What changed in this filing

/stocks — the workspaceLOADING

Item 2. Management’s Discussion and Analysis

2025-11-06 compared with 2025-08-07 · 114 added, 72 removed, 264 unchanged (41% of the section changed)

27 unchanged sentences

In addition, we offer support services with fixed fees covering the support periods.

A selection of our cell engineering tools offerings are described below.

Recent advances in machine-learning (ML), molecular simulation, and other computational techniques hold great promise to improve our ability to program cells.

We believe our Foundry is well-positioned to build the kind of large, well-structured datasets that such computational approaches need to succeed.

In time, we believe computational approaches will reduce the need for certain kinds of experiments (for example, we already use ML to make protein and enzyme design projects more efficient).

To this end, we have introduced two new data generation services to provide high-quality data at the scale, price, and speed that AI-powered drug development demands:

• Our Functional Genomics Datapoints services generate large, high fidelity transcriptomic and phenotypic datasets in the disease context of our customers’ choice to power AI models of cell and disease biology for use in target identification, target validation, and drug discovery;

• Our Antibody Developability Datapoints services generate biophysical antibody characterization developability datasets for our customers to use in AI model training and validation.

Reconfigurable Automation Cart (“RAC”) Systems

Ginkgo Automation’s capabilities build on years of internal expertise, encompassing hardware design, software integration, and applications development, epitomized in our offering of RACs:

our Reconfigurable Automation Cart systems.

The modularity and flexibility of the RACs enables high walkway time, high uptime, and high throughput experimentation for high-mix biological workflows like the kinds performed in Ginkgo’s Foundry and in our partners’ labs.

In addition to providing advanced automation hardware and software, Ginkgo Automation’s deployments to third party customers include access to Catalyst Flow, a fully remote, active error resolution and troubleshooting support service.

Catalyst Flow’s proactive monitoring is expected to enable Ginkgo’s scientists and engineers to identify and resolve approximately 80-90% of system errors remotely, without the need for our customers to initiate tickets.

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.

7 unchanged sentences

Our cell engineering platform is a key enabling technology and source of intellectual property for our customers’ products.

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.

We typically structure customer contracts for Cell Engineering services to include some combination of the following:

We earn Cell Engineering revenue for our R&D services.

For each of our end-to-end cell engineering programs, we charge customers fees for the services we provide, typically structured as fixed fees, although we also have cost reimbursement arrangements.

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.

Commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types.

We charge customers fees for the services we provide in our cell engineering tools offerings.

Typically, these fees are structured as a fixed fee for a fixed scope of work.

Fees for our data generation products (“Datapoints”), which provide large, biological datasets for customers to train their AI models, synthesizing and testing the output of customer existing models, and generating datasets for lead selection, hit selection, or a variety of other data science applications, are typically earned over a shorter period of time (weeks to months) than for end-to-end cell engineering solutions which may be multi-year programs.

Fees for our automation solutions are typically earned over a period that covers design, build, and deployment and range from six to twelve months.

In addition, we offer support services with fixed fees covering the support periods.

We typically structure customer contracts for Cell Engineering services to include one or more of the following:

• upfront payments upon execution of an agreement or other fixed payments, which are generally recognized over the period of performance;

16 unchanged sentences

Our customers obtain license rights to the output of our services, which are primarily the optimized strains or cell lines, in order to manufacture and commercialize products derived from that licensed strain or cell line.

Generally, the terms of these

agreements provide that we receive some combination of:

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.

64 unchanged sentences

Reductions in force are expected to be substantially completed in 2025, subject to compliance with applicable laws.

While we have substantially completed the majority of our facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions.

While we have substantially completed the majority of our facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities is expected to extend into 2026 or may not occur prior to termination of such lease, depending on market conditions.

Additionally, restructuring expenses related to potential asset impairments or contract amendments or terminations for any facilities no longer in use or underutilized could be material.

4 unchanged sentences

Loss on investments includes the change in fair value of our marketable equity securities in publicly traded companies and impairment losses recognized on non-marketable equity securities in privately held companies.

Loss on Deconsolidation of Subsidiary

Loss on deconsolidation of subsidiary pertains to our deconsolidation of our former foreign subsidiary Altar SAS (“Altar”) in the third quarter of 2024 as a result of a sale.

