Biggest changeOur income tax provision may be significantly affected by changes to our estimates. 82 Table of Contents Results of Operations Comparison of the Years Ended December 31, 2023 and 2022 The following table presents our result of operations for the periods indicated: Years Ended December 31, (in thousands) 2023 2022 Change Cell Engineering revenue $ 143,531 $ 143,666 $ (135) Biosecurity revenue: Product 28,949 35,455 (6,506) Service 78,975 298,585 (219,610) Total revenue 251,455 477,706 (226,251) Costs and operating expenses: Cost of Biosecurity product revenue 7,481 20,646 (13,165) Cost of Biosecurity service revenue 46,524 183,570 (137,046) Research and development (1) 580,621 1,052,643 (472,022) General and administrative (1) 385,025 1,429,799 (1,044,774) Impairment of lease assets 96,210 — 96,210 Total operating expenses 1,115,861 2,686,658 (1,570,797) Loss from operations (864,406) (2,208,952) 1,344,546 Other income (expense): Interest income 57,217 20,262 36,955 Interest expense (93) (106) 13 Loss on equity method investments (2,635) (43,761) 41,126 Loss on investments (54,827) (53,335) (1,492) Change in fair value of warrant liabilities 5,168 124,970 (119,802) (Loss) gain on deconsolidation of subsidiaries (42,502) 31,889 (74,391) Other income (expense), net 9,138 7,634 1,504 Total other income (expense), net (28,534) 87,553 (116,087) Loss before income taxes (892,940) (2,121,399) 1,228,459 Income tax benefit (71) (15,027) 14,956 Net loss (892,869) (2,106,372) 1,213,503 Loss attributable to non-controlling interest — (1,443) 1,443 Net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders $ (892,869) $ (2,104,929) $ 1,212,060 (1) R&D and G&A expenses included a significant charge for stock-based compensation expense as a result of the modification of the vesting terms of RSUs and related earnout shares (as further described above in “Modification of Equity Awards in Connection with 83 Table of Contents SRNG Business Combination”).
Biggest changeResults of Operations Comparison of the Years Ended December 31, 2024 and 2023 The following table presents our result of operations for the periods indicated: Year Ended December 31, (in thousands) 2024 2023 Change Cell Engineering revenue $ 173,972 $ 143,531 $ 30,441 Biosecurity revenue: Service 53,071 78,975 (25,904) Product — 28,949 (28,949) Total revenue 227,043 251,455 (24,412) Costs and operating expenses: Cost of Biosecurity service revenue 38,549 46,524 (7,975) Cost of Biosecurity product revenue — 7,481 (7,481) Cost of other revenue 5,999 — 5,999 Research and development (1) 424,061 580,621 (156,560) General and administrative (1) 246,161 385,025 (138,864) Impairment of lease assets — 96,210 (96,210) Goodwill impairment 47,858 — 47,858 Restructuring charges 24,172 — 24,172 Total operating expenses 786,800 1,115,861 (329,061) Loss from operations (559,757) (864,406) 304,649 Other income (expense): Interest income 38,612 57,217 (18,605) Interest expense (94) (93) (1) Loss on equity method investments — (2,635) 2,635 Loss on investments (28,827) (54,827) 26,000 Loss on deconsolidation of subsidiaries (7,013) (42,502) 35,489 Change in fair value of warrant liabilities 5,701 5,168 533 Other income, net 3,870 9,138 (5,268) Total other income (expense) 12,249 (28,534) 40,783 Loss before income taxes (547,508) (892,940) 345,432 Income tax benefit (479) (71) (408) Net loss $ (547,029) $ (892,869) $ 345,840 71 Table of Contents (1) The following table presents the allocation of stock-based compensation expense, inclusive of employer payroll taxes.
Investing Activities Net cash used in investing activities for the year ended December 31, 2023, primarily consisted of purchases of property and equipment of $40.8 million associated with Foundry capacity and capability investments, relinquishment of $43.0 million in cash upon the deconsolidation of Zymergen, offset by $4.4 million in proceeds from the sale of equipment.
Net cash used in investing activities for the year ended December 31, 2023 primarily consisted of purchases of property and equipment of $40.8 million associated with Foundry capacity and capability investments, relinquishment of $43.0 million in cash upon the deconsolidation of Zymergen, offset by $4.4 million in proceeds from the sale of equipment.
Financing Activities Net cash used in financing activities for the year ended December 31, 2023, primarily consisted of principal payments on finance leases and payments of contingent consideration related to business acquisitions.
Net cash used in financing activities for the year ended December 31, 2023 primarily consisted of principal payments on finance leases and payments of contingent consideration related to business acquisitions.
We typically structure Cell Engineering revenue to include some combination of the following: • service fees, which may comprise cash and/or non-cash consideration, in the form of: ◦ upfront payments upon consummation of an agreement or other fixed payments that are generally recognized over our period of performance; ◦ reimbursement for costs incurred for R&D services; ◦ milestone payments upon the achievement of specified technical criteria; plus, • downstream value share payments in the form of: ◦ milestone payments, which may comprise cash and/or non-cash consideration, upon the achievement of specified commercial criteria; ◦ royalties on sales of products from or comprising engineered organisms; ◦ royalties related to cost of goods sold reductions realized by our customers; or, • downstream value share in the form of equity interests in our customer. ◦ downstream value share in the form of equity interest appreciation is not recognized as revenue but is expected to contribute to future cash flows upon liquidation, the amount and timing of which is inherently unpredictable.
