Metagenomi, Inc.

Item 5. Other Information.

There have been no material changes to the procedures by which security holders may recommend nominees to the Company’s Board since the Company last provided disclosure in response to the requirements of Item 407(c)(3) of Regulation S-K.

During the quarter ended September 30, 2025, no director or “officer” of the Company, as defined in Rule 16a-1(f) under the Exchange Act, adopted orterminated a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” as each term is defined in Item 408(a) of Regulation S-K.

Departure of Chief Executive Officer

On November 5, 2025, Brian C. Thomas, Ph.D. resigned from his position as the Company’s Chief Executive Officer and Chairman (the “Chair”) of the board of directors of the Company (the “Board”) effective as of November 6, 2025. Dr. Thomas will remain on the Board as a director. On November 5, 2025, the Board appointed Dr. Willard Dere as Chair of the Board, effective as of November 6, 2025.

In connection with Dr. Thomas’s resignation as Chief Executive Officer, the Company and Dr. Thomas entered into a transition agreement (the “Transition Agreement”). In accordance with the terms of the Transition Agreement, Dr. Thomas shall receive one hundred sixty-five thousand dollars ($166,500.00), at the rate of fifty-five thousand dollars ($55,500.00) per month for three months, less applicable withholdings for three months from the first regular payroll date following November 6, 2025. Additionally, Dr. Thomas shall receive a prorated 2025 bonus of $399,600.

Appointment of Chief Executive Officer and Grant of Equity Awards

On November 5, 2025, the Board appointed Jian Irish, Ph.D., M.B.A, the Company’s current President and Chief Operating Officer, as President and Chief Executive Officer and principal executive officer of the Company, effective as of November 6, 2025.

Dr. Irish, 61, has served as the Company’s President since November 2021 and its Chief Operating Officer since January 2021. Prior to joining the Company, Dr. Irish held positions as Senior Vice President, Global Head of Manufacturing and Senior Vice President of Supply Chain at Kite Pharma (now a subsidiary of Gilead) from September 2016 to December 2020. Dr. Irish served as Interim Chief Operating Officer of Affini-T Therapeutics from January 2021 to January 2022. Dr. Irish also served as Interim Chief Technology Officer and a board member for Fosun Kite, a joint venture between Kite Pharma and Fosun Pharma, from October 2018 to April 2020. From December 2014 to August 2016, Dr. Irish held positions as Vice President of Biologics Supply, Outsourcing, Partnerships, and External Manufacturing and Vice President of Product Development at Sanofi. From January 2000 to September 2014, Dr. Irish held various leadership positions at Amgen in operations, including Executive Director of JAPAC Supply, Executive Director of Contract Manufacturing, Officer for Kirin-Amgen JV, and Global Operations Team Leader. Dr. Irish currently serves as an advisor to Ori Biotech, and previously served as an advisor to ORCA Biosystems and ViTToria Biotherapeutics. Dr. Irish received a B.S. in chemical engineering from East China University of Science and Technology, an M.S. and Ph.D. in pharmaceutical sciences from Chiba University, and an M.B.A. from University of California, Los Angeles, Anderson School of Management.

In connection with Dr. Irish’s appointment as the Company’s President and Chief Executive Officer, the Company and Dr. Irish entered into an executive employment agreement on November 6, 2025 (the “Irish Employment Agreement”). The Irish Employment Agreement provides for Dr. Irish’s at-will employment. The base salary for Ms. Irish was increased from $564,000 to $670,000 effective November 16, 2025, and her target annual bonus amount was increased from 50% to 60% of her annual base salary. In addition, Dr. Irish will be granted equity awards on December 1, 2025 (the “Grant Date”). The equity awards will consist of 225,000 options to purchase the Company’s common stock (the “Options”) with an exercise price equal to the closing price of the common stock on the Grant Date, which will vest with 25% of such Options vesting on November 6, 2026, and the remainder vesting in 36 equal monthly installments thereafter, so long as Dr. Irish continues to provide services to the Company through such date; and 37,500 restricted stock units (the “RSUs”), which will vest with 25% of the RSUs vesting on December 5, 2026, and the remainder vesting in 12 equal quarterly installments thereafter, so long as Dr. Irish continues to provide services to the Company through such date. Further, on December 1, 2025, Dr. Irish will be granted an additional equity award consisting of 211,000 RSUs (the “Additional RSUs”), which will vest with 50% of the Additional RSUs vesting on December 5, 2026 and 2027, respectively. Dr. Irish is eligible to participate in the employee benefit plans available to the Company’s employees, subject to the terms of such plans.

