ $325 - $340+ FY2022 Forecast First Revision (May 16) 60 $165 - $180 $210+ $375 - $390+ Second Revision (August 15) 60 $165 - $180 $260+ $425 - $440+ I I 13 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#14Agenda Introduction Jason Kelly, Co-Founder and CEO Q2 2022 Financial Update Mark Dmytruk, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Anna Marie Wagner, SVP Corporate Development Property of Ginkgo Bioworks - 14 Q2 2022 UPDATE & BUSINESS REVIEW#15We believe... 1 Zymergen and Bayer will improve our platform and drive better customer outcomes The pending additions of Zymergen and Bayer's ag biologicals assets are expected to meaningfully benefit our platform and customers, adding both entirely new capabilitie as well as driving system-wide improvements 2 We remain focused on our cash runway and achieving profitability We are focused on maintaining our multi-year cash runway and driving toward long-term profitability. In addition to general fiscal discipline, our business model affords several levers we can pull, including scale economics on the platform as well as the types of programs we take on 3 Sustainability is fundamental to our strategy ESG is not window dressing for Ginkgo, it's in our DNA. We believe our framework of care has enabled us to take advantage of key strategic opportunities while furthering o mission and is critical to our long-term sustainable performance 15 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#16We believe... 1 Zymergen and Bayer will improve our platform and drive better customer outcomes The pending additions of Zymergen and Bayer's ag biologicals assets are expected to meaningfully benefit our platform and customers, adding both entirely new capabilitie as well as driving system-wide improvements 2 We remain focused on our cash runway and achieving profitability 3 Sustainability is fundamental to our strategy 16 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#17Zymergen and Bayer transactions expected to be valuable platform additions Transactions build on our successful history of opportunistic M&A and technology acquisition integrations Zymergen Integration of Zymergen's automation and technical capabilities is expected to improve Ginkgo's platform capabilities across verticals • Technology fits well into Ginkgo's roadmap and is expected to drive efficiency for customer programs • Zymergen plans to continue its ongoing standalone optimization plans, and Ginkgo will support Zymergen's efforts to realize value from its product portfolio All-stock transaction implied $300M market cap at signing (¹) ● 0.9179x exchange ratio fixed at signing implied 5.25% pro forma ownership by Zymergen shareholders post-transaction • Expected to close by Q1 2023 READ MORE (1) Based on Ginkgo's closing price on Friday, July 22, 2022 (2) Ginkgo owns 70% of Cooksonial Bayer Bayer transaction expected to open up agricultural biologicals market and contribute significant new capabilities West Sacramento Joyn Dissolution New Bayer Collaboration Ginkgo Receives WesSac facility, strain collection, team Platform assets from Joyn and royalty on Bayer net sales of NFix product via Cooksonia (2) Bayer Receives READ MORE $83M consideration NFix program and certain IP rights from Joyn 3 year collaboration with Bayer to advance multiple programs • Ginkgo's largest ever cell programming contract (in terms of R&D service fees) • Opportunity for standard royalty-based downstream value 17 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#18These transactions complement each other, opening new market opportunities and improving our platform capabilities for our customers End Market Asset purchase deepens ag biologicals vertical expertise • Leading "translational research" capabilities enhance our offering and will allow us to make these capabilities broadly available to the ag biologicals market Collaboration provides significant revenue opportunity • Ginkgo's largest ever cell programming contract (in terms of R&D service fees) • Ability to work with new customers on the platform B A BAYER R JOYN BIO z zymergen ✓ Expanded TAM ✔ New capabilities Broad platform improvements Automation and software built with flexibility in mind complements Ginkgo's strengths • Believe we can quickly deploy Zymergen's scalable architecture alongside Ginkgo's own automation capabilities • Talent fits within and is expected to accelerate scaling plans Data organization and analysis tools can help us take advantage of our codebase assets General Purpose Capabilities 18 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#19We believe... 