We typically structure Cell Engineering revenue to include some combination of the following: • service fees, which may comprise cash and/or non-cash consideration, in the form of: ◦ upfront payments upon consummation of an agreement or other fixed payments that are generally recognized over our period of performance; ◦ reimbursement for costs incurred for R&D services; ◦ milestone payments upon the achievement of specified technical criteria; plus, when applicable, • downstream value share payments in the form of: ◦ milestone payments, which may comprise cash and/or non-cash consideration, upon the achievement of specified commercial criteria; ◦ royalties on sales of products from or comprising engineered organisms; ◦ royalties related to cost of goods sold reductions realized by our customers; or, • downstream value share in the form of equity interests in our customer. ◦ downstream value share in the form of equity interest appreciation is not recognized as revenue but is expected to contribute to future cash flows upon liquidation, the amount and timing of which is inherently unpredictable.
See Note 8 to the consolidated financial statements in Part II, Item 8 of this Annual Report on Form 10-K for more information. Purchase Obligations In August 2023, we entered into a five-year strategic cloud and AI partnership with Google Cloud, which includes minimum annual commitments to purchase cloud hosting services.
See Note 9 to the consolidated financial statements in Part II, Item 8 of this Annual Report on Form 10-K for more information. Purchase Obligations In August 2023, we entered into a five-year strategic cloud and AI partnership with Google Cloud, which includes minimum annual commitments to purchase cloud hosting services.
The activities above incur the following expenses: • laboratory supplies, consumables and related services provided under agreements with third parties and in-licensing arrangements; • personnel compensation and benefits; and • rent, facilities, depreciation, software, professional fees and other direct and allocated overhead expenses. We expense R&D costs as incurred.
The activities above incur the following expenses: • personnel compensation and benefits; • rent, facilities, depreciation, software, professional fees and other direct and allocated overhead expenses; and • laboratory supplies, consumables and related services provided under agreements with third parties and in-licensing arrangements. We expense R&D expenses as incurred.
Generally, the terms of these agreements provide that we receive some combination of: (1) service fees in the form of (i) upfront payments upon consummation of the agreement or other fixed payments, (ii) reimbursement for costs incurred for R&D services and (iii) milestone payments upon the achievement of specified technical criteria, plus (2) downstream value share payments in the form of (i) milestone payments upon the achievement of specified commercial criteria, (ii) royalties on sales of products 79 Table of Contents from or comprising engineered organisms arising from the collaboration or licensing agreement and (iii) royalties related to cost of goods sold reductions realized by our customers.
Generally, the terms of these agreements provide that we receive some combination of: (1) service fees in the form of (i) upfront payments upon consummation of the agreement or other fixed payments, (ii) reimbursement for costs incurred for R&D services and (iii) milestone payments upon the achievement of specified technical criteria, plus (2) downstream value share payments in the form of (i) milestone payments upon the achievement of specified commercial criteria, (ii) royalties on sales of products from or comprising engineered organisms arising from the collaboration or licensing agreement and/or (iii) royalties related to cost of goods sold reductions realized by our customers.
We earn Cell Engineering revenue for our R&D services as well as through a share of the value of products created using our platform.
We earn Cell Engineering revenue for our R&D services as well as generally through a share of the value of products created using our platform.
Revenue Recognition Cell Engineering Revenue For certain Cell Engineering revenue agreements, we recognize revenue over the period of performance using a measure of progress based on costs incurred to date relative to total expected costs (i.e., cost-to-cost method). A significant level of judgment is involved in estimating the total expected costs.
Revenue Recognition Cell Engineering Revenue For certain Cell Engineering revenue contracts, we recognize revenue over the period of performance using a measure of progress based on costs incurred to date relative to total expected costs (i.e., cost-to-cost method). A significant level of judgment is involved in estimating the total expected costs.
These service offerings generally consist of multiple promised goods and services including, but not limited to, sample collection, sample storage and transportation, outsourced laboratory analysis, access to results reported through a web-based portal, analytical reporting of results, and overall program management.
These service offerings generally consist of goods and services including, but not limited to, sample collection, sample storage and transportation, outsourced laboratory analysis, access to results reported through a web-based portal, analytical reporting of results, and overall program management.
See Notes 5 and 16 of our audited consolidated financial statements included elsewhere in this Annual Report on Form 10-K for further details of our investments in and the material terms of our agreements with our Platform Ventures and Structured Partnerships.
See Notes 6 and 16 of our audited consolidated financial statements included elsewhere in this Annual Report on Form 10-K for further details of our investments in and the material terms of our agreements with our Platform Ventures and Structured Partnerships.
Actual results may differ materially from those anticipated in these forward-looking statements as a result of many factors, including those discussed in Item 1A. “Risk Factors” and “Cautionary Note Regarding Forward-Looking Statements” elsewhere in this Annual Report on Form 10-K. 73 Table of Contents Overview Our mission is to make biology easier to engineer.
Actual results may differ materially from those anticipated in these forward-looking statements as a result of many factors, including those discussed in Item 1A. “Risk Factors” and “Cautionary Note Regarding Forward-Looking Statements” elsewhere in this Annual Report on Form 10-K. Overview Our mission is to make biology easier to engineer.
Further, this section of this Form 10-K generally discusses 2023 and 2022 items and year-to-year comparisons between 2023 and 2022. For discussion related to 2021 items and year-to-year comparisons between 2022 and 2021 that are not included in this Form 10-K, please refer to Part II, Item 7.
Further, this section of this Form 10-K generally discusses 2024 and 2023 items and year-to-year comparisons between 2024 and 2023. For discussion related to 2022 items and year-to-year comparisons between 2023 and 2022 that are not included in this Form 10-K, please refer to Part II, Item 7.
