Flagship VentureLabs IV SC 13D/ASeres Therapeutics / Flagship VentureLabs IV ownership change

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

UNDER THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 2)*

Seres Therapeutics, Inc.

(Name of Issuer)

Common Stock, $0.001 par value per share

(Title of Class of Securities)

81750R 10 2

(CUSIP Number)

Noubar B. Afeyan, Ph.D.

Flagship Pioneering

55 Cambridge Parkway, Suite 800E

Cambridge, MA 02142

(617) 868-1888

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

July 5, 2022

(Date of Event Which Requires Filing of Statement on Schedule 13D)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), checking the following box.  ☐

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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EXPLANATORY NOTE

This Amendment No. 2 (this “Amendment”) amends and supplements the Schedule 13D (the “Schedule 13D”) filed by the Reporting Persons (as defined below) on June 28, 2019, as amended, with respect to the shares of common stock, $0.001 par value per share (“Common Stock”), of Seres Therapeutics, Inc. (the “Company” or the “Issuer”). Except as specifically provided herein, this Amendment does not modify any of the information previously reported in the Schedule 13D.

Item 2 of the Schedule 13D is hereby amended and restated as follows:

This Schedule 13D is being filed by the following persons (each a “Reporting Person”):

The principal business of each Reporting Person is the venture capital investment business. The principal business address of each Reporting Person is 55 Cambridge Parkway, Suite 800E, Cambridge, Massachusetts 02142.

During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

During the last five years, none of the Reporting Persons has been party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding were or are subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

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Item 4 is hereby amended to include the following:

On July 5, 2022, Nutritional LTP and Flagship Fund VII purchased 2,912,748 shares and 5,825,495 shares, respectively, of the Issuer’s Common Stock in a registered direct offering (the “July 2022 Offering”) at a price per share of $3.15.

Item 5(a)-(c) is hereby amended and restated as follows:

(a)-(b) The information set forth in rows 7 through 13 of the cover pages to this Schedule 13D is incorporated by reference. The percentage set forth in row 13 is based on 124,008,086 outstanding shares of Common Stock following the July 2022 Offering, as disclosed in the Issuer’s Form 424(b)(5) prospectus supplement filed with the Securities and Exchange Commission on June 30, 2022.

VentureLabs IV, Flagship Fund IV and Flagship Fund IV-Rx directly hold 2,734,994 shares, 4,434,600 shares, and 1,283,282 shares of Common Stock, respectively. Flagship Fund IV, as the manager of VentureLabs IV, may be deemed to beneficially own the shares directly held by VentureLabs IV. Flagship Fund IV GP, as the general partner of the Flagship Fund IV Funds, may be deemed to beneficially own the shares directly held by the Flagship Fund IV Funds.

Nutritional LTP directly holds 5,875,711 shares of Common Stock. Nutritional LTP GP, as the general partner of Nutritional LTP, may be deemed to beneficially own the shares directly held by Nutritional LTP.

Flagship Fund VI directly holds 2,962,963 shares of Common Stock. Flagship Fund VI GP, as the general partner of Flagship Fund VI, may be deemed to beneficially own the shares directly held by Flagship Fund VI.

Flagship Fund VII directly holds 5,825,495 shares of Common Stock. Flagship Fund VII GP, as the general partner of Flagship Fund VII, may be deemed to beneficially own the shares directly held by Flagship Fund VII.

Flagship Pioneering, as the manager of each of Flagship Fund VI GP and Flagship Fund VII GP, may be deemed to beneficially own the shares held directly by Flagship Fund VI and Flagship Fund VII.

Dr. Afeyan, as the sole manager of each of Flagship Fund IV GP and Nutritional LTP GP and as CEO, sole shareholder and director of Flagship Pioneering, may be deemed to beneficially own the shares directly held by each of the Flagship IV Funds, Nutritional LTP, Flagship Fund VI and Flagship Fund VII. Dr. Afeyan also holds 363,165 shares of Common Stock directly, in addition to 12,853 shares of Common Stock held by a trust for the benefit of Dr. Afeyan’s children.

(c) On July 5, 2022, Nutritional LTP and Flagship Fund VII purchased 2,912,748 shares and 5,825,495 shares, respectively, of the Issuer’s Common Stock in connection with the Issuer’s July 2022 Offering. The purchase price was $3.15 per share.

Item 6 is hereby amended to include the following:

In connection with the July 2022 Offering, the Issuer entered into a Securities Purchase Agreement (the “Non-Affiliate Purchase Agreement”) with certain institutional accredited investors named therein, including certain of the Reporting Persons. Pursuant to the Non-Affiliate Purchase Agreement, the Issuer agreed to issue and sell an aggregate of 31,238,094 shares of Common Stock at a purchase price of $3.15 per share pursuant to an effective shelf registration statement on Form S-3, as amended (File No. 333-244401) and a related prospectus supplement filed with the Securities and Exchange Commission.

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The Non-Affiliate Purchase Agreement contains customary representations, warranties and agreements by the Company, customary conditions to closing, indemnification obligations of the Company and the Purchasers, including for liabilities under the Securities Act of 1933, as amended (the “Securities Act”), other obligations of the parties and termination provisions.

The foregoing description of the Non-Affiliate Purchase Agreement is not complete and is qualified in its entirety by reference to the full text of the Non-Affiliate Purchase Agreement, a copy of which is filed as Exhibit 99.2 and is incorporated by reference herein.

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SIGNATURE

After reasonable inquiry and to the best of its knowledge and belief, the undersigned certifies that the information set forth in this Statement is true, complete and correct.

Dated: July 7, 2022

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JOINT FILING AGREEMENT

The persons below hereby agree that the Schedule 13D to which this agreement is attached as an exhibit, as well as all future amendments to such Schedule 13D, shall be filed jointly on behalf of each of them. This agreement is intended to satisfy the requirements of Rule 13d-1(k)(1)(iii) under the Securities Exchange Act of 1934.

Dated: July 7, 2022

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