| Item 1. | |
| (a) | Name of issuer:
Generate Biomedicines, Inc. |
| (b) | Address of issuer's principal executive offices:
101 South Street, Suite 900, Somerville, MA 02143 |
| Item 2. | |
| (a) | Name of person filing:
The names of the persons filing this report (collectively, the "Reporting Persons") are:
(i) Flagship Pioneering Fund VI, L.P. ("Flagship Fund VI").
(ii) Flagship Pioneering Fund VI General Partner LLC ("Flagship Fund VI GP").
(iii) Pioneering Medicines 02, LLC ("PM02").
(iv) Flagship Pioneering Fund VII, L.P. ("Flagship Fund VII").
(v) Flagship Pioneering Fund VII General Partner LLC ("Flagship Fund VII GP").
(vi) Nutritional Health LTP Fund, L.P. ("Nutritional LTP").
(vii) Nutritional Health LTP Fund General Partner LLC ("Nutritional LTP GP").
(viii) Flagship Pioneering Special Opportunities Fund II, L.P. ("Flagship Opportunities Fund II").
(ix) Flagship Pioneering Special Opportunities Fund II General Partner LLC ("Flagship Opportunities Fund II GP").
(x) FPN II, L.P. ("FPN II Fund").
(xi) FPN General Partner LLC ("FPN GP").
(xii) Flagship VentureLabs VI, LLC ("VentureLabs VI" and together with Flagship Fund VI, PM02, Flagship Fund VII, Nutritional LTP, Flagship Opportunities Fund II and FPN II Fund, the "Flagship Funds").
(xiii) Flagship VentureLabs VI Manager LLC ("VentureLabs VI Manager" and together with Flagship Fund VI GP, Flagship Fund VII GP, Nutritional LTP GP, Flagship Opportunities Fund II GP and FPN GP, the "Flagship GPs").
(xiv) Flagship Pioneering, LLC ("Flagship Pioneering").
(xv) Noubar B. Afeyan, Ph.D. ("Dr. Afeyan"). |
| (b) | Address or principal business office or, if none, residence:
The address of the principal business office of each of the Reporting Persons is:
c/o Flagship Pioneering
55 Cambridge Parkway, Suite 800E
Cambridge, Massachusetts 02142 |
| (c) | Citizenship:
(i) Flagship Fund VI: Delaware
(ii) Flagship Fund VI GP: Delaware
(iii) PM02: Delaware
(iv) Flagship Fund VII: Delaware
(v) Flagship Fund VII GP: Delaware
(vi) Nutritional LTP: Delaware
(vii) Nutritional LTP GP: Delaware
(viii) Flagship Opportunities Fund II: Delaware
(ix) Flagship Opportunities Fund II GP: Delaware
(x) FPN II Fund: Ontario, Canada
(xi) FPN GP: Delaware
(xii) VentureLabs VI: Delaware
(xiii) VentureLabs VI Manager: Delaware
(xiv) Flagship Pioneering: Delaware
(xv) Dr. Afeyan: United States |
| (d) | Title of class of securities:
Common Stock, $0.001 par value per share |
| (e) | CUSIP No.:
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| Item 3. | If this statement is filed pursuant to §§ 240.13d-1(b) or 240.13d-2(b) or (c), check whether the person filing is a: |
| (a) |  Broker or dealer registered under section 15 of the Act (15 U.S.C. 78o);
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| (b) | Bank as defined in section 3(a)(6) of the Act (15 U.S.C. 78c);
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| (c) | Insurance company as defined in section 3(a)(19) of the Act (15 U.S.C. 78c);
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| (d) | Investment company registered under section 8 of the Investment Company Act of 1940 (15 U.S.C. 80a-8);
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| (e) | An investment adviser in accordance with § 240.13d-1(b)(1)(ii)(E);
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| (f) | An employee benefit plan or endowment fund in accordance with § 240.13d-1(b)(1)(ii)(F);
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| (g) | A parent holding company or control person in accordance with § 240.13d-1(b)(1)(ii)(G);
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| (h) | A savings associations as defined in Section 3(b) of the Federal Deposit Insurance Act (12 U.S.C. 1813);
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| (i) | A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act of 1940 (15 U.S.C. 80a-3);
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| (j) | A non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J). If filing as a non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J),
please specify the type of institution:
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| (k) | Group, in accordance with Rule 240.13d-1(b)(1)(ii)(K).
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| | |
| Item 4. | Ownership |
| (a) | Amount beneficially owned:
The information required by this item with respect to each Reporting Person is set forth in Rows 5 through 9 and 11 of the cover page to this Schedule 13G. The ownership percentages reported are based on 128,192,484 shares of Common Stock outstanding as of March 31, 2026, as reported by the Issuer in its Quarterly Report on Form 10-Q filed on May 7, 2026. Flagship Fund VI GP is the general partner of Flagship Fund VI and may be deemed to beneficially own the shares held directly by Flagship Fund VI. Flagship Fund VII is the majority equity holder of PM02 and may be deemed to beneficially own the shares held directly by PM02. Charles R. Carelli, Jr., Chief Financial Officer of Flagship Pioneering, is the sole manager of PM02. Flagship Fund VII GP is the general partner of Flagship Fund VII and may be deemed to beneficially own the shares held directly by each of PM02 and Flagship Fund VII. Nutritional LTP GP is the general partner of Nutritional LTP and may be deemed to beneficially own the shares held directly Nutritional LTP. Flagship Opportunities Fund II GP is the general partner of Flagship Opportunities Fund II and may be deemed to beneficially own the shares held directly by Flagship Opportunities Fund II. FPN GP is the general partner of FPN II Fund and may be deemed to beneficially own the shares held directly by FPN II Fund. VentureLabs VI Manager is the manager of VentureLabs VI and may be deemed to beneficially own the shares held directly by VentureLabs VI. Flagship Pioneering, as the manager of each of the Flagship GPs, and Dr. Afeyan, as the ultimate control person of Flagship Pioneering, may each be deemed to beneficially own the shares held directly by the Flagship Funds. |
| (b) | Percent of class:
See Item 4(a). %
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| (c) | Number of shares as to which the person has:
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| | (i) Sole power to vote or to direct the vote:
See Row 5 of cover page for each Reporting Person.
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| | (ii) Shared power to vote or to direct the vote:
See Row 6 of cover page for each Reporting Person.
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| | (iii) Sole power to dispose or to direct the disposition of:
See Row 7 of cover page for each Reporting Person.
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| | (iv) Shared power to dispose or to direct the disposition of:
See Row 8 of cover page for each Reporting Person.
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| Item 5. | Ownership of 5 Percent or Less of a Class. |
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| Item 6. | Ownership of more than 5 Percent on Behalf of Another Person. |
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Not Applicable
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| Item 7. | Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company or Control Person. |
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Not Applicable
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| Item 8. | Identification and Classification of Members of the Group. |
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Not Applicable
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| Item 9. | Notice of Dissolution of Group. |
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Not Applicable
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Rule 13d-1(d)