The net change in operating assets and liabilities was primarily due to (i) a $50.1 million decrease in accounts receivable from collections of Biosecurity receivables and the end of COVID-19 testing in schools in the third quarter of 2023, (ii) a $10.5 million decrease in prepaid expenses and other current assets primarily from depletion of inventory coinciding with the reduction of Biosecurity product revenue in the third quarter plus the timing of directors and officers insurance payments in the prior year, (iii) a $9.3 million decrease in operating lease right-of-use assets from lease incentives received, (iv) a $16.9 million increase in accrued expenses and other current liabilities primarily from accrued litigation costs, partially offset by (v) a $35.9 million decrease in deferred revenue and (vi) a $22.8 million decrease in operating lease liabilities from rent payments.
The net change in operating assets and liabilities was primarily driven by (i) a $50.1 million decrease in accounts receivable from collections of Biosecurity receivables and the end of COVID-19 testing in schools in 2023, (ii) a $10.5 million decrease in prepaid expenses and other current assets primarily from depletion of inventory coinciding with the reduction of Biosecurity product revenue plus the timing of directors and officers insurance payments in the prior year, (iii) a $9.3 million decrease in operating lease right-of-use assets from lease incentives received, (iv) a $16.9 million increase in accrued expenses and other current liabilities primarily from accrued litigation costs, partially offset by (v) a $35.9 million decrease in deferred revenue and (vi) a $22.8 million decrease in operating lease liabilities from rent payments.
In general, these agreements stipulate that we are entitled to compensation for service revenue as services are performed and for product revenue upon delivery of diagnostic test kits. The timing of revenue recognition depends on the identified performance obligations but is generally recognized ratably over time or as results are reported to the customer.
In general, these agreements stipulate that we are entitled to compensation for service revenue as services are performed, and for product revenue, prior to 2024, upon delivery of diagnostic test kits. The timing of revenue recognition depends on the identified performance obligations but is generally recognized over time or as results are reported to the customer.
We are also engaged in a series of smaller partnerships that generate revenues through biosecurity services and R&D. We generate service revenue through the sale of our end-to-end biomonitoring and bioinformatic support services.
We are also engaged in a series of smaller partnerships that generate revenues through biosecurity services and R&D. We generate service revenue through the sale of our end-to-end biomonitoring and bioinformatics support services.
We view the upfront non-cash consideration as prepayments for licenses which will be granted in the future as we complete mutually agreed upon technical development plans. In these instances, we also receive cash consideration for the R&D services performed by us on a fixed fee or cost-plus basis.
We view the upfront non-cash consideration as prepayments for licenses which will be granted in the future as we complete mutually agreed upon technical development plans. In these instances, we also receive cash consideration for the R&D services 67 Table of Contents performed by us on a fixed fee or cost-plus basis.
Customer arrangements which involve non-cash consideration generally fall into two categories: Platform Ventures and Structured Partnerships. 75 Table of Contents Platform Ventures Platform Ventures enable Ginkgo to partner with leading multinationals and financial investors to form new ventures in identified market segments with potential to benefit from synthetic biology.
Customer arrangements which involve non-cash consideration generally fall into two categories: Platform Ventures and Structured Partnerships. Platform Ventures Platform Ventures enable Ginkgo to partner with leading multinationals and financial investors to form new ventures in identified market segments with potential to benefit from synthetic biology.
In exchange for an equity position in the venture, we contribute license rights to our proprietary cell programming technology and intellectual property, while our partners contribute relevant industry expertise, other resources and venture funding. We also provide R&D services for which we receive cash consideration on a fixed-fee or cost-plus basis. Platform Ventures include: Motif FoodWorks, Inc.
In exchange for an equity position in the venture, we contribute license rights to our proprietary cell programming technology and intellectual property, while our partners contribute relevant industry expertise, other resources and venture funding. We also provide R&D services for which we receive cash consideration on a fixed-fee or cost-plus basis.
As of December 31, 2023, we had federal net operating loss carryforwards of approximately $1.0 billion, of which $139.2 million will begin to expire in 2029 and $884.1 million can be carried forward indefinitely.
As of December 31, 2024, we had federal net operating loss carryforwards of approximately $1.2 billion, of which $139.2 million will begin to expire in 2029 and $1.1 billion can be carried forward indefinitely.
Components of Results of Operations Revenue Cell Engineering Revenue We generate Cell Engineering revenue through the execution of license and collaboration agreements whereby customers obtain license rights to our proprietary technology and intellectual property for use in the development and commercialization of engineered organisms and derived products.
Components of Results of Operations Revenue Cell Engineering Revenue We generate Cell Engineering revenue primarily through license and collaboration agreements, under which customers obtain rights to our proprietary technology and intellectual property for use in the development and commercialization of engineered organisms and derived products.
As of December 31, 2023, we had cash and cash equivalents of $944.1 million which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Annual Report on Form 10-K.
As of December 31, 2024, we had cash and cash equivalents of $561.6 million, which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Annual Report on Form 10-K.
When estimating total expected costs, we make assumptions and estimates regarding the contracted scope of work, tasks required to complete each project, technical and schedule risks associated with the science, the expected duration of each project, and the total amount of internal and 89 Table of Contents external (i.e., subcontractor) resources required.
When estimating total expected costs, we make assumptions and estimates regarding the contracted scope of work, tasks required to complete each project, technical and schedule risks associated with the science, the expected duration of each project, and the total amount of internal and external resources required.
Additionally, we negotiate a value share with our customers (typically in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform.
Additionally, we have historically negotiated a value share with our customers (in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform.
We grant the customer a prepaid Cell Engineering services credit in exchange for the upfront non-cash consideration, which can be drawn down as payment for R&D services performed under mutually agreed upon development plans.
We issued the customer a prepaid Cell Engineering services credit in exchange for the upfront non-cash consideration, which can and has been drawn down as payment for R&D services performed under mutually agreed upon development plans.