1 Zymergen and Bayer will improve our platform and drive better customer outcomes 2 We remain focused on our cash runway and achieving profitability We are focused on maintaining our multi-year cash runway and driving toward long-term profitability. In addition to general fiscal discipline, our business model affords several levers we pull, including scale economics on the platform as well as the types of programs we take on 3 Sustainability is fundamental to our strategy 19 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#20Cash runway and profitability are important in this environment, and our underwriting and structuring of the Zymergen and Bayer deals reflects that zymergen BAYER BAYER JOYN BIO Significant cost efficiencies in Zymergen transaction means recurring OpEx investment is minimal • Zymergen to progress independently planned cost and program rationalization prior to close • Post-close, Ginkgo will complete restructuring, and core Zymergen team is expected to fill significant planned hiring by Ginkgo, which is expected to accelerate growth and result in minimal additional employee costs • Upside if able to monetize Zymergen's product pipeline or restructure real estate obligations Bayer collaboration fees expected to significantly offset incremental run-rate OpEx from new ag biologicals capabilities • Some cost optimization through combination, including ability to leverage Ginkgo's platform capabilities ● Multi-year Bayer anchor contract expected to provide strong base of demand while we build base of new customers in this space, which could create significant opportunities for growth Ginkgo's -$1.4B cash balance as of 6/30/22 provides margin of safety, allowing us to lean into high ROI opportunities Transactions structured with the intention of minimizing incremental recurring operating costs Meaningful revenue opportunity from ag vertical expansion and increased efficiency and probability of success from horizontal platform improvements 20 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#21Significant incremental upside opportunities in Zymergen transaction that could improve financial case 1 Product Portfolio • Zymergen exploring strategic alternatives for its Advanced Materials and Drug Discovery businesses 2 o Sale(s) could create additional cash proceeds and reduce operating expenses o Spin-out could reduce costs, create a new customer for Ginkgo, and provide an opportunity for additional upside through equity appreciation • Not contemplated in base case runway and revenue forecasts, but believe product portfolio is strong, and Zymergen has already received serious inbound interest in the portfolio since announcement Real Estate Rationalization • Ginkgo assuming a present value of ~$186 million in total future lease liabilities(1) (including ~$30 million in 2023) in connection with Zymergen's real estate portfolio, largely due to their new HQ in Emeryville, CA o Note: the merger agreement provides protections related to cost overruns so minimal uncertainty re: build-out costs • We will actively evaluate real estate portfolio rationalization, and any successful effort to mitigate the lease liability could represent meaningful upside to the base case and further reduce incremental cash burn from the Zymergen transaction (1) Represents the lump sum present value across Zymergen's leases Ginkgo's vision fits well with where Zymergen is in its transformation Over the last year, Zymergen has simplified its business into 3 core areas: Advanced Materials, Drug Discovery, and Automation Previously Zymergen was focused on pursuing many discrete product opportunities Advanced Materials Drug Discovery Automation & Tech Platform (and enabling SW/Data and biological assets) Ginkgo's expertise in creating and supporting NewCos will support Zymergen's plans to explore standalone opportunities for the product areas ON Advanced Materials • Independent product portfolio in areas like water repellency, advanced polymers, and enzymes • Zymergen may explore standing up a NewCo in the space and/or selling certain product concepts to strategic acquirers Drug Discovery Long-term goal to develop owned therapeutic assets, potentially as another NewCo • Certain enabling technologies may remain at Ginkgo and enable therapeutics developers Core technology assets that Ginkgo will integrate into its platform to improve its service offering to customers Excerpt from M&A Strategy Update Call (July 25, 2022) The site of Zymergen's new HQ in Emeryville 21 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#22While we're focused on costs in this environment, our business