Change in Fair Value of Warrant Liabilities

2 unchanged sentences

(“SRNG”) on September 16, 2021, and were initially issued in connection with SRNG’s initial public offering.

Warrant liabilities are remeasured at fair value at each balance sheet date and have substantially no value as of June 30, 2025.

Warrant liabilities are remeasured at fair value at each balance sheet date and have substantially no value as of September 30, 2025.

Other Income (Expense), Net

11 unchanged sentences

Results of Operations

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

Comparison of the Three and Nine Months Ended September 30, 2025 and 2024

The following table presents our result of operations for the periods indicated:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(in thousands) 2025 2024 Change

18 unchanged sentences

Interest income, net 5,742 9,251 (3,509) 17,906 31,275 (13,369)

Loss on investments (229) (6,826) 6,597 (3,922) (9,370) 5,448

Gain (loss) on investments 3,684 (6,912) 10,596 (238) (16,282) 16,044

Loss on deconsolidation of subsidiary — (7,013) 7,013 — (7,013) 7,013

Change in fair value of warrant liabilities — 1,528 (1,528) — 5,701 (5,701)

Other income (expense), net (163) 1,572 (1,735) (5,348) 2,821 (8,169)

Total other income 4,958 5,954 (996) 3,057 18,076 (15,019)

Total other income (expense) 9,263 (1,574) 10,837 12,320 16,502 (4,182)

Loss before income taxes (80,754) (56,778) (23,976) (232,206) (439,649) 207,443

2 unchanged sentences

(1) Total stock-based compensation expense, inclusive of employer payroll taxes, was allocated as follows (in thousands):

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

2025 2024 2025 2024

5 unchanged sentences

Cell Engineering Revenue

Cell Engineering revenue was $39.1 million for the three months ended June 30, 2025, compared to $36.2 million for the three months ended June 30, 2024, an increase of $2.9 million.

This increase was primarily due to an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S.

government (healthcare and defense sectors), partially offset by the recognition of $4.5 million in non-cash revenue from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024.

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.

Cell Engineering revenue was $29.4 million for the three months ended September 30, 2025, compared to $75.1 million for the three months ended September 30, 2024, a decrease of $45.7 million.

This decrease was primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024.

Cell Engineering revenue was $106.7 million for the nine months ended September 30, 2025, compared to $139.2 million for the nine months ended September 30, 2024, a decrease of $32.4 million.

This decrease was primarily due to the

recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, the recognition of $4.5 million in non-cash revenue 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 decreases in revenue for certain programs with customers in the industrial biotechnology industry.

These decreases were partially offset by 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) and an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S.

government (healthcare and defense sectors).

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.

Cell Engineering revenue recognized relating to non-cash consideration decreased from $48.0 million for the three months ended September 30, 2024 to zero for the three months ended September 30, 2025, and from $60.1 million for the nine months ended September 30, 2024 to $9.9 million for the nine months ended September 30, 2025, primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, and 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, 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.

Biosecurity Revenue

Biosecurity revenue was $10.5 million for the three months ended June 30, 2025, compared to $20.0 million for the three months ended June 30, 2024, a decrease of $9.5 million.

This decrease was primarily due to lower revenue related to a program with the U.S.

Biosecurity revenue was $20.6 million for the six months ended June 30, 2025, compared to $30.1 million for the six months ended June 30, 2024, a decrease of $9.5 million.

This decrease was primarily due to lower revenue related to a program with the U.S.

Biosecurity revenue was $9.5 million for the three months ended September 30, 2025, compared to $14.0 million for the three months ended September 30, 2024, a decrease of $4.5 million.

This decrease was primarily due to lower revenue related to programs with the U.S.

government and a foreign government.

Biosecurity revenue was $30.0 million for the nine months ended September 30, 2025, compared to $44.0 million for the nine months ended September 30, 2024, a decrease of $14.0 million.

This decrease was primarily due to lower revenue related to a programs with the U.S.

government and a foreign government.

Cost of Biosecurity Revenue

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.

The cost of Biosecurity revenue was $17.4 million for the six months ended June 30, 2025, compared to $21.0 million for the six months ended June 30, 2024, a decrease of $3.6 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.

The cost of Biosecurity revenue was $8.2 million for the three months ended September 30, 2025, compared to $10.0 million for the three months ended September 30, 2024, a decrease of $1.8 million.