Material Cash Requirements We anticipate that our expenditures will exceed our revenue through at least the next 12 months from the date of filing of this Annual Report on Form 10-K, as we: • continue our R&D, activities under existing and new programs and further invest in our Foundry and Codebase; • hire additional personnel and secure facilities to support our expanding R&D efforts; • develop and expand our offerings, including Biosecurity; 87 Table of Contents • upgrade and expand our operational, financial and management systems and support our operations; • acquire and integrate companies, assets or intellectual property that advance our company objectives; and • maintain, expand, and protect our intellectual property.
Material Cash Requirements We anticipate that our expenditures will exceed our revenue through at least the next 12 months from the date of filing of this Annual Report on Form 10-K, as we: • continue our R&D activities under existing and new programs and further invest in our Foundry and Codebase; • develop and expand our offerings, including Biosecurity; • upgrade, expand or adapt our operational, financial and management systems and support our operations; • potentially acquire and integrate companies, assets or intellectual property that advance our company objectives; • maintain, expand, and protect our intellectual property; and • continue our restructuring actions.
(3) Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) due diligence, legal, consulting and accounting fees associated with acquisitions, (ii) post-acquisition employee retention bonuses and severance payments, (iii) the fair value adjustments to contingent consideration liabilities resulting from acquisitions, (iv) acquired intangible assets expensed as in-process research and development, and (v) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs, net of insurance recovery.
(5) Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) due diligence, legal, consulting and accounting fees associated with acquisitions, (ii) post-acquisition employee retention bonuses and severance payments, (iii) the fair value adjustments to contingent consideration liabilities resulting from acquisitions, and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs, net of insurance recovery.
Management’s Discussion and Analysis of Financial Condition and Results of Operations in our 2022 Form 10-K, filed with the United States Securities and Exchange Commission on March 13, 2023. This discussion contains forward-looking statements that reflect our plans, estimates and beliefs that involve risks and uncertainties.
Management’s Discussion and Analysis of Financial Condition 64 Table of Contents and Results of Operations in our 2023 Form 10-K, filed with the United States Securities and Exchange Commission on February 29, 2024. This discussion contains forward-looking statements that reflect our plans, estimates and beliefs that involve risks and uncertainties.
Before the fourth quarter of 2023, we generated product revenue by selling lateral flow assay (“LFA”) diagnostic test kits, polymerase chain reaction (“PCR”) sample collection kits, and pooled test kits associated with COVID-19 tests to customers on a standalone basis.
Prior to 2024, we generated product revenue by selling lateral flow assay (“LFA”) diagnostic test kits, polymerase chain reaction (“PCR”) sample collection kits, and pooled test kits associated with COVID-19 tests to customers on a standalone basis.
Leases We have various noncancelable operating leases for office and laboratory space, with significant leases expiring between 2030 and 2036. As of December 31, 2023 , we have minimum rental commitments under noncancellable operating leases of $43.6 million in 2024 and $387.5 million thereafter.
Leases We have various noncancelable operating leases for office and laboratory space, with significant leases expiring between 2030 and 2036. As of December 31, 2024 , we have minimum rental commitments under noncancellable operating leases of $61.2 million in 2025 and $662.5 million thereafter.
We are building the future bioeconomy with our customers and partners, and we envision the future of biosecurity as a global immune system equipped with the capabilities to prevent, detect, and respond to biological threats.
We are building the future bioeconomy with our customers and partners, and we envision the future of biosecurity as a global immune system equipped with the capabilities to rapidly and reliably identify, monitor, prevent, and mitigate biological threats.
Certain customer agreements contain payment in the form of shares of equity securities or other financial instruments that are convertible into equity upon a triggering event. Any non-cash consideration is measured at the estimated fair value of the non-cash consideration at contract inception.
Certain customer contracts include payment in the form of equity securities or other financial instruments that convert into equity upon a triggering event. Any non-cash consideration is measured at its estimated fair value at contract inception.
Costs and Operating Expenses Cost of Biosecurity Product Revenue Before the fourth quarter of 2023, cost of Biosecurity product revenue consisted of costs associated with the sale of diagnostic and sample collection test kits, which included costs incurred to purchase test kits from third parties.
Cost of Biosecurity Product Revenue Prior to 2024, the cost of Biosecurity product revenue consisted of costs associated with the sale of diagnostic and sample collection test kits, which included costs incurred to purchase test kits from third parties.
While our significant accounting policies are described in more detail in Note 2 to our audited consolidated financial statements appearing elsewhere in this Annual Report on Form 10-K, we believe the following accounting policies used in the preparation of our consolidated financial statements require the most significant judgments and estimates.
The effects of material revisions in estimates, if any, are reflected in our consolidated financial statements prospectively from the date of change in estimates. 77 Table of Contents While our significant accounting policies are described in more detail in Note 2 to our audited consolidated financial statements appearing elsewhere in this Annual Report on Form 10-K, we believe the following accounting policies used in the preparation of our consolidated financial statements require the most significant judgments and estimates.
Biosecurity Revenue We offer biomonitoring and bioinformatic support services internationally as well as domestically. We are currently offering biomonitoring and bioinformatic support services domestically through our partnerships with the CDC and XpresCheck, and internationally through our international programs, including those in Qatar, Rwanda and Ukraine.
Biosecurity Revenue We offer biosecurity services through our two core offerings: Canopy and Horizon. We are currently offering biomonitoring and bioinformatics support services domestically through our partnerships with the CDC and XpresCheck, and internationally through our international programs, including those in Qatar and Ukraine.
Loss on Equity Method Investments Loss on equity method investments includes our share of losses from certain of our equity method investments under the hypothetical liquidation at book value (“HLBV”) method.