model has several unique levers we can pull to drive towards profitability Platform Scale Our platform benefits from scale Physical scale drives decreasing unit costs to execute work, which can drive lower costs to customers as well as improve margins The learnings generated from executing more work can drive efficiencies in our work as well, yielding improved outcomes and higher probability of technical success (and downstream value) CODEBASE LOWER FOUNDRY COST STRUCTURE, IMPROVED PROGRAM TECHNICAL SUCCESS ADD NEW PROGRAM DEMAND FOR MORE PROGRAMS LOWER COST PER PROGRAM VALUE SHARE (ROYALTY/EQUITY) CUSTOMER VALVE PROPOSITION Program Risk Sharing We can adjust how we structure contracts based on market conditions and our priorities (e.g. near-term cash vs. longer-term value) Risk to Revenue High Upfront Fees No / Low Downstream Value (e.g. a traditional CRO model) No / Low Upfront Fees High Downstream Value When profitable / well capitalized, can lean into our differentiated p(success) Can shift focus towards need to preserve cash cost-covering upfront fees if Return if Successful Program Choice We can direct business development efforts towards programs with a higher probability of success and lower expected effort (e.g. CDKS) higher lower Standard Cell Program (Standardized CDK modules in any configuration) TDP Module TDP Module p(success) Cost to Ginkgo CDK-Enabled Cell Program (Mix of modular work and new capabilities) TDP Module TDP Module lower higher Bespoke Cell Program (Primarily new biology or capabilities) Non-standard engineering loop Non-standard engineering loop 22 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#23We believe... 1 Zymergen and Bayer will improve our platform and drive better customer outcomes 2 We remain focused on our cash runway and achieving profitability 3 Sustainability is fundamental to our strategy ESG is not window dressing for Ginkgo, it's in our DNA. We believe our framework of care has enabled us to take advantage of key strategic opportunities while furthering o mission and is critical to our long-term sustainable performance 23 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#24Caring at Ginkgo READ MORE 2021 Sustainability Report We care... and that drives everything we do "We believe that caring about people and the planet now requires being able to imagine a better world. And we believe that programming biology offers us an opportunity to imagine and build such a world, because biology grows and builds in a regenerative way, it adapts and evolves, and fundamentally it is us and our environment. Our mission is to make biology easier to engineer so that we can more easily imagine what that future looks like and achieve it together." 24 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#25Our investors also care... and we believe investors will increasingly need to focus on the sustainability of their portfolios Our approach to sustainable investing and ESG integration builds upon [our] active management legacy, with the understanding that every company has a specific subset of relevant ESG issues that are vital to long-term fundamental success... Our process avoids reliance on external scoring systems in favor of integrating sustainability analysis with long-term fundamental analysis, with a goal of generating superior performance for our investors. With this context in mind, we'd like to thank you for the example Ginkgo sets as a company that understands the intertwined nature of sustainability and strategy. In particular, we are impressed by the company's ability to grow and cultivate partnerships throughout the synbio community, which are likely to benefit long-term growth, effectiveness, and returns. We also note your proactive approach to employee ownership and voting structure, and your far-ranging work to develop an ethos of care throughout the company and the broader field. In the months and years to come, we look forward to assessing how these foundational strategies link to longer-term scientific and commercial success. Though for some investors this type of letter is an administrative process, for our team this is a core investment process, with the intention of highlighting the potential for long-term value creation for all stakeholders. The challenges of our current environment present unique opportunities for companies to extend their own potential and to contribute to thriving individuals, systems, society, and planet. We are grateful for your leadership. Excerpt from 2022 Annual Letter to Ginkgo from $175 billion AUM fundamental asset manager 25 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#26Ginkgo