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Ginkgo Bioworks Holdings, Inc. (DNA)·Q3 2025 Earnings Summary

Executive Summary

  • Q3 2025 revenue was $38.84M, down 56% YoY due to a $45M non-cash deferred revenue release in the prior year; ex that, revenue fell 11% YoY. Adjusted EBITDA was $(55.7)M, and GAAP net loss was $(80.8)M .
  • Versus S&P Global consensus, revenue was essentially in line ($38.94M est. vs $38.84M actual), but EPS missed (−$1.24 est. vs −$1.45 actual) and EBITDA missed materially (−$22.29M est. vs −$74.10M actual); management cited a $21M Google Cloud shortfall expense in Q3 as a driver of profitability pressure (settled for $14M in Oct) . Revenue*, EPS*, EBITDA* estimates and actual EBITDA* from S&P Global.
  • FY25 outlook reaffirmed: total revenue $167–$187M, Cell Engineering $117–$137M, Biosecurity ≥$40M (Biosecurity guide was lowered to ≥$40M in Q2 from ≥$50M in Q1, and maintained in Q3) .
  • Cash burn improved to $28M in Q3 (vs $114M in Q3’24; −75% YoY) and period-end cash, cash equivalents and marketable securities were $462M, supporting continued investment in AI-enabled automation tools .

What Went Well and What Went Wrong

  • What Went Well

    • Cash preservation and burn: “Cash burn in the third quarter of 2025 was $28 million, down from $114 million… a 75% decrease,” driven by restructuring .
    • Strategic wins: BARDA award up to $22.2M to develop mAb biomanufacturing innovations and produce an anti-filovirus countermeasure; Bayer multi‑year partnership extension in ag biologicals .
    • AI-enabled automation narrative: CEO emphasized AI “reasoning models controlling lab automation” and Ginkgo’s “reconfigurable automation carts,” positioning for on-prem autonomous labs; showcased Boston “frontier autonomous lab” scaling to 46 instruments on 36 RACs .

  • What Went Wrong

    • Profitability miss: Adjusted EBITDA deteriorated to $(55.7)M (vs $(20.0)M in Q3’24) and EBITDA to $(72.3)M, with CFO calling out a $21M Google Cloud shortfall expense in Q3 and lapping prior-year $45M non‑cash revenue .
    • Segment softness: Cell Engineering revenue fell to $29.4M (−61% YoY; slightly down ex-$45M prior-year non‑cash item); Biosecurity declined to $9.5M (from $14.0M) .
    • Program rationalization: Revenue-generating programs declined to 102 (−5% YoY) due to ongoing restructuring/program rationalization .

Financial Results

Headline financials (actuals)

MetricQ1 2025Q2 2025Q3 2025
Total Revenue ($M)$48.32 $49.60 $38.84
Diluted EPS$(1.68) $(1.10) $(1.45)
Adjusted EBITDA ($M)$(47.45) $(28.06) $(55.71)

Segment revenue

Segment Revenue ($M)Q1 2025Q2 2025Q3 2025
Cell Engineering$38.23 $39.13 $29.38
Biosecurity$10.09 $10.47 $9.46

Profitability and cash

MetricQ1 2025Q2 2025Q3 2025
EBITDA ($M)$(81.58) $(50.87) $(72.33)
Adjusted EBITDA ($M)$(47.45) $(28.06) $(55.71)
Cash, Cash Equivalents + Marketable Securities ($M)$517 $474 $462

KPI snapshots

KPIQ1 2025Q2 2025Q3 2025
Revenue‑generating programs (count)123 —102
Cash burn ($M)$58 —$28

Consensus vs actual (Q3 2025)

MetricConsensusActualBeat/Miss
Revenue ($M)$38.95*$38.84 In line/slight miss
Primary EPS$(1.24)*$(1.45) Miss
EBITDA ($M)$(22.29)*$(74.10)*Miss

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

Context on YoY dynamics: Management noted Q3’24 included $45M of non‑cash deferred revenue release (Motif), creating a 56% YoY headline decline; excluding that item, Q3’25 revenue was down 11% YoY .

Guidance Changes

MetricPeriodPrevious GuidanceCurrent GuidanceChange
Total RevenueFY 2025$167–$187M (Q2 guide) $167–$187M (Q3 reaffirm) Maintained
Cell Engineering RevenueFY 2025$117–$137M (Q2 guide) $117–$137M (Q3 reaffirm) Maintained
Biosecurity RevenueFY 2025≥$40M (Q2 guide; lowered from ≥$50M in Q1) ≥$40M (Q3 reaffirm) Maintained (after Q2 cut)