This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S.

The cost of Biosecurity revenue was $25.6 million for the nine months ended September 30, 2025, compared to $31.0 million for the nine months ended September 30, 2024, a decrease of $5.4 million.

This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S.

Cost of Other Revenue

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.

The cost of other revenue was $4.6 million for the three months ended September 30, 2025, compared to $2.0 million for the three months ended September 30, 2024, an increase of $2.6 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.

These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024.

Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.

The cost of other revenue was $9.5 million for the six months ended June 30, 2025, compared to $1.9 million for the six months ended June 30, 2024, an increase of $7.6 million.

The cost of other revenue was $14.1 million for the nine months ended September 30, 2025, compared to $3.9 million for the nine months ended September 30, 2024, an increase of $10.2 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.

These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024.

Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.

1 unchanged sentence

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

$19.8 million for the six months ended June 30, 2025 and 2024, respectively.

Research personnel costs, including stock-based compensation, is our largest expense, totaling $19.3 million and $31.2 million for the three months ended September 30, 2025 and 2024, respectively, and $73.3 million and $152.5 million for the nine months ended September 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 for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 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.

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.

Research and development expenses were $124.3 million for the six months ended June 30, 2025, compared to $270.7 million for the six months ended June 30, 2024, a decrease of $146.4 million.

This decrease was primarily driven by reductions of $39.5 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $27.0 million in stock-based compensation expense (inclusive of employer payroll taxes), $22.3 million in rent and facilities expenses, $19.8 million in acquired in-process research and development expense, $13.6 million in laboratory supplies, $11.6 million in information technology expenses, $6.4 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), and $6.2 million in other operating expenses.

Research and development expenses were $69.4 million for the three months ended September 30, 2025, compared to $77.0 million for the three months ended September 30, 2024, a decrease of $7.7 million.

This decrease was primarily driven by reductions of $15.0 million in personnel-related compensation and benefits expenses, $8.0 million in rent and facilities expenses, $4.4 million in depreciation and amortization, $2.2 million in laboratory supplies, $2.0 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $1.1 million in temporary labor and contractors, and $0.6 million in other operating expenses.

These decreases were partially offset by an increase of $22.5 million in information technology expenses primarily due to a shortfall in contractually committed spending related to our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and $3.1 million in stock-based compensation expense (inclusive of employer payroll taxes).

Research and development expenses were $193.6 million for the nine months ended September 30, 2025, compared to $347.7 million for the nine months ended September 30, 2024, a decrease of $154.0 million.

This decrease was primarily driven by reductions of $54.6 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $30.3 million in rent and facilities expenses, $23.8 million in stock-based compensation expense (inclusive of employer payroll taxes), $19.8 million in acquired in-process research and development expense, $15.8 million in laboratory supplies, $8.4 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $6.3 million in depreciation and amortization, $4.5 million in temporary labor, and contractors and $1.5 million in other operating expenses.

These decreases were partially offset by an increase of $11.0 million in information technology expenses primarily due to a shortfall in contractually committed spending related to the our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q).

General and Administrative Expenses

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.

General and administrative expenses were $45.0 million for the three months ended September 30, 2025, compared to $52.3 million for the three months ended September 30, 2024, a decrease of $7.3 million.

This decrease was primarily driven by reductions of $6.4 million in personnel-related compensation and benefits expenses, $1.9 million in allocated overhead expenses (reclassified from R&D to G&A), $1.2 million of stock-based compensation expense (inclusive of employer payroll taxes), $1.4 million in earnout remeasurement expenses, $1.4 million in professional fees, and $0.7 million in other operating expenses.

These decreases were partially offset by an increase of $5.7 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.

General and administrative expenses were $92.3 million for the six months ended June 30, 2025, compared to $136.6 million for the six months ended June 30, 2024, a decrease of $44.3 million.

This decrease was primarily driven by reductions of $18.3 million in professional fees, $15.1 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $14.4 million in stock-based compensation expense (inclusive of employer payroll taxes), $6.5 million in earnout remeasurement expenses, $4.2 million in temporary labor and contractors, and $9.0 million in other operating expenses.

General and administrative expenses were $137.3 million for the nine months ended September 30, 2025, compared to $188.9 million for the nine months ended September 30, 2024, a decrease of $51.6 million.