Bioworks- 2021 Sustainability Report Our Approach to Sustainability: Caring How Our Platform is Used Engineers often say that technology is neutral; however, we believe that we cannot remain neutral when it comes to the use of powerful technologies- we care about how our platform is used and about the impact it has on the world. Our long-term commitment to care drives our engagement with our customers who seek positive long- term impact, efforts in building large- scale biosecurity technology, and culture and modes of governance. Ginkgo is building a horizontal platform for programming cells across organisms in any market and to address some of the most difficult environmental and societal challenges. We recognize that humans did not invent biology-rather, biology invented us-so we must have humility about the current limits of our understanding. Our culture is built on care. For us, that means transparency, diversity, employee ownership, engagement, and a deep, humble respect for biology. Transparency is essential to how we operate, to enable sharing of the insights and tools that enable our platform to grow, as well as to build trust and accountability with all of our stakeholders. We have advocated for more transparency in our industry, including supporting Environmental The Impact of Cell Programming Social Technology Isn't Neutral Governance Ownership is the First Step in Caring GMO ("Genetically Modified Organism") labeling, and seek to educate policymakers and the general public about the benefits and risks of synthetic biology through our advocacy efforts. Many of the initiatives and activities that we pursue to realize our commitment to caring are detailed on the following pages. 16 28 52 About Ginkgo Bioworks 26 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#27Our Impact: Cell Programming We believe the world is recognizing that biology will be a necessary tool to combat our most pressing challenges; we expect our focus on the responsible deployment of biology can benefit from that increasing interest Cell Programming is Addressing Our Most Challenging Environmental and Social Issues Pharma & Biotech • Antibody therapeutic development • Nucleic acid vaccine production • Antibiotic discovery and manufacturing • Microbiome therapeutics • Gene and cell therapies Industrials & Environment • Wastewater remediation • Renewable chemicals • Pollutant degradation . Sustainable building materials . Carbon sequestration Food & Agriculture • Animal protein replacement • Brewing & baking • Fertilizer reduction • Pest control • Animal feed and aquaculture Consumer & Technology • Flavors, fragrances, and cannabinoids • Skin microbiome • Haircare and skincare proteins • Textiles and dyes • Electronic coatings THE WHITE HOUSE WASHINGTON BRIEFING ROOM FACT SHEET: CHIPS and Science Act Will Lower Costs, Create Jobs, Strengthen Supply Chains, and Counter China AUGUST 09, 2022 STATEMENTS AND RELEASES Bloomberg How the Senate's Big Climate Bill Eliminates 4 Billion Tons of Emissions The Inflation Reduction Act would avoid 24 tons of climate emissions for every new ton it creates, say researchers who have analyzed the legislation. By Zahra Hirji August 4, 2022 at 4:22 PM EDT Updated on August 4, 2022 at 9:49 PM EDT The CHIPS and Science Act names synthetic biology as a key focus area for National Science Foundation funding The Inflation Reduction Act passed by Congress seeks to create a carbon capture industry that could create meaningful opportunities for synthetic biology 27 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#28Our Impact: Biosecurity Our COVID response efforts were not simply opportunistic, they built upon years of work in biosecurity... Bloomberg The DNA Cops Who Make Sure the World's Deadliest Viruses Aren't Rebuilt Ginkgo Bioworks is helping stop a new class of lethal biological weapons from being created. By Rebecca Spalding June 27, 2018 at 5:00 AM EDT SCIENCES ENGINEERING-MEDICINE CONSENSUS STUDY REPORT BIODEFENSE IN THE AGE OF Synthetic Biology P THE APOLLO PROGRAM FOR BIODEFENSE WINNING THE RACE AGAINST BIOLOGICAL THREATS A RECOMMENDATION BY THE BIPARTISAN COMMISSION ON BIODEFENSE January 2021 NTI Insight Report Biosecurity Innovation and Risk Reduction: A Global Framework for Accessible, Safe and Secure DNA Synthesis In collaboration with the Nuclear Threat Initiative (NT) WORLD ECONOMIC FORUM COMMITTED TO IMPROVING THE STATE 28 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#29Our Impact: Biosecurity ...and have built a foundation from which we plan to develop a more robust industry CDC launches