Ginkgo Bioworks Holdings, Inc.

Previous wording

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 U.S. Centers for Disease Control and Prevention and XpresCheck, and internationally through our international programs, including those in Qatar and Ukraine. We are also engaged in a series of smaller partnerships that generate revenues through biosecurity services and R&D.

Current wording

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 U.S. Centers for Disease Control and Prevention and XpresCheck, and internationally through our international programs. We are also engaged in a series of smaller partnerships that generate revenues through biosecurity services and R&D.

Previous wording

We expense R&D costs as incurred. Our R&D expenses were lower in the first quarter of 2025 compared to the first quarter of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024 as we rationalize our current development programs and prioritize our investments in our Foundry, Codebase and cell engineering tools offerings. We expect that our R&D 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 R&D expenses could increase in 2025 due to employee incentive programs offered or additional costs and expenses arising from these restructuring actions. The nature, timing, and estimated costs required to support our growth will be dependent on advances in technology, our ability to attract new customers, and the rate of market penetration within our existing customer industries.

Current wording

We expense R&D costs as incurred. Our R&D expenses were lower in the first half of 2025 compared to the first half of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024 as we rationalize our current development programs and prioritize our investments in our Foundry, Codebase and cell engineering tools offerings. We expect that our R&D 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 R&D expenses could increase in 2025 due to employee incentive programs offered or additional costs and expenses arising from these restructuring actions. The nature, timing, and estimated costs required to support our growth will be dependent on advances in technology, our ability to attract new customers, and the rate of market penetration within our existing customer industries.

Previous wording

Our G&A expenses were lower in the first quarter of 2025 compared to the first quarter of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024, as we began reducing our operational overhead. 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. Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, and other inorganic growth initiatives.

Current wording

Our G&A expenses were lower in the first half of 2025 compared to the first half of 2024, primarily due to our restructuring plan announced and commenced in the second quarter of 2024, as we began reducing our operational overhead. 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. Conversely, we intend to maintain a strategic and opportunistic approach regarding inorganic G&A expenses arising from mergers, acquisitions, and other inorganic growth initiatives.

Previous wording

Other income (expense), 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.

Current wording

Other income (expense), net primarily consists of changes in the fair value of notes receivable that we elected to account for under the fair value option and sublease rent income for the comparative periods in 2024.

Previous wording

Comparison of the Three Months Ended March 31, 2025 and 2024

Current wording

Comparison of the Three and Six Months Ended June 30, 2025 and 2024

Previous wording

Cell Engineering revenue was $38.2 million in the three months ended March 31, 2025, compared to $27.9 million in the three months ended March 31, 2024, an increase of $10.3 million. This increase was primarily due to the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc. (“BiomEdit”) contract in the first quarter of 2025 (see Note 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q).

Current wording

Cell Engineering revenue was $77.4 million for the six months ended June 30, 2025, compared to $64.1 million for the six months ended June 30, 2024, an increase of $13.3 million. This increase was primarily due to the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc.

Previous wording

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 $3.8 million in the three months ended March 31, 2024 to $8.7 million in the three months ended March 31, 2025, primarily due to the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025, partially offset by lower non-cash revenue from other customers.

Current wording

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 decreased from $8.2 million for the three months ended June 30, 2024 to $1.2 million for the three months ended June 30, 2025, and from $12.1 million for the six months ended June 30, 2024 to $9.9 million for the six months ended June 30, 2025, primarily due to the recognition of $4.5 million from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024 and lower non-cash revenue from other customers, offset by the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025.

Previous wording

The cost of Biosecurity revenue was $8.0 million in the three months ended March 31, 2025, compared to $9.2 million in the three months ended March 31, 2024, a decrease of $1.2 million. This decrease was primarily due to cost reductions implemented during the first quarter of 2025 as well as timing of revenue recognition.

Current wording

The cost of Biosecurity revenue was $9.4 million for the three months ended June 30, 2025, compared to $11.8 million for the three months ended June 30, 2024, a decrease of $2.4 million. This decrease was primarily due to cost reductions implemented during the first quarter of 2025 as well as a reduction in activities supporting a program with the U.S. government.

Previous wording

The cost of other revenue was $4.1 million in three months ended March 31, 2025 and zero in the three months ended March 31, 2024. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which began in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.