Upon termination of Dr. Irish’s employment by us without Cause or her resignation for Good Reason outside of a Change in Control Period, as such terms are defined in the Irish Employment Agreement, subject to (i) Dr. Irish resigning from all positions, (ii) signing a General Release (as defined in the Irish Employment Agreement) in a form and manner satisfactory to the Company, (iii) the General Release becoming irrevocable and fully effective, all within sixty (60) days after the date of termination, and (iv) Dr. Irish not breaching any of the post-employment covenants and contractual obligations to the Company, Dr. Irish shall be entitled to (A) a lump sum payment equal to twelve (12) months of her then current base salary and target bonus in the amount of 1.0 times Dr. Irish’s target bonus, payable within sixty (60) days following her termination, and (B) if Dr. Irish was participating in the Company’s group health plan immediately prior to the termination date, a monthly cash payment for twelve (12) months in an amount equal to Dr. Irish’s and her eligible dependents monthly COBRA premium. In addition, and subject to the same conditions, upon a termination by us without Cause or her resignation for Good Reason during the Change in Control Period, she shall be entitled to (A) a lump sum payment equal to eighteen (18) months of her then current base salary and target bonus in the amount of 1.5 times her target bonus, in a lump sum amount payable within sixty (60) days following the Date of Termination, (B) if Dr. Irish was participating in the Company’s group health plan immediately prior to the termination date, a monthly cash payment for eighteen (18) months in an amount equal to Dr. Irish’s and her eligible dependents monthly COBRA premium, and (C) full acceleration of her then outstanding and unvested time-based vesting equity awards.

The foregoing description of the Irish Employment Agreement is qualified in its entirety by reference to the full text of the Irish Employment Agreement, a copy of which will be filed as an exhibit to the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.

There are no arrangements or understandings between Dr. Irish and any other persons pursuant to which Dr. Irish was appointed as Chief Executive Officer of the Company. In addition, there are no family relationships between Dr. Irish and any director or executive officer of the Company, and there are no transactions involving Dr. Irish requiring disclosure under Item 404(a) of Regulation S-K.

Entry into Employment Agreement with Pamela Wapnick, M.B.A. and Grant of Equity Awards

On November 6, 2025, the Company executed an executive employment agreement with Ms. Wapnick (the “Wapnick Employment Agreement”), for the expanded position of Chief Financial Officer. The Wapnick Employment Agreement provides for Ms. Wapnick’s at-will employment. The base salary for Ms. Wapnick was increased from $461,000 to $500,000 effective November 16, 2025, and her target annual bonus amount was increased from 40% to 45% of her annual base salary. Ms. Wapnick is eligible to participate in the employee benefit plans available to the Company’s employees, subject to the terms of such plans. In addition, Ms. Wapnick will be granted equity awards, consistent with the Company’s company-wide equity retention grant on the December 1, 2025. The equity award will consist of 120,000 RSUs, which will vest with 50% of such RSUs vesting on December 5, 2026 and 2027, respectively, so long as Ms. Wapnick continues to provide services to the Company through such date.

Upon termination of Ms. Wapnick’s employment by us without Cause or her resignation for Good Reason outside of the Change in Control Period, as such terms are defined in the Wapnick Employment Agreement, subject to (i) Ms. Wapnick resigning from all positions, (ii) signing a General Release (as defined in the Wapnick Employment Agreement) in a form and manner satisfactory to the Company, (iii) the General Release becoming irrevocable and fully effective, all within sixty (60) days after the date of termination, and (iv) Ms. Wapnick not breaching any of the post-employment covenants and contractual obligations to the Company, Ms. Wapnick shall be entitled to (A) a lump sum payment equal to nine (9) months of her then current base salary and her target bonus prorated to the date her employment ended, payable within sixty (60) days following her termination, and (B) if Ms. Wapnick was participating in the Company’s group health plan immediately prior to the termination date, a monthly cash payment for nine (9) months in an amount equal to Ms. Wapnick’s and her eligible dependents monthly COBRA premium. In addition, and subject to the same conditions, upon a termination by us without Cause or her resignation for Good Reason during the Change in Control Period, she shall be entitled to (A) a lump sum payment equal to twelve (12) months of her then current base salary and target bonus, in a lump sum amount payable within sixty (60) days following the date of termination, (B) if Ms. Wapnick was participating in the Company’s group health plan immediately prior to the termination date, a monthly cash payment for twelve (12) months in an amount equal to Ms. Wapnick’s and her eligible dependents monthly COBRA premium, and (C) full acceleration of her then outstanding and unvested time-based vesting equity awards.

The foregoing description of the Wapnick Employment Agreement is qualified in its entirety by reference to the full text of the Wapnick Employment Agreement, a copy of which will be filed as an exhibit to the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.