Traveler-based SARS-CoV-2 Genomic Surveillance Program May 27, 2022 "This Traveler-based SARS-CoV-2 genomic surveillance program is a model of pathogen detection that can be used as an early warning system for pandemics and other outbreaks affecting international travelers" - Dr. Cindy R. Friedman Ginkgo Bioworks and First Serv Announce Plans to Develop and Implement Innovative Global Biosecurity Capabilities in Qatar May 18, 2022 Today announced we were awarded a contract with the CDC to expand this early warning program Early Warning International Ginkgo Bioworks and the Rwanda Development Board Announce Plans to Develop and Implement New Biosecurity Capabilities in Rwanda Aug 11, 2022 Concentric by Ginkgo crosses 10 million samples tested and expands testing and sequencing capabilities to detect monkeypox and other pathogens, as part of scaling its global biosecurity infrastructure JUNE 24, 2022 Emerging Threats CAN health WHO declares monkeypox a public health emergency of international concern By Carma Hassan and Carolyn Sung, CNN Updated 10:57 AM ET, Sat July 23, 2022 The New York Times As Monkeypox Spreads, U.S. Declares a Health Emergency By Sheryl Gay Stolberg and Apoorva Mandavilli Aug. 4, 2022 29 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#30Social: Technology Isn't Neutral Technology isn't Neutral The individuals who build new technologies have significant power. We embed our values into the platforms and products that we make. As individuals, our worldview and our privilege profoundly affect what problems we choose to solve, what risks we choose to accept, and what safeguards we put in place. And in biology, these choices are all the more critical. But right now, the direction of the bioeconomy is largely driven by those with the most privilege. At Ginkgo, we believe that as an industry leader, it is our responsibility to better share that power for the benefit of our stakeholders and communities. Employee Diversity Race O O O White Asian Female Male Supply Chain Diversity Underrepresented minority Undisclosed More than 40% of our supplier base Is diverse More than 30% of our spend within supply chain goes to diverse suppliers 59% 21% Gender 12% 8% 43% 57% Gender X 0.3% Data accurate for Ginkgo's employees based in the U.S. STEM aire Age PRESENTED BY GINKGO BIOWORKS ¡GEM synbiobeta | BENJAMIN FRANKLIN CUMMINGS BLACK QUEER INSTITUTE OF TECHNOLOGY Under 30 30 to 50 Over 50 lassBioEd 29% 63% 8% AFRICA CDC TOWN HALL In STEM and Healthcare Penn BIOTA BEATS GINKGO BioBuilder Bridge 30 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#31Ownership is the First Step in Caring Class A 79% Bioworkers Own Class B Shares, Which Hold 10 Votes per Share O As of December 31, 2021 Class B 21% Outstanding Shares among Founders and Employees The individuals who work at Ginkgo and build our platform care deeply about how that platform is used and the impact our company will have in the world. Ownership is the first step in caring how our platform is used, and, as employees, we have an outsized influence on how our platform is developed and deployed. We believe a workforce with strong equity ownership will make the wise decisions needed to build long- term value for our company, and to build a company whose long-term impacts make them proud. That is why we have implemented a multi-class stock structure that permits all employees (current and future), not just Founders, to hold high-vote (10 votes per share) common stock. We believe that our multi-class stock structure will help maintain the long-term mentality we have benefited from as a Founder-led company. Our team is supported by a strong, experienced, and diverse Board of Directors... and we're thrilled to have recently welcomed our newest board member, Dr. Kathy Hannan Jason Kelly FOUNDER Christian Henry AUDIT COMMITTEE CHAIR Reshma Shetty FOUNDER Shyam Sankar COMPENSATION COMMITTEE CHAIR Marijn Dekkers Prior Experience CHAIRPERSON Harry E. Sloan Reshma Kewalramani NOMINATING AND CORPORATE GOVERNANCE COMMITTEE CHAIR Arie Belldegrun Kathy Hopinkah Hannan, PhD, CPA - Board Director ● Director at Annaly Capital Management, Otis Worldwide, Carpenter Technology ● Chair of the Board of Trustees, Smithsonian National Museum of the American Indian Sr. Partner & Vice Chair, KPMG LLC ● Chair of the Board of Directors of Girl Scouts of the USA Commissioner for the Tribal Employment Rights Office National Advisory Council on Indian Education 31 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#32Let's build the world we want to see GINKGO BIOWORKS#33Agenda Introduction Jason Kelly, Co-Founder and CEO Q2 2022 Financial Update Mark Dmytruk, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Anna Marie Wagner, SVP Corporate Development 33 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#34APPENDIX 04 Pe 2#35Cell Program Counts New Programs Current Active Programs Cumulative Programs (1) Last Twelve Months Ended June 30, 2022 Three Months Ended June 30, 2022 13 73 129 2021 7 46 85 Six Months Ended June 30, 2022 24 77 129 2021 11 51 85 LTM (1) 2022 44 New Programs: New Programs represent the number of unique programs commenced within the reporting period. As new programs have multi-year durations, we view this metric as an indication of future Foundry revenue growth. 