This decrease was primarily driven by reductions of $21.4 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $19.7 million in professional fees, $15.6 million in stock-based compensation expense (inclusive of employer payroll taxes), $7.9 million in earnout remeasurement expenses, $5.7 million in allocated overhead expenses (reclassified from R&D to G&A), $4.4 million in temporary labor and contractors, and $5.9 million in other operating expenses.

These decreases were partially offset by an increase of $29.0 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.

Goodwill Impairment

During both the three and six months ended June 30, 2024, we recorded a full impairment of the $47.9 million goodwill balance related to our Cell Engineering reporting unit.

During the nine months ended September 30, 2024, we recorded a full impairment of the $47.9 million goodwill balance related to our Cell Engineering reporting unit.

Restructuring Charges

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 were $1.7 million and $2.9 million for the three months ended September 30, 2025 and 2024, respectively, and $10.7 million and $20.0 million for the nine months ended September 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.

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.

Interest Income, Net

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.

Interest income, net was $12.2 million for the six months ended June 30, 2025, compared to $22.0 million for the six months ended June 30, 2024, a decrease of $9.9 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Loss on Investments

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.

Interest income, net was $5.7 million for the three months ended September 30, 2025, compared to $9.3 million for the three months ended September 30, 2024, a decrease of $3.5 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Interest income, net was $17.9 million for the nine months ended September 30, 2025, compared to $31.3 million for the nine months ended September 30, 2024, a decrease of $13.4 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.

Gain (Loss) on Investments

Gain on investments was $3.7 million for the three months ended September 30, 2025.

Loss on investments was $6.9 million for the three months ended September 30, 2024.

Loss on investments was $0.2 million and $16.3 million for the nine months ended September 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.

Loss on Deconsolidation of Subsidiary

In the third quarter of 2024, we recorded a $7.0 million loss on our deconsolidation of our former foreign subsidiary Altar as a result of a sale.

Change in Fair Value of Warrant Liabilities

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 change in fair value of warrant liabilities was zero for both the three and nine months ended September 30, 2025, compared to gains of $1.5 million and $5.7 million for the three and nine months ended September 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.

As of September 30, 2025, these warrant liabilities had substantially no value.

Other Income (Expense), Net

We recorded a net other expense amount of $0.9 million for the three months ended June 30, 2025, compared to a net other expense amount of $0.8 million for the three months ended June 30, 2024, a decrease of $0.1 million.

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.

We recorded a net other expense amount of $0.2 million for the three months ended September 30, 2025, compared to a net other income amount of $1.6 million for the three months ended September 30, 2024, a decrease of $1.7 million.

We recorded a net other expense amount of $5.3 million for the nine months ended September 30, 2025, compared to a net other income amount of $2.8 million for the nine months ended September 30, 2024, a decrease of $8.2 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.

5 unchanged sentences

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 Zymergen Bankruptcy, and certain other income and expenses.

We believe that the use of EBITDA and Adjusted EBITDA provides an additional tool for investors to use in evaluating ongoing operating results and trends because it eliminates the effect of financing activities, investing activities, and certain non-cash charges and other items that are not related to our core operating performance or affect comparability period over period.

We believe that the use of EBITDA and Adjusted EBITDA provides an additional tool for investors to use in evaluating ongoing operating

results and trends because it eliminates the effect of financing activities, investing activities, and certain non-cash charges and other items that are not related to our core operating performance or affect comparability period over period.

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.

3 unchanged sentences

A reconciliation of EBITDA and Adjusted EBITDA to net loss, the most directly comparable GAAP financial measure, is presented below:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(in thousands) 2025 2024 2025 2024

11 unchanged sentences

57 (796) (4,478) 6,110

Loss on investments 229 6,826 3,922 9,370

Loss (gain) on investments (3,684) 6,912 238 16,282

Loss on deconsolidation of subsidiary — 7,013 — 7,013

Change in fair value of warrant liabilities — (1,528) — (5,701)

1 unchanged sentence

Adjusted EBITDA $ (55,707) $ (20,014) $ (131,219) $ (236,216)

(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.

(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.

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

(2) Includes $0.3 million and $0.2 million in employer payroll taxes for the three months ended September 30, 2025 and 2024, respectively, and $0.9 million and $2.9 million for the nine months ended September 30, 2025 and 2024, respectively.