Earnings Call Themes & Trends

TopicPrevious Mentions (Q1, Q2)Current Period (Q3)Trend
AI + Autonomous Labs (RACs)Q1: Expanding tools businesses (Data Points, Automation); RACs enable rapid, expandable integrated automation; highlighted new diagnostics customer and 25+ rack setup . Q2: Automation/Datapoints positioned as critical AI tools; PNNL anaerobic platform; launched ADME service .CEO emphasized “reasoning models controlling lab automation,” Boston “frontier autonomous lab” scaling to 46 instruments on 36 RACs; goal to sell large general‑purpose autonomous labs; demo invites .Intensifying focus; moving from concept/proof points toward scaled commercial rollout.
Government/Defense WorkQ1: 28 US Gov projects, ~$180M contracted + unfunded potential; ARPA‑H WHEAT $29M prime; biosecurity Canopy & Horizon platforms . Q2: Continued gov’t traction (PNNL; tools positioning) .BARDA BioMaP award up to $22.2M for mAbs; exposure to US gov business discussed; shutdown impact minimal .Pipeline sustained; gov funding a key pillar for growth and backlog visibility.
Cost Actions & Cash BurnQ1: Run-rate cost reduction $205M; cash burn Q1 $58M; targeting Adj. EBITDA breakeven by end 2026 . Q2: Achieved $250M annualized cost reduction target; Adj. EBITDA improved to $(28)M .Cash burn reduced to $28M in Q3 (−75% YoY); “no bank debt”; focus shifting from cost takeout to growth investments .Sustained improvement; pivot toward growth investment underway.
Google Cloud Commitment——CFO: Q3 included $21M shortfall expense; Oct amendment reduced go‑forward commitment by >$100M and extended term to six years; settled shortfall for $14M .
Biosecurity Trend/GuideQ1: Biosecurity revenue ≥$50M guide; passive monitoring vision . Q2: Guide lowered to ≥$40M .Reaffirmed ≥$40M; segment revenue $9.5M; 19% segment gross margin .Guide stabilized at lower level; margin modest.
Ag Bio (Bayer)——Bayer partnership extended; nitrogen fixation focus .

Management Commentary

  • Strategic pivot to tools-led growth: “We went from just offering research solutions… [and] expanded into the tool space with our Data Points, automation, and reagents businesses… AI reasoning models controlling robotics in the lab [and] neural nets trained on biological data” .
  • Capital discipline: “After Q3, we have $462 million in cash and cash equivalents and no bank debt… we’re going to hear less about cost takeouts in 2026 and a lot more about our investments for growth” .
  • On RACs commercialization roadmap: “I’d like to see… a large biopharma… purchase of a very large system with an intent for a general‑purpose autonomous lab” in 2026 .
  • Google Cloud contract reset: “We were able to reduce our go forward commitment by over $100 million and extended out the period by 2x… puts us right where we want to be” .

Q&A Highlights

  • Government exposure and shutdown impact: “Shutdown has not had a big impact… we have a good amount of exposure to the government overall… BARDA and ARPA‑H awards” .
  • RACs milestones and commercialization: Management targets 50+ internal scientists ordering simultaneously in 2026 and seeks a large biopharma purchase of a general-purpose autonomous lab .
  • Long-term revenue mix: CEO envisions 2030 mix skewing ~80/20 toward tools vs services, with biosecurity potentially large depending on monitoring infrastructure adoption .
  • Google Cloud commitments: Q3 included a $21M shortfall; in Oct, Ginkgo reduced future commitments by >$100M and extended timeline to six years; shortfall settled for $14M .

Estimates Context

  • Q3 2025 vs S&P Global consensus: revenue essentially in line ($38.95M est. vs $38.84M actual), EPS worse (−$1.24 est. vs −$1.45 actual), EBITDA worse (−$22.29M est. vs −$74.10M actual). Management attributed EBITDA pressure to a one‑time $21M Google Cloud shortfall expense and lapping prior-year $45M non‑cash deferred revenue release . Revenue*, EPS*, EBITDA* estimates and actual EBITDA* from S&P Global.
  • Implications: Street models may trim near‑term profitability (EBITDA/loss) while keeping FY revenue broadly intact given reaffirmed guidance; carry‑forward benefit from lower Google Cloud commitments should aid out‑years. Values marked with an asterisk (*) are retrieved from S&P Global.

Key Takeaways for Investors

  • Revenue largely in line, but profitability underperformed on one‑time cloud obligation and deferred revenue comp headwinds; FY revenue guidance reaffirmed, de‑risked by gov’t awards .
  • Cash runway appears solid ($462M cash + securities; reduced cash burn), enabling continued investment in AI‑enabled automation tools and on‑prem autonomous lab deployments .
  • Tools strategy (RACs, Data Points) is the core medium‑term growth vector; watch for a large biopharma autonomous lab deal and increasing tool revenue contribution as catalysts .
  • Biosecurity guide stabilized at ≥$40M after Q2 reset; execution on U.S. monitoring infrastructure and BARDA/ARPA‑H programs can provide upside optionality .
  • Google Cloud contract reset reduces multi‑year spend commitments (>$100M reduction) and removes a Q3‑specific headwind; forward margin trajectory should improve absent similar items .
  • Segment focus: Cell Engineering softness this quarter reflected prior‑year non‑cash revenue comp and program rationalization; track program count, tool attach, and biopharma wins for reacceleration .
  • Trading setup: Near‑term sentiment hinges on evidence of tools monetization (orders/deployments), sustained burn improvement, and additional government/commercial wins; EBITDA miss was notable but tied to identifiable, non‑recurring factors .

Additional Supporting Data

EBITDA Margin % trend (S&P Global)

MetricQ1 2025Q2 2025Q3 2025
EBITDA Margin %−141.42%*−92.88%*−190.81%*

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

Recent press releases referenced

  • Q3 2025 earnings PR and financials
  • BARDA award up to $22.2M
  • Bayer partnership extension
  • Q2 2025 earnings PR and 8‑K exhibit
  • Q1 2025 earnings PR

Notes on non‑GAAP

  • Adjusted EBITDA excludes items including stock‑based comp, restructuring, fair value changes, investment gains/losses; reconciliations provided in exhibits .
  • Prior‑year non‑cash deferred revenue release ($45M) elevated Q3’24 revenue; Q1’25 included $7–7.5M similar non‑cash items .

Citations

  • 8‑K/Press release figures and guidance:
  • Q3 call commentary:
  • Q2 results and guidance:
  • Q1 results and call:
  • BARDA/Bayer releases:

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