Executive Summary

Q2 revenue of $49.6M beat S&P Global consensus of $41.6M*, while GAAP EPS of $(1.10) beat $(1.57)*; Adjusted EBITDA improved to $(28.1)M from $(99.2)M YoY driven by reduced OpEx .
Cell Engineering grew 8% YoY to $39.1M while Biosecurity fell to $10.5M; management reaffirmed FY25 total revenue ($167–$187M) and Cell Engineering ($117–$137M) but cut Biosecurity to “at least $40M” from “at least $50M” .
Management achieved its $250M annualized cost-reduction run-rate three months early and ended Q2 with $474M in cash and marketable securities, supporting the path to Adjusted EBITDA breakeven by end of 2026 .
Strategic pivot to tools accelerated: PNNL awarded a $4.66M automation workcell; Ginkgo launched a US-based, price-matched ADME profiling service and its first reagent (cell-free protein synthesis) aimed at AI-enabled science .
Potential stock reaction catalysts: revenue/EPS beat and cost discipline versus a lowered Biosecurity outlook and ongoing real-estate carrying cost drag ($12.4M in Q2) .

What Went Well and What Went Wrong

What Went Well
- Achieved $250M annualized cost savings a quarter early; Adjusted EBITDA improved to $(28.1)M from $(99.2)M YoY and sequentially from $(47.5)M in Q1 .
- Commercial momentum in tools: $4.66M PNNL anaerobic automation system; launched ADME service with price-match guarantee and first reagent product (cell-free protein synthesis) .
- CEO tone on positioning for AI: “Our platform is proving to be a critical engine for AI in biology… backed by rigorous financial discipline” .
What Went Wrong
- Biosecurity revenue halved YoY to $10.5M; FY25 Biosecurity guidance cut to “at least $40M” due to international contract timing uncertainty .
- Ongoing carrying cost of excess space was $12.4M in Q2, a cash drag that is “not related to driving revenue right now” and dependent on a soft sublease market .
- Total revenue down YoY to $49.6M vs $56.2M as Biosecurity weakness offset Cell Engineering growth .

Financial Results

Quarterly trend (oldest → newest):

Metric	Q4 2024	Q1 2025	Q2 2025
Total Revenue ($M)	$43.8	$48.3	$49.6
GAAP Net Loss ($M)	$(107.5)	$(91.0)	$(60.3)
GAAP Basic EPS ($)	$(2.00)	$(1.68)	$(1.10)
Adjusted EBITDA ($M)	$(57.1)	$(47.5)	$(28.1)
Cash & Equivalents ($M)	$561.6	$312.4	$203.6
Marketable Securities ($M)	—	$204.5	$270.1

Q2 actual vs S&P Global consensus:

Metric	Q2 2025 Actual	Q2 2025 Consensus	Surprise
Revenue ($M)	$49.6	$41.6*	+$8.0M; +19% (beat)
GAAP Primary EPS ($)	$(1.10)	$(1.57)*	+$0.47 (less negative; beat)
EBITDA ($M)	$(46.1)*	$(51.0)*	+$4.9M (less negative; beat)

Values with asterisk (*) are from S&P Global.

Segment performance:

Segment	Q2 2024	Q1 2025	Q2 2025
Cell Engineering Revenue ($M)	$36.2	$38.2	$39.1
Cell Engineering Operating Loss ($M)	$(83.0)	$(31.6)	$(9.9)
Biosecurity Revenue ($M)	$20.0	$10.1	$10.5
Biosecurity Operating Loss ($M)	$(3.4)	$(5.2)	$(4.8)

Selected KPIs and cost items:

KPI / Cost Item	Q2 2024	Q1 2025	Q2 2025
Revenue-generating programs (count)	—	—	120
Cash burn ($M)	~$110	—	~$38
“Excess space” carrying cost ($M)	$7.4	$11.7	$12.4
Cash + Marketable Securities ($M)	—	$516.9 (312.4+204.5)	~$474 (203.6+270.1)

Notes: EBITDA and EPS comparisons to consensus use S&P Global data*; Adjusted EBITDA is a non-GAAP metric as defined by the company .