Current wording

The cost of other revenue was $5.4 million for the three months ended June 30, 2025, compared to $1.9 million for the three months ended June 30, 2024, an increase of $3.5 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which began in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.

Previous wording

Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform, which includes our Foundry and Codebase assets, to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $30.7 million and $62.2 million for the three months ended March 31, 2025 and 2024, respectively. We also acquired and expensed in-process research and development primarily through the issuance of our equity, aggregating to zero and $16.9 million for the three months ended March 31, 2025 and 2024, respectively. Our remaining research and development costs are comprised primarily of rent and related facilities costs, information technology costs, depreciation pertaining to facilities and equipment, laboratory consumables, contract services and routine costs and fees.

Current wording

Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform, which includes our Foundry and Codebase assets, to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $23.7 million and $58.3 million for the three months ended June 30, 2025 and 2024, respectively, and $54.4 million and $120.5 million for the six months ended June 30, 2025 and 2024, respectively. We also acquired and expensed in-process research and development primarily through the issuance of our equity, aggregating to zero and $3.0 million for the three months ended June 30, 2025 and 2024, respectively, and zero and

Previous wording

Research and development expenses were $70.9 million for the three months ended March 31, 2025, compared to $136.5 million for the three months ended March 31, 2024, a decrease of $65.5 million. This decrease was primarily driven by reductions in stock-based compensation expense of $14.9 million (inclusive of employer payroll taxes), $16.9 million in acquired in-process research and development, $16.6 million in personnel-related compensation and benefits expenses, $6.6 million in rent and facilities expenses, $5.7 million in information technology expenses, $5.2 million in laboratory supplies, $2.3 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), and $3.5 million in other operating expenses. These decreases were partially offset by an increase of $6.2 million in outside services, primarily due to a loss recorded under a supply agreement related to a shortfall in meeting a minimum annual purchase commitment.

Current wording

Research and development expenses were $53.4 million for the three months ended June 30, 2025, compared to $134.2 million for the three months ended June 30, 2024, a decrease of $80.9 million. This decrease was primarily driven by reductions of $23.0 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $15.7 million in rent and facilities expenses, $12.0 million in stock-based compensation expense (inclusive of employer payroll taxes), $8.4 million in laboratory supplies, $5.9 million in information technology expenses, $3.0 million in acquired in-process research and development expense, $2.9 million in depreciation and amortization, $2.2 million in outside services, $1.8 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), and $6.0 million in other operating expenses.

Previous wording

General and administrative expenses were $49.0 million for the three months ended March 31, 2025, compared to $70.3 million for the three months ended March 31, 2024, a decrease of $21.2 million. This decrease was primarily driven by reductions in stock-based compensation expense of $8.4 million (inclusive of employer payroll taxes), $12.3 million in professional fees, $5.7 million in personnel-related compensation and benefits expenses, $2.3 million in temporary labor and contractors, and $4.1 million in other operating expenses. These decreases were partially offset by an increase of $11.6 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.

Current wording

General and administrative expenses were $43.3 million for the three months ended June 30, 2025, compared to $66.3 million for the three months ended June 30, 2024, a decrease of $23.0 million. This decrease was primarily driven by reductions of $9.4 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $6.1 million in earnout remeasurement expenses, $6.1 million in professional fees, $6.0 million of stock-based compensation expense (inclusive of employer payroll taxes), $1.9 million in temporary labor and contractors, and $5.2 million in other operating expenses. These decreases were partially offset by an increase of $11.6 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.

Previous wording

In the three months ended March 31, 2025, we incurred restructuring charges of $5.3 million in connection with our restructuring plan, which was announced and commenced in the second quarter of 2024, primarily affecting the Cell Engineering segment. These charges primarily consisted of employee termination costs from the reduction in force. See

Current wording

Restructuring charges were $3.7 million and $17.1 million for the three months ended June 30, 2025 and 2024, respectively, and $8.9 million and $17.1 million for the six months ended June 30, 2025 and 2024, respectively. Restructuring charges relate to our restructuring plan, which was announced and commenced in the second quarter of 2024, primarily affecting the Cell Engineering segment. These charges primarily consisted of employee termination costs from the reduction in force. See Note 3 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details.

