Ginkgo Bioworks Holdings, Inc.

17. Significant Collaboration Agreements and Transactions with Related Parties

The Company’s significant transactions with its related parties are primarily comprised of revenue generating activities under collaboration and license agreements.

Platform Ventures

The Company has partnered with other investors, including investors who were also Company investors at the time, to form business ventures, including Motif FoodWorks, Inc. in 2018 (“Motif”), Allonnia, LLC in 2019 (“Allonnia”), Arcaea, LLC in 2021 (“Arcaea”), Verb Biotics, LLC in 2021 (“Verb”), Ayana Bio, LLC in 2021 (“Ayana”) and BiomEdit, LLC in 2022 (“BiomEdit”) (collectively “Platform Ventures”). Each of these entities is privately held with the Company holding common equity interests in each.

The Company initially consolidated Ayana and Verb at formation as variable interests where the Company was initially the primary beneficiary, subsequently deconsolidating both in 2022 when it was concluded that was no longer the case. With respect to the investments in Motif, Allonnia, Arcaea, and BiomEdit, the Company concluded these entities represent variable interest entities, however the Company has never been the primary beneficiary of these entities. The Company accounts for its investments in Platform Ventures under the equity method.

Concurrently with the launch of each of the Platform Ventures, the Company received common equity and, with respect to Arcaea, subsequently received additional common equity. The Company generally granted each Platform Venture licenses to certain of the Company’s intellectual property and executed Technical Development Agreements (“TDAs”) that established terms under which the Company would provide technical research and development services to those entities, generally in return for fees on a fixed fee or cost-plus basis for services provided.

The common equity investments in each of the Platform Ventures were initially recorded at the then fair values determined at inception of the investments. The Company is recognizing earnings and losses on these equity method investments using the HLBV method. Accordingly, the carrying values of each of the Platform Ventures investments were reduced to zero immediately following the Company’s investments. There is no commitment for the Company to provide further financial support to these Platform Ventures, and therefore the carrying value of the equity method investments will not be reduced below zero.

The relationship with the Platform Ventures is as vendor-customer relationships and is within the scope of ASC 606, as the provision of services and corresponding license rights are considered a part of the Company’s ordinary activities. The common equity issued to the Company represent non-cash consideration under revenue contracts. While TDAs executed by the parties provides payment terms for future services, the TDAs do not provide for any transfer of goods or services between the parties as the Company contemplated provided licenses and services upon execution of future contemplated TDPs.

With the exception of Ayana and Verb, the Company’s performance obligations under the initial arrangements consisted of a number of estimated materials rights provided to the Platform Ventures (BiomEdit having four and Arcaea, Allonia and Motif havingten) to future technical research and development services and commercial licenses under individual TDPs that the Company expected to execute. These material rights equated in aggregate to the fair values of the common equity issued by each of the Platform Ventures to the Company and represented advanced payment for the license rights, which would be granted upon the execution of future applicable TDPs. As there would be no additional payment for these license rights when future TDPs are executed, the Company determined that there are material rights associated with each of the contemplated TDPs under each of the TDAs. The value of the material rights are included in deferred revenue until recognized as revenue. The material rights are recorded as non-current deferred revenue until such time as the parties execute an applicable TDP inclusive of the material rights.

For each TDP underlying a material right, the transaction price consists of (i) either a fixed fee or, if a cost-plus arrangement, variable consideration for the most likely amount of estimated consideration to be received and (ii) non-cash consideration allocated to the material right. As the services performed by the Company under a TDP inclusive of a material right, the Company creates or enhances an asset that the Platform Ventures controls, the Company satisfies the performance obligation and recognizes revenue over time using an input method that compares total costs incurred relative to total estimated cost to complete to estimate progress under the contract. Any revisions to the estimated total budgeted costs to complete, and the resulting impact on revenue recognition, are reflected in the period of the change through a cumulative catch-up adjustment.

In August 2024, the Company and Motif mutually terminated its services agreements with no adjustment to the original consideration. As a result, the Company has no further obligation to perform services for Motif and, accordingly, the then remaining $45.4 million in material rights deferred revenue has been recognized in full as revenue during the year ended December 31, 2024.

In March 2025, the Company and BiomEdit mutually terminated its services agreements with no adjustment to the original consideration. As a result, the Company has no further obligation to perform services for BiomEdit, and accordingly, the then remaining $7.5 million in material rights deferred revenue has been recognized in full as revenue during the year ended December 31, 2025. BiomEdit is no longer considered a significant related party due to a reduction of the Company’s equity ownership interest that occurred during the year ended December 31, 2025.

Genomatica, Inc.

The Company has also partnered with Genomatica, Inc. (“Genomatica”), a previously established business that is privately held. Genomatica is deemed a variable interest entity, however the Company has never been the primary beneficiary of this entity

In 2016, the Company purchased Series A preferred stock of Genomatica, Inc. for $15.0 million and entered into a collaboration agreement, which was subsequently terminated in September 2018, whereby the Company received $40.0 million of Series B preferred stock in Genomatica in exchange for providing Genomatica with up to $40.0 million in services at no charge to Genomatica. The agreements between the Company and Genomatica were determined to be within the scope of ASC 606 directly or by analogy. The Company recognized the revenue for the combined performance obligations using an over-time input method.

The Company concluded the preferred stock investments were not in-substance common stock and therefore did not qualify for accounting as an equity method investment and should be accounted for as equity security under the measurement alternative for equity investments that do not have a readily determinable fair value. As of December 31, 2024, the Company determined that the investment had substantially no value. During the years ended December 31, 2024, and 2023, the Company recorded impairment losses of $11.9 million, and $33.0 million, respectively, related to its investment in Genomatica preferred stock.

Related Party Transactions

Significant related party transactions included in the consolidated balance sheet, excluding the Company’s investments and equity method investments, are summarized below (in thousands):

Significant related party transactions included in the consolidated statements of operations and comprehensive loss, excluding the losses on the Company’s investments and equity method investments, are summarized below (in thousands):

Refer to Notes 7 for additional details on the Company’s investments and equity method investments held in its related parties.