Interest Income Interest income consists primarily of interest earned on our cash and cash equivalents. Loss on Equity Method Investments Loss on equity method investments includes our share of losses from certain of our equity method investments under the hypothetical liquidation at book value (“HLBV”) method.
Under this agreement, we are obligated to spend a minimum of $58.0 million over the four-year term, with approximately $17.6 million payable in the next 12 months and $23.0 million thereafter.
Under this agreement, we are obligated to spend a minimum of $58.0 million over the four-year term, with approximately $24.8 million payable in 2025 and $4.8 million thereafter.
Non-cash adjustments primarily consisted of $70.5 million of depreciation and amortization, $229.9 million of stock-based compensation, $57.5 million loss on investments including equity method investments, $9.2 million loss on the change in fair value of contingent consideration liabilities, $28.3 million of non-cash lease expense, $121.4 million in impairments of long-lived assets, and $42.5 million loss on deconsolidation of Zymergen. 88 Table of Contents Net cash used in operating activities for the year ended December 31, 2022 consisted of net loss of $2.1 billion, adjusted for net change in operating assets and liabilities of $37.0 million and non-cash charges of $1.9 billion.
Non-cash adjustments primarily consisted of $70.5 million of depreciation and amortization, $229.9 million of stock-based compensation, $57.5 million loss on investments including equity method investments, $9.2 million loss on the change in fair value of contingent consideration liabilities, $28.3 million of non-cash lease expense, $121.4 million in impairments of long-lived assets, and $42.5 million loss on deconsolidation of Zymergen.
We define Adjusted EBITDA as EBITDA adjusted for stock-based compensation expense, gain or loss on equity method investments, gain or loss on investments, change in fair value of warrant liabilities, gain or loss on deconsolidation of subsidiaries, transaction and integration costs associated with planned, completed or terminated mergers and acquisitions, including related litigation costs, acquired in-process research and development expenses, impairment charges, costs associated with the Zymergen Bankruptcy, and other income and expenses.
We define Adjusted EBITDA as EBITDA adjusted for stock-based compensation expense, gain or loss on equity method investments, gain or loss on investments, change in fair value of warrant liabilities, gain or loss on deconsolidation of subsidiaries, transaction and integration costs associated with planned, completed or terminated mergers and acquisitions, including related litigation costs, restructuring and impairment charges (inclusive of impairments of goodwill and long-lived assets), costs associated with the bankruptcy filing of our former subsidiary, Zymergen (the “Zymergen 74 Table of Contents Bankruptcy”), and certain other income and expenses.
As of December 31, 2023, the remaining aggregate commitment was $286.1 million, with approximately $14.4 million payable in the next 12 months and $271.7 million thereafter. In March 2022, we entered into a four-year noncancelable supply agreement with Twist for the purchase of diverse products including synthetic DNA.
As of December 31, 2024, the remaining aggregate commitment was $279.3 million, with approximately $44.3 million payable in 2025 and $235.0 million thereafter. In March 2022, we entered into a four-year noncancelable supply agreement with Twist for the purchase of diverse products including synthetic DNA.
Actual results may differ from these estimates under different assumptions or conditions. On an ongoing basis, we evaluate our judgments and estimates in light of changes in circumstances, facts and experience. The effects of material revisions in estimates, if any, are reflected in our consolidated financial statements prospectively from the date of change in estimates.
Actual results may differ from these estimates under different assumptions or conditions. On an ongoing basis, we evaluate our judgments and estimates in light of changes in circumstances, facts and experience.
Cell Engineering revenue also includes transactions with Startup Structured Partnerships where, as part of these transactions, we received upfront non-cash consideration in the form of current equity interests or financial instruments that are convertible into equity upon a triggering event.
These arrangements are further described in Notes 6 , 7 , 16 and 20 of our audited consolidated financial statements included elsewhere in this Annual Report on Form 10-K.Cell Engineering revenue also includes transactions with Startup Structured Partnerships where, as part of these transactions, we received upfront non-cash consideration in the form of current equity interests or financial instruments that are convertible into equity upon a triggering event.
The impact of the modification on stock-based compensation expense has significantly diminished by the end of 2023. General and Administrative Expenses General and administrative (“G&A”) expenses consist primarily of costs for personnel in executive, business development, finance, human resources, legal and other corporate administrative functions.
General and Administrative Expenses General and administrative (“G&A”) expenses consist primarily of costs for personnel in executive, business development, finance, human resources, legal and other corporate administrative functions.
In 2023 and 2022, we entered into 6 and 11 Startup Structured Partnerships, respectively, and received prepayments of service fees in the form of equity securities or convertible financial instruments in the amount of $18.9 million and $30.7 million, respectively, that is recognized as revenue over our period of performance. Our Legacy Structured Partnerships are described below: Genomatica, Inc.
In 2024, we did not enter into 66 Table of Contents any new Startup Structured Partnerships. In 2023, we entered into six Startup Structured Partnerships and received prepayments of service fees in the form of equity securities or convertible financial instruments in the amount of $18.9 million that is recognized as revenue over our period of performance.
The first, critical step in realizing this future is to build a robust early warning system for biological threats—this is the primary focus of Ginkgo’s Biosecurity business. Our biosecurity offering includes biomonitoring and bioinformatic support services internationally as well as domestically.
The first, critical step in realizing this future is to build a robust early warning system for biological threats—this is the primary focus of Ginkgo’s Biosecurity business. 65 Table of Contents Our primary biosecurity customers are governments.
As of December 31, 2023, we had state net operating loss carryforwards of approximately $998.2 million, of which $869.2 million will begin to expire in 2030 and $129.0 million can be carried forward indefinitely. As of December 31, 2023, we had foreign net operating losses of approximately $1.7 million, which can be carried forward indefinitely.