88 129 Current Active Programs: Current Active Programs represent the number of unique programs for which we performed R&D services in the reporting period. We view this metric as an indication of current period and future Foundry revenue. Cumulative Programs: Cumulative Programs represent the cumulative number of unique programs Ginkgo has commenced. We view this metric as an indication of our competitive advantage and as a leading indicator of the mid- to long-term potential economic value derived from downstream value share arrangements. The cumulative number of programs also contributes to Codebase, which accumulates with each additional program we conduct over time and drives better experimental direction and improves the odds of technical success in current and future programs. 35 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#36Adjusted EBITDA Reconciliation (Unaudited) In millions of USD Net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders Interest (income) expense, net Income tax (benefit) provision Depreciation and amortization EBITDA Stock-based compensation 1 Loss on equity method investments Loss (gain) on investments Change in fair value of warrant liabilities Gain on deconsolidation of subsidiary Merger and acquisition related expenses In-process research and development 4 Other 5 Adjusted EBITDA 2 3 Three Months Ended June 30, 2022 2021 ($668.8) ($1.7) ($0.0) $9.6 ($660.9) $607.3 $10.0 $38.7 ($23.5) $0.0 $2.7 $1.6 $0.9 ($23.3) ($53.9) $0.5 ($0.4) $7.2 ($46.7) $14.5 $3.8 ($2.8) $0.0 $0.0 $0.0 $0.0 ($6.4) ($37.5) Six Months Ended June 30, 2021 ($127.5) $1.0 ($0.6) $12.8 2022 ($1,259.3) ($1.3) ($0.2) $19.1 ($1,241.7) $1,266.3 $30.2 $38.2 ($108.5) ($15.9) $6.6 $1.6 $0.3 ($22.9) ($114.4) $14.6 $31.2 ($15.4) $0.0 $0.0 $0.0 $0.0 ($4.8) ($88.7) (1) For the three and six months ended June 30, 2022, includes employer payroll taxes of $0.8 million and $7.0 million, respectively. (2) Represents losses on equity method investments under the hypothetical liquidation at book value method, net of losses attributable to non-controlling interests. (3) Represents transaction and integration costs directly related to mergers and acquisitions including (i) due diligence, legal and other professional fees associated with acquisitions and (ii) the fair value adjustments to contingent consideration liabilities resulting from acquisitions. In the second quarter of 2022, we redefined Adjusted EBITDA to exclude the impact of merger and acquisition related expenses. We elected to recast our previous first quarter 2022 Adjusted EBITDA calculation to exclude these costs and conform to the new presentation. (4) Represents acquired intangible assets expensed to research and development associated with a business acquisition. (5) For the three and six months ended June 30, 2022, includes change in fair value of Access Bio Convertible Notes. For the three and six months ended June 30, 2021, includes change in fair value of Access Bio Convertible Notes and gain related to a settlement payment from Amyris. 36 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#37Stock-Based Compensation (Unaudited) In millions of USD Total Stock-Based Compensation Amount included in Research and Development expenses: Stock-Based Compensation Employer Payroll Taxes Related to Stock-Based Compensation Amount included in General and Administrative expenses: Stock-Based Compensation Employer Payroll Taxes Related to Stock-Based Compensation Three Months Ended June 30, 2021 $14.5 2022 $607.3 217.3 216.8 0.5 390.0 389.7 0.3 0.0 0.0 0.0 14.5 14.5 0.0 % YoY NM NM NM NM NM NM NM Six Months Ended June 30, 2022 $1,266.3 483.6 477.8 5.8 782.7 781.5 1.2 2021 $14.6 0.0 0.0 0.0 14.6 14.6 0.0 % YoY NM NM NM NM NM NM NM Modification of Equity Awards in Connection with Business Combination Prior to becoming a public company in September 2021, Ginkgo granted restricted stock units ("RSUS") with both a service-based vesting