Guidance Changes

Metric	Period sop	Period	Previous Guidance	Current Guidance
Total Revenue	FY 2025	$167–$187M	$167–$187M	Maintained
Cell Engineering Revenue	FY 2025	$117–$137M	$117–$137M	Maintained
Biosecurity Revenue	FY 2025	At least $50M	At least $40M	Lowered
Adj. EBITDA Breakeven Target	Timeline	End of 2026 (narrative)	End of 2026 (reiterated)	Maintained

Earnings Call Themes & Trends

Topic	Q4 2024 (prior 2)	Q1 2025 (prior 1)	Q2 2025 (current)	Trend
Life Science Tools (Automation & Datapoints)	Highlighted expansion; GLBRC automation selection; Datapoints traction	New dataset (GDPa1), first diagnostics automation customer (Aura)	PNNL $4.66M anaerobic platform; ADME service with price-match; first reagent (cell-free protein synthesis)	Accelerating
Cost reductions & profitability	Run-rate savings $190M; breakeven by end-2026	$205M run-rate; target $250M by Q3’25	$250M run-rate achieved early; Adjusted EBITDA improvement; cash margin of safety	Improving
Biosecurity outlook	FY25 “at least $50M”	Reaffirmed “at least $50M”	Cut to “at least $40M”; international contract timing uncertainty	Softening
AI / Lab-in-the-loop automation	Demonstrations & positioning	Initial traction	Emphasis on general-purpose, AI-enabled labs; cloud-enabled labs narrative	Rising focus
Real estate/sublease headwind	—	$11.7M carrying cost	$12.4M carrying cost; sublease market soft	Persistent headwind
Government programs/backlog	Multi-year awards (HaDEA)	~$180M USG projects and backlog	PNNL contract; continued gov’t focus	Steady

Management Commentary

“We hit that target [the $250M annual run rate cost savings] a quarter early… we now have $474 million in cash and cash equivalents with no bank debt… [so] we can be strategic about engaging with capital markets.” — Jason Kelly, CEO .
“Total Adjusted EBITDA in [Q2] was negative $28 million, improved from negative $99 million [YoY]… cash burn in [Q2] was $38 million, down from $110 million in [Q2 2024].” — Steve Coen, CFO .
“Automation is going to be a huge part of our future business… we’re solving for general purpose automation… a platform akin to the lab bench.” — Jason Kelly .
On Biosecurity: “We brought [FY25] down from $50M+ to $40M+… based on the international side… certain contracts… not be in place [yet].” — Jason Kelly .

Q&A Highlights

Revenue drivers and M&A: Management expects automation/tools to be a growing revenue driver over time; no immediate acquisition plans though the market is fluid .
ADME service and AI models: Primary monetization is data generation; open to building/partnering on models; publishing datasets (e.g., on Hugging Face) to seed an ecosystem .
Profit path levers: Further targeted cost actions, revenue growth from tools/solutions, and progress on subleasing underutilized space; sublease market is a key risk .
Deployment model flexibility: Services can prove value and then be “lifted and shifted” on-prem via Ginkgo’s rack hardware for customers with in-house needs .

Estimates Context

Q2 beats vs S&P Global: revenue $49.6M vs $41.6M*; GAAP EPS $(1.10) vs $(1.57); EBITDA $(46.1)M vs $(51.0)M* — broad-based beats driven by Cell Engineering growth and cost reductions .
Forward quarters: S&P Global models Q3 revenue ~$38.9M* and EPS $(1.24), Q4 revenue ~$37.7M and EPS $(1.80), implying modest sequential declines as tools scale up.
Analyst revisions likely: Better-than-expected Q2 and reinforced cost discipline may support upward EPS revisions (less negative), though the Biosecurity guide cut could temper revenue expectations*.