Previous wording

Interest income, net was $6.1 million in the three months ended March 31, 2025, compared to $11.7 million in the three months ended March 31, 2024, a decrease of $5.6 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Current wording

Interest income, net was $6.1 million for the three months ended June 30, 2025, compared to $10.3 million for the three months ended June 30, 2024, a decrease of $4.2 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Previous wording

Loss on investments was $3.7 million and $2.5 million in the three months ended March 31, 2025 and 2024, respectively. The $1.1 million increase was primarily driven by fluctuations in the stock prices of marketable equity securities, partially offset by lower impairment losses on our non-marketable equity investments in privately held companies compared to the same period in 2024. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable.

Current wording

Loss on investments was $0.2 million and $6.8 million for the three months ended June 30, 2025 and 2024, respectively, and $3.9 million and $9.4 million for the six months ended June 30, 2025 and 2024, respectively. The change was primarily driven by fluctuations in the stock prices of marketable equity securities, partially offset by lower impairment losses on our non-marketable equity investments in privately held companies, compared to the same periods in 2024. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable.

Previous wording

The change in fair value of warrant liabilities was zero for the three months ended March 31, 2025, compared to a gain of $0.9 million for the three months ended March 31, 2024. The fair value of warrant liabilities is primarily driven by fluctuations in the value of our common stock. An increase or decrease in the value of our common stock results in a loss or gain, respectively, in the fair value of warrant liabilities. As of March 31, 2025, these warrant liabilities had substantially no value.

Current wording

The change in fair value of warrant liabilities was zero for both the three and six months ended June 30, 2025, compared to gains of $3.2 million and $4.2 million for the three and six months ended June 30, 2024, respectively. The fair value of warrant liabilities is primarily driven by fluctuations in the value of our common stock. An increase or decrease in the value of our common stock results in a loss or gain, respectively, in the fair value of warrant liabilities. As of June 30, 2025, these warrant liabilities had substantially no value.

Previous wording

We recorded a net other expense amount of $4.3 million in the three months ended March 31, 2025, compared to a net other income amount of $2.0 million in the three months ended March 31, 2024, a decrease of $6.3 million. This decrease was primarily due to a loss on the change in fair value of a note receivable accounted for under the fair value option recorded in the first quarter of 2025.

Current wording

We recorded a net other expense amount of $5.2 million for the six months ended June 30, 2025, compared to a net other income amount of $1.2 million for the six months ended June 30, 2024, a decrease of $6.4 million. This decrease was primarily due to losses on the change in fair value of a note receivable accounted for under the fair value option recorded in 2025.

Previous wording

(1)All periods include non-cash revenue when earned, including $7.5 million recognized in the three months ended March 31, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.

Current wording

(1)All periods include non-cash revenue when earned, including $7.5 million recognized in the six months ended June 30, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.

Previous wording

(2)Includes $0.4 million and $1.6 million in employer payroll taxes for the three months ended March 31, 2025 and 2024, respectively.

Current wording

(2)Includes $0.3 million and $1.1 million in employer payroll taxes for the three months ended June 30, 2025 and 2024, respectively, and $0.6 million and $2.7 million for the six months ended June 30, 2025 and 2024, respectively.

Previous wording

(4)Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero and $16.9 million for the three months ended March 31, 2025 and 2024, respectively.

Current wording

(4)Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero and $3.0 million for the three months ended June 30, 2025 and 2024, respectively, and zero and $19.8 million for the six months ended June 30, 2025 and 2024, respectively.

Previous wording

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. As of March 31, 2025, we had cash and cash equivalents and marketable securities of $516.9 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 Quarterly Report on Form 10-Q.

Current wording

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. As of June 30, 2025, we had cash and cash equivalents and marketable securities of $473.7 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 Quarterly Report on Form 10-Q.

Previous wording

•develop and expand our offerings;

Current wording

•develop and expand our tools offerings;

Previous wording

•upgrade, expand or adapt our operational, financial and management systems and support our operations;

Current wording

•upgrade or adapt our operational, financial and management systems and support our operations;

Previous wording

Net cash used in operating activities for the three months ended March 31, 2025 consisted of a net loss of $91.0 million, adjusted for net change in operating assets and liabilities of $11.6 million and non-cash charges of $51.0 million. The net change in operating assets and liabilities was primarily due to (i) a $12.5 million decrease in deferred revenue primarily from a one-time release of a deferred revenue balance associated with a terminated customer contract, (ii) a $4.8 million decrease in operating lease liabilities from rent payments, and (iii) a $4.7 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $6.4 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation under a supplier agreement, and (v) a $3.7 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $20.4 million of stock-based compensation expense, $15.4 million of depreciation and amortization, $7.4 million non-cash lease expense, a $4.0 million change in fair values of various assets and liabilities, and a $3.7 million loss on investments.