condition and a performance-based vesting condition, defined as a change in control or an initial public offering (both as defined in the underlying award agreement). Ginkgo historically did not recognize any stock-based compensation expense associated with these awards due to the performance-based vesting condition. As of December 31, 2021, there was $2.2 billion of unrecognized stock-based compensation expense related to the above catch-up adjustment for those RSUS and Earnout RSUS that had not yet fully met the service-based vesting condition as of December 31, 2021. This amount will be recognized over a weighted-average period of 1.6 years, of which $650.1 million was recognized in the first quarter and $594.0 million in the second quarter of 2022. As previously disclosed, on November 17, 2021 the board of directors modified the vesting terms of RSUs, such that Ginkgo's business combination with Soaring Eagle Acquisition Corp. was deemed to have met the performance condition for vesting. This was accounted for as a modification and resulted in a catch-up adjustment of approximately $1.5 billion of incremental stock-based compensation expense in the fourth quarter of 2021 (calculated based on the number of RSUS impacted, which had been granted since 2015, at the share price of $13.59 on November 17, 2021). Stock-based compensation expense also increased by $173.5 million in the fourth quarter of 2021 related to RSU earnout shares ("Earnout RSUS") which were also subject to the same performance condition as the underlying RSUS. 37 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#38Foundry Revenue (Unaudited) In thousands of USD, except percentages Related Parties Third Parties Foundry Revenue Three Months Ended June 30, 2022 % of Total 2021 10,962 10,630 $21,592 18% 82% 100% 7,973 36,269 $44,242 % of Total 51% 49% 100% 2022 21,501 44,229 $65,730 Six Months Ended June 30, % of Total 33% 67% 100% 2021 23,622 20,474 $44,096 % of Total 54% 46% 100% Related Parties: Related parties include Platform Ventures and certain Structured Partnerships. See notes to our condensed consolidated financial statements for additional information related to transactions with related parties. Third Parties: Includes all other customers 38 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#39Segment Information (Unaudited) In millions of USD Revenue: Foundry Biosecurity Total Revenue Segment cost of revenue: Biosecurity Segment research and development expense: Foundry Biosecurity Total segment research and development expense Segment general and administrative expense: Foundry Biosecurity Total segment general and administrative expense Segment operating income (loss): Foundry Biosecurity Total segment operating income (loss) Operating expenses not allocated to segments: Stock-based compensation Depreciation and amortization Other Loss from operations Three Months Ended June 30, 2021 % YoY 2022 $44 100 145 64 63 0 63 37 12 49 (55) 24 (32) 607 9 (1) (647) $22 22 44 17 41 4 45 15 5 20 (34) (5) (38) 15 ܢ ܘ 7 0 (60) 105% 355% 231% 274% 54% (90%) 40% 149% 144% 147% (62%) NM 18% NM 34% NM NM Six Months Ended June 30, 2022 2021 % YoY $66 247 313 149 110 1 111 63 26 89 (108) 71 (36) 1,266 19 0 (1,321) $44 44 88 41 49% 467% 257% 72 53% 28 (97%) 99 12% (56) (35) (90) 266% 28 127% 167% 10 37 137% 15 12 0 (117) (94%) NM 60% NM 50% NM NM 39 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW#40Share Supplement Shares in millions Basic Shares (1) RSUS (2) Illustrative Fully-Diluted Share Count Options (Treasury-stock method)(3) Fully-Diluted Shares Memo: Remaining Earnout Shares Outstanding(4) Memo: Shares Underlying Warrants (public and private)(5) 1,624.3 214.3 18.3 1,856.9 160.5 51.8 (1) Common stock outstanding as of 8/8/2022 per Q2 2022 10-Q face less outstanding earnout shares as of 6/30/2022 for which the service and/or price (between $15 and $20 per share) vesting conditions have not yet been met. (2) Non-vested RSUS as of 6/30/2022. See Note 9 to Q2 2022 financial statements. (3) Outstanding options as of 6/30/2022. Treasury-stock method based on Ginkgo VWAP during Q2 2022. Excludes earnout options. See Note 9 to Q2 2022 financial statements. (4) Outstanding earnout shares as of 6/30/2022, includes shares for which the service and/or price (between $15 and $20 per share) vesting conditions have not yet been met. See Note 13 to Q2 2022 financial statements. (5) Warrants to purchase Class A common stock outstanding as of 6/30/2022, with an exercise price of $11.50. See Note 13 to Q2 2022 financial statements. 40 Property of Ginkgo Bioworks Q2 2022 UPDATE & BUSINESS REVIEW