As of December 31, 2024, we had state net operating loss carryforwards of approximately $1.2 billion, of which $991.7 million will begin to expire in 2030 and $162.3 million can be carried forward indefinitely. As of December 31, 2024, we had federal research and development tax credit carryforwards of approximately $37.7 million, which will begin to expire in 2029.
These metrics may change or be substituted for additional or different metrics as our business develops.
We may in the future report on key business metrics, which metrics may change or be substituted for additional or different metrics as our business develops.
Provision for Income Taxes Income taxes are recorded in accordance with ASC 740 , Income Taxes (“ASC 740”), which provides for deferred taxes using an asset and liability approach. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our audited consolidated financial statements or tax returns.
We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our audited consolidated financial statements or tax returns.
(2) For the year ended December 31, 2023, includes $25.2 million impairment loss on lab equipment and $96.2 million impairment loss on a right-of-use asset and the related leasehold improvements associated with an exited Zymergen leased facility.
Impairment of Lease Assets In 2023, we recognized an impairment loss of $96.2 million related to a right-of-use asset and the associated leasehold improvements for an exited Zymergen leased facility.
Cash Flows The following table provides information regarding our cash flows for each period presented: Year Ended December 31, (in thousands) 2023 2022 Net cash (used in) provided by: Operating activities $ (295,500) $ (252,198) Investing activities (80,693) (67,394) Financing activities (3,216) 95,337 Effect of exchange rate changes (588) 908 Net decrease in cash, cash equivalents and restricted cash $ (379,997) $ (223,347) Operating Activities Net cash used in operating activities for the year ended December 31, 2023 consisted of net loss of $892.9 million, adjusted for net change in operating assets and liabilities of $29.8 million and non-cash charges of $567.5 million.
Cash Flows The following table provides information regarding our cash flows for each period presented: Year Ended December 31, (in thousands) 2024 2023 Net cash used in: Operating activities $ (319,585) $ (295,500) Investing activities (62,236) (80,693) Financing activities (1,739) (3,216) Effect of exchange rate changes (281) (588) Net decrease in cash, cash equivalents and restricted cash $ (383,841) $ (379,997) 76 Table of Contents Operating Activities Net cash used in operating activities for the year ended December 31, 2024 consisted of a net loss of $547.0 million, adjusted for a net decrease in cash due to changes in operating assets and liabilities of $89.7 million and non-cash charges of $317.1 million.
This includes costs incurred for sample collection equipment and materials, outsourced laboratory analysis, access to results reported through our proprietary web-based portal, and reporting of results to public authorities. 80 Table of Contents Additionally, the cost of Biosecurity service revenue includes direct labor cost associated with bioinformatics, lab network management, delivery logistics, and customer support.
Costs and Operating Expenses Cost of Biosecurity Service Revenue The cost of Biosecurity service revenue consists of costs related to our biomonitoring and bioinformatics support services. This includes costs incurred for sample collection equipment and materials, outsourced laboratory analysis, access to results reported through our proprietary web-based portal, and reporting of results to government and non-government customers.
Research and Development Expenses The nature of our business, and primary focus of our activities, generates a significant amount of R&D expenses. R&D expenses represent costs incurred by us for the following: • development, operation, expansion and enhancement of our Foundry and Codebase; and • development of new offerings, such as Biosecurity.
R&D expenses represent costs incurred by us for the following: • development, operation, expansion and enhancement of our Foundry and Codebase; 68 Table of Contents • costs incurred to deliver our end-to-end cell engineering solutions offering to customers; and • development of new offerings, such as Biosecurity.
As we add new programs, our portfolio of programs with this “downstream” value potential grows. 74 Table of Contents With a mission to make biology easier to engineer, we have always recognized the need to invest in biosecurity as a key component of our platform.
In addition, we offer support services with fixed fees covering the support periods. Biosecurity With a mission to make biology easier to engineer, we have always recognized the need to invest in biosecurity as a key component of our platform.
Other Income (Expense), Net Other income (expense), net primarily consists of sublease rent income, changes in fair value of notes receivable that we elected to account for under the fair value option and loss on disposal of equipment.
Other Income, Net Other income, net primarily consists of sublease rent income and changes in fair value of notes receivable that we elected to account for under the fair value option. Provision for Income Taxes Income taxes are recorded in accordance with ASC 740 , Income Taxes , which provides for deferred taxes using an asset and liability approach.
Liquidity and Capital Resources Sources of Liquidity Upon the closing of the SRNG Business Combination in September 2021, we received net proceeds totaling approximately $1,509.6 million, inclusive of $760.0 million from investments from certain accredited investors for 76 million shares of our Class A common stock at a price of $10.00 per share.
Accordingly, all common shares presented herein have been retrospectively adjusted to reflect the reverse stock split. Sources of Liquidity Upon the closing of our merger with SRNG in September 2021, we received net proceeds totaling approximately $1.5 billion, inclusive of $760.0 million from investments from certain accredited investors for 1.9 million shares of our Class A common stock.
Royalties did not comprise a material amount of our revenue during any of the periods presented. Cell Engineering revenue includes transactions with Platform Ventures and Legacy Structured Partnerships where, as part of these transactions, we received an equity interest in such entities.
There has been no material impact on our revenue recognition policies to date from the announced changes in our new commercial terms and Cell Engineering offerings. Cell Engineering revenue includes transactions with Platform Ventures and Legacy Structured Partnerships where, as part of these transactions, we received an equity interest in such entities.
Under the HLBV method, we absorb losses as a common unit holder prior to preferred unit holders due to a substantive profit-sharing agreement where the preferred unit holders receive preferential distribution rights. Because we have no commitment to fund the losses of our equity method investees, no further losses on these investments were recognized during the periods presented.