(3) Restructuring charges primarily consist of employee termination costs from the reduction in force commenced in June 2024.

4 unchanged sentences

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.

Not included in this adjustment are acquired in-process research and development expenses, which totaled zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively.

Liquidity and Capital Resources

2 unchanged sentences

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.

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.

common stock.

As of September 30, 2025, we had cash and cash equivalents and marketable securities of $461.9 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.

At-The-Market Program

On August 7, 2025, we filed a universal shelf registration statement on Form S-3, which was declared effective by the SEC on August 14, 2024, on which we registered for sale up to $500 million of any combination of our Class A common stock, preferred stock, warrants, and/or units from time to time and at prices and on terms that we may determine.

On September 4, 2025, the Company entered into a Sales Agreement (the “Sales Agreement”) with Allen & Company LLC (“Allen”), who is acting as the sales agent (the “Agent”), pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $100.0 million (the “Shares”) through or directly to the Agent in one or more at-the-market (“ATM”) offerings.

Since inception of the Sales Agreement through September 30, 2025, the Company has issued 975,300 shares of Class A common stock under the ATM Sales Agreement for net proceeds of $9.4 million.

We currently intend to use the net proceeds from this offering for general corporate purposes, which may include, but are not limited to, financing our operations, technology development, working capital and capital expenditures.

Material Cash Requirements

7 unchanged sentences

The following table provides information regarding our cash flows for each period presented:

Six Months Ended June 30,

Nine Months Ended September 30,

(in thousands) 2025 2024

Net cash used in:

Net cash provided by (used in):

Operating activities $ (123,381) $ (277,150)

4 unchanged sentences

Operating Activities

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.

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.

Net cash used in operating activities for the nine months ended September 30, 2025 consisted of a net loss of $232.0 million, adjusted for net change in operating assets and liabilities of $20.5 million and non-cash charges of $129.1 million.

The net change in operating assets and liabilities was primarily due to (i) a $27.2 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 $18.8 million decrease in operating lease liabilities from rent payments, and (iii) a $0.3 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $17.0 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation, and (v) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received.

Non-cash adjustments primarily consisted of $60.5 million of stock-based compensation expense,

$45.3 million of depreciation and amortization, $22.4 million non-cash lease expense, a $1.5 million change in fair values of various assets and liabilities, $2.5 million accretion of discount on marketable securities, and a $0.3 million loss on investments.

Net cash used in operating activities for the nine months ended September 30, 2024 consisted of a net loss of $439.5 million, adjusted for a net decrease in cash due to changes in operating assets and liabilities of $91.8 million and non-cash charges of $254.2 million.

The net change in operating assets and liabilities was primarily driven by a $31.1 million decrease in accounts payable, accrued expenses and other current liabilities primarily due to the payment or release of restructuring-related accruals and litigation costs, a $67.8 million decrease in deferred revenue primarily from a one-time release of a deferred revenue balance associated with a terminated customer contract, and a $11.4 million decrease in operating lease liabilities from rent payments, partially offset by a $19.2 million decrease in operating lease right-of-use assets from lease incentives received.

Non-cash adjustments primarily consisted of $47.4 million in depreciation and amortization, $91.8 million in stock-based compensation expense, $16.3 million loss on investments, $20.6 million non-cash lease expense, $19.8 million in acquired in-process research and development expense, and $47.9 million in goodwill impairment.

Investing Activities

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.

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.

Net cash used in investing activities for the nine months ended September 30, 2025 primarily consisted of purchases of marketable debt securities of $401.8 million, maturities of marketable debt securities of $73.6 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.

Net cash used in investing activities for the nine months ended September 30, 2024 primarily consisted of $48.8 million in purchases of property and equipment related to Foundry capacity and capability investments, $5.4 million paid for the acquisition of certain Zymergen assets, and $4.0 million in proceeds from the sale of investment securities.

Financing Activities

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

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.

Net cash provided by financing activities for the nine months ended September 30, 2025 primarily consisted of $10.0 million in net proceeds from an ATM offering and $0.3 million of principal payments on finance leases.

Net cash used in financing activities for the nine months ended September 30, 2024 primarily consisted of $0.7 million of principal payments on finance leases and $0.9 million in payments of contingent consideration related to business acquisitions.

Critical Accounting Estimates

3 unchanged sentences

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 2. Management’s Discussion and Analysis