Current wording

Net cash used in operating activities for the six months ended June 30, 2025 consisted of a net loss of $151.3 million, adjusted for net change in operating assets and liabilities of $34.3 million and non-cash charges of $93.8 million. The net change in operating assets and liabilities was primarily due to (i) a $23.7 million decrease in deferred revenue primarily from one-time releases of deferred revenue balances associated with terminated customer contracts and the recognition of previously deferred revenue, (ii) a $11.6 million decrease in operating lease liabilities from rent payments, and (iii) a $0.4 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $5.1 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation under a supplier agreement, and (v) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $42.7 million of stock-based compensation expense, $31.2 million of depreciation and amortization, $14.9 million non-cash lease expense, a $1.1 million change in fair values of various assets and liabilities, and a $4.0 million loss on investments.

Previous wording

Net cash used in operating activities for the three months ended March 31, 2024 consisted of a net loss of $165.9 million, adjusted for a net change in operating assets and liabilities of $0.3 million and non-cash charges of $76.3 million. The net change in operating assets and liabilities was primarily due to (i) a $10.9 million increase in accounts payable, accrued expenses and other current liabilities and (ii) a $6.8 million increase in accounts receivable, partially offset by (iii) a $4.1 million decrease in operating lease liabilities from rent payments and (iv) a $2.9 million decrease in deferred revenue. Non-cash adjustments primarily consisted of $40.8 million of stock-based compensation expense, $16.8 million of in-process research and development expense from asset acquisitions, $12.9 million of depreciation and amortization, and $5.6 million of non-cash lease expense.

Current wording

Net cash used in operating activities for the six months ended June 30, 2024 consisted of a net loss of $383.1 million, adjusted for net change in operating assets and liabilities of $6.2 million and non-cash charges of $203.3 million. The net change in operating assets and liabilities was primarily due to (i) a $10.9 million increase in accounts payable, accrued expenses and other current liabilities primarily due to restructuring-related accruals, (ii) a $14.4 million decrease in operating lease right-of-use assets from lease incentives received, partially offset by (iii) a $17.0 million decrease in deferred revenue and (iv) a $3.9 million decrease in operating lease liabilities from rent payments. Non-cash adjustments primarily consisted of $30.2 million of depreciation and amortization, $77.9 million of stock-based compensation expense, $9.4 million loss on investments, $13.1 million non-cash lease expense, $19.8 million in acquired in-process research and development expense, and $47.9 million of goodwill impairment.

Previous wording

Net cash used in investing activities for the three months ended March 31, 2025 primarily consisted of purchases of marketable debt securities of $191.2 million and purchases of property and equipment of $7.6 million related to the build-out of new office and laboratory space near our headquarters.

Current wording

Net cash used in investing activities for the six months ended June 30, 2025 primarily consisted of purchases of marketable debt securities of $320.1 million, maturities of marketable debt securities of $65.0 million, and purchases of property and equipment of $7.7 million related to the build-out of new office and laboratory space near our headquarters.

Previous wording

Net cash used in investing activities for the three months ended March 31, 2024 primarily consisted of purchases of property and equipment of $6.7 million associated with Foundry capacity and capability investments and $5.4 million paid for the acquisition of Zymergen.

Current wording

Net cash used in investing activities for the six months ended June 30, 2024 primarily consisted of purchases of property and equipment of $33.7 million associated with Foundry capacity and capability investments and $5.4 million paid for the acquisition of Zymergen.

Previous wording

Net cash used in financing activities for the three months ended March 31, 2025 primarily consisted of principal payments on finance leases.

Current wording

Net cash used in financing activities for the six months ended June 30, 2025 primarily consisted of principal payments on finance leases.

Previous wording

Net cash used in financing activities for the three months ended March 31, 2024 primarily consisted of principal payments on finance leases and payments of contingent consideration related to business acquisitions.

Current wording

Net cash used in financing activities for the six months ended June 30, 2024 primarily consisted of principal payments on finance leases and payments of contingent consideration related to business acquisitions.