The 2023 loss represented our share of losses from certain equity method investees resulting from the application of the HLBV method. Under the HLBV method, as a common unit holder, we absorb losses before preferred unit holders due to a substantive profit-sharing agreement that grants preferred unit holders preferential distribution rights.
Change in Fair Value of Warrant Liabilities Change in fair value of warrant liabilities includes the change in fair value of private placement warrants (“Private Placement Warrants”) and publicly traded warrants (“Public Warrants”), which are classified as liabilities and were assumed as part of the SRNG Business Combination. Warrant liabilities are marked to market at each balance sheet date.
Change in Fair Value of Warrant Liabilities The change in fair value of warrant liabilities reflects adjustments to the fair value of private placement warrants (“Private Placement Warrants”) and warrants formerly publicly traded on the NYSE (“Public Warrants”). These warrants, classified as liabilities, were assumed as part of our merger with Soaring Eagle Acquisition Corp.
We evaluate our measure of progress to recognize revenue for these agreements at each reporting date and, as necessary, adjust the measure of progress and related revenue recognition. We also evaluate contract modifications and amendments to determine whether any changes should be accounted for prospectively or on a cumulative catch-up basis.
If a material right is identified, the option is treated as a separate performance obligation, and the revenue allocated to the option is deferred until the option is either exercised or expires. We also evaluate contract modifications and amendments to determine whether any changes should be accounted for as a separate contract, prospectively or on a cumulative catch-up basis.
The change in fair value of warrant liabilities is primarily driven by changes in the value of our common stock. Increases or decreases in the value of our common stock results in a loss or gain, respectively, on the change in fair value of warrant liabilities.
Increases or decreases in the value of our common stock result in a loss or gain, respectively, in the fair value of warrant liabilities. There was substantially no value related to these warrant liabilities as of December 31, 2024.
Impairment of Long-Lived Assets We review our long-lived assets for impairment whenever events or changes in circumstances indicate that the carrying value of an asset may not be recoverable. Recoverability is measured by comparing the book values of the assets to the expected future net undiscounted cash flows that the assets are expected to generate.
Changes in these assumptions can materially affect the fair value of the non-cash consideration and, consequently, the total revenue recognized for the contract. Impairment of Long-Lived Assets We review our long-lived assets and asset groups for impairment whenever events or changes in circumstances indicate that the carrying value of the assets may not be recoverable.
As of December 31, 2023, we had federal research and development tax credit carryforwards of approximately $40.4 million, which will begin to expire in 2029. As of December 31, 2023, we also had state research and development and investment tax credit carryforwards of approximately $30.1 million, which will begin to expire in 2030.
As of December 31, 2024, we also had state research and development and investment tax credit carryforwards of approximately $30.2 million, which will begin to expire in 2030. 70 Table of Contents Income taxes are determined at the applicable tax rates adjusted for non-deductible expenses, R&D tax credits and other permanent differences.
Additionally, services revenue increased due to the launch of New Programs and was partially offset by the completion of certain programs. As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration.
As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration. Cell Engineering revenue recognized relating to non-cash consideration increased from $48.5 million in 2023 to $61.4 million in 2024.
For equity securities and financial instruments received that are not actively traded, we generally engage a third-party valuation specialist to determine the estimated fair value of the upfront non-cash consideration. The fair value is generally determined based on a recent round of financing or by using a scenario-based valuation model.
For equity securities and financial instruments that are not actively traded, we generally determine the estimated fair value by referencing a recent financing round or utilizing a scenario-based valuation model. Significant unobservable inputs are used in these valuations, including expectations regarding future financings of the customer, scenario dates and probabilities, expected volatility, discount rates, and recovery rates.
(Loss) Gain on Deconsolidation of Subsidiaries In 2023, we recorded a $42.5 million loss on our deconsolidation of Zymergen following Zymergen's bankruptcy filing in October 2023. In 2022, we recorded a $31.9 million gain on our deconsolidation of Verb and Ayana equal to the fair value of our retained interest in each entity measured as of the deconsolidation date.
Loss on Deconsolidation of Subsidiaries In 2024, we recorded a $7.0 million loss on the deconsolidation of our former foreign subsidiary Altar as a result of a sale of this business. In 2023, we recorded a $42.5 million loss on the deconsolidation of Zymergen following Zymergen's bankruptcy filing in October 2023.
We compensate for these limitations by providing a reconciliation of EBITDA and Adjusted EBITDA to their most directly comparable GAAP financial measure. 86 Table of Contents The following table reconciles net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders to EBITDA and Adjusted EBITDA for the years ended December 31, 2023 and 2022, respectively: Year Ended December 31, (in thousands) 2023 2022 Net loss attributable to Ginkgo Bioworks Holdings, Inc. stockholders $ (892,869) $ (2,104,929) Interest income (57,217) (20,262) Interest expense 93 106 Income tax benefit (71) (15,027) Depreciation and amortization 70,507 42,552 EBITDA (879,557) (2,097,560) Stock-based compensation (1) 234,908 1,940,920 Impairment of long-lived assets (2) 121,404 — Merger and acquisition related expenses (3) 70,771 46,229 Loss on investments 54,827 53,335 Loss (gain) on deconsolidation of subsidiaries 42,502 (31,889) Loss on equity method investments (4) 2,635 45,315 Change in fair value of warrant liabilities (5,168) (124,970) Change in fair value of notes receivable 2,295 (4,153) Adjusted EBITDA $ (355,383) $ (172,773) (1) For the years ended December 31, 2023 and 2022, includes $5.0 million and $10.3 million, respectively, in related employer payroll taxes.
A reconciliation of EBITDA and Adjusted EBITDA to net loss, the most directly comparable GAAP financial measure, is presented below: Year Ended December 31, (in thousands) 2024 2023 Net loss (1) $ (547,029) $ (892,869) Interest income (38,612) (57,217) Interest expense 94 93 Income tax benefit (479) (71) Depreciation and amortization 63,020 70,507 EBITDA (523,006) (879,557) Stock-based compensation (2) 115,299 234,908 Impairment expense (3) 53,654 121,404 Restructuring charges (4) 24,172 — Merger and acquisition related expenses (5) 4,417 61,189 Loss on equity method investments — 2,635 Loss on investments 28,827 54,827 Loss on deconsolidation of subsidiaries 7,013 42,502 Change in fair value of warrant liabilities (5,701) (5,168) Change in fair value of convertible notes 2,014 2,295 Adjusted EBITDA $ (293,311) $ (364,965) (1) All periods include non-cash revenue when earned, including $45.4 million in the year ended December 31, 2024, recognized pursuant to the termination of revenue contracts with Motif.
Total stock-based compensation expense, inclusive of employer payroll taxes, was allocated as follows (in thousands): Year Ended December 31, 2023 2022 Research and development $ 148,861 $ 738,821 General and administrative 86,047 1,202,099 Total $ 234,908 $ 1,940,920 Cell Engineering Revenue Cell Engineering revenue remained relatively flat in 2023 compared to 2022, decreasing by $0.1 million.
Year Ended December 31, (in thousands) 2024 2023 Research and development $ 57,723 $ 148,861 General and administrative 57,576 86,047 Total $ 115,299 $ 234,908 Cell Engineering Revenue Cell Engineering revenue was $174.0 million in 2024, compared to $143.5 million in 2023, an increase of $30.4 million.
Our non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for performance measures calculated in accordance with GAAP.
In 2024, we updated our definition of Adjusted EBITDA to no longer exclude the impact of acquired in-process research and development expenses. Accordingly, the comparable 2023 period has been recast to conform to the revised definition. Our non-GAAP financial measures have limitations as analytical tools and should not be considered in isolation or as a substitute for GAAP performance measures.
The net change in operating assets and liabilities was primarily due to (i) a decrease in accounts receivable of $55.0 million from increased Biosecurity collections, partially offset by (ii) increase in prepaid expenses and other current assets of $8.5 million primarily due to prepaid insurance for directors and officers, (iii) decrease in accounts payable of $10.8 million due to timing of invoices, (iv) decrease in accrued expenses and other current liabilities of $39.6 million, (v) decrease in deferred revenue of $36.4 million, and (vi) lease incentives received of $13.2 million offset by (vii) $10.8 million decrease in operating lease liabilities from rent payments.
The net change in operating assets and liabilities was primarily driven by a $40.4 million decrease in accrued expenses and other current liabilities primarily due to the payment or release of restructuring-related accruals and litigation costs, a $68.6 million decrease in deferred revenue primarily from a one-time release of a deferred revenue balance associated with a terminated customer contract, and a $14.9 million decrease in operating lease liabilities from rent payments, partially offset by a $23.5 million decrease in operating lease right-of-use assets from lease incentives received and a $10.1 million decrease in prepaid expenses and other current assets, primarily driven by the derecognition of an insurance receivable and a reduction in contract renewals resulting from our restructuring actions.
We anticipate that our G&A expenses attributable to organic business activities will either remain consistent or decline in 2024 as compared to 2023, reflecting a stabilization in our operational overhead. Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, and other non-organic growth initiatives.
We expect that our G&A expenses will either remain consistent or decline in 2025 as compared to 2024, reflecting the stabilization of our operational overhead and the impact of our restructuring actions. However, our G&A expenses could increase in 2025 due to employee incentive programs offered or additional costs and expenses arising from these restructuring actions.
Other Income (Expense), Net Other income (expense), net increased $1.5 million in 2023 compared to 2022 primarily due to a $6.6 million unfavorable change in fair value of notes receivable offset by a $6.0 million increase in sublease rent income from Zymergen subleases prior to deconsolidation and a $2.6 million decrease in loss on disposal of equipment.
Other Income, Net Other income, net was $3.9 million in 2024, compared to $9.1 million in 2023, a decrease of $5.3 million. This decrease was primarily due to reduced sublease rent income following the deconsolidation of Zymergen.
The impact of the modification on stock-based compensation expense has significantly diminished by the end of 2023. Impairment of Lease Assets Impairment of lease assets relates to impairment losses recognized on a right-of-use asset and the related leasehold improvements associated with a Zymergen facility that we exited in the third quarter of 2023.
Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, and other inorganic growth initiatives. Impairment of Lease Assets Impairment of lease assets relates to impairment losses recognized on a right-of-use asset and the related leasehold improvements associated with exited leased facilities.
These arrangements are further described in Notes 5 , 6 , 16 and 20 of our audited consolidated financial statements included elsewhere in this Annual Report on Form 10-K.
Our recent strategic business and asset acquisitions are described in detail in Note 4 of our audited consolidated financial statements included elsewhere in this Annual Report on Form 10-K. Generating Economic Value Through Cell Programs Our cell engineering platform is a key enabling technology and source of intellectual property for our customers’ products.
In September 2023, Zymergen exited and ceased use of a leased facility which resulted in a $96.2 million impairment to reduce the carrying value of the right-of-use asset and the related leasehold improvements to their estimated fair value.
During 2023, Zymergen permanently ceased use of and vacated the leased space, which triggered an impairment analysis and resulted in a write-down of the carrying value of the assets to their estimated fair value. Goodwill Impairment In 2024, we recorded goodwill impairment expense of $47.9 million related to our Cell Engineering reporting unit, further discussed within “Critical Accounting Estimates” below.