Metagenomi Therapeutics, Inc.

EXECUTIVE COMPENSATION

This section provides an overview of the compensation awarded to, earned by, or paid to our principal executive officer and our two most highly compensated executive officers (other than our principal executive officer) who were serving as executive officers at the end of 2024, in respect of their service to us for the fiscal year ended December 31, 2024. We refer to these individuals as our named executive officers (“NEOs”). Our NEOs for the fiscal year ended December 31, 2024 were:

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Brian C. Thomas, Ph.D., our Chief Executive Officer (“CEO”);

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Jian Irish, Ph.D., M.B.A., our President and Chief Operating Officer; and

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Pamela Wapnick, M.B.A., our Chief Financial Officer.

2024 Summary Compensation Table

(1)

The amounts reported in this column reflect one time special bonuses paid to Dr. Thomas and Dr. Irish for performance during the applicable fiscal year.

(2)

The amounts reported in this column represent the aggregate grant date fair value of equity awards granted to our named executive officers or materially modified during the applicable fiscal year, as calculated in accordance with FASB ASC Topic 718. Such grant date value does not take into account any estimated forfeitures related to service-based vesting conditions. The assumptions used in the grant date fair value of the awards are described in Note 11 – Stock-Based Compensation to our audited consolidated financial statements appearing in our 2024 Annual Report. For fiscal year 2023, the awards consisted of profits interests granted to the named executive officers, which were exchanged in 2024 for unvested restricted common stock in connection with the Reorganization. The amounts reported for fiscal year 2023 include the incremental amount recognized as a result of the amendment to the LLC agreement to include a “catch-up” feature, in the aggregate amount of $4,564,081. For fiscal year 2024, the awards consisted of restricted stock units granted to our NEOs.

(3)

The amounts reported in this column represent the aggregate grant date fair value of stock options granted to our named executive officers during the applicable fiscal year, as calculated in accordance with FASB ASC Topic 718. Such grant date value does not take into account any estimated forfeitures related to service-based vesting conditions. The assumptions used in the grant date fair value of the awards are described in Note 11 – Stock-Based Compensation to our audited consolidated financial statements appearing in our 2024 Annual Report.

(4)

The amounts reported represent annual bonuses under our annual cash bonus program based on achievement of company performance and individual performance during the applicable fiscal year.

(5)

The amounts reported in this column for 2024 reflect an employer matching contribution on the employee’s behalf under our 401(k) plan.

(6)

2024 is Ms. Wapnick’s first year as an NEO, therefore no 2023 compensation data is shown for Ms. Wapnick.

Overview

Our executive compensation program is designed to attract, motivate and retain key employees who we believe best represent our Company values and can make significant contributions towards achieving our commitment of developing curative therapeutics for patients using our proprietary, comprehensive metagenomics-derived genome editing toolbox. Our executive compensation program’s purpose is to incentivize them based on the achievement of key performance goals, and to align their interests with the interests of our stockholders. Under this program, our NEOs’ compensation is based on the achievement of key strategic and business goals that were developed based on the Company’s mission. The program consists of a combination of base salary, an annual cash bonus, long-term equity incentive compensation and other employee benefits generally available to our employees, and is designed to align our executive compensation program with the interests of our stockholders by reflecting a pay-for-performance philosophy that supports our business strategy. At the same time, the Board believes that the program does not encourage excessive risk-taking by management.

Our compensation committee is generally responsible for determining the compensation of our executive officers. In setting executive base salaries and bonuses and granting equity incentive awards, the compensation committee considers compensation for comparable positions in the market, the historical compensation levels of our executive officers, internal equity, our desire to motivate our employees to achieve short- and long-term results that are in the best interests of our stockholders, and a long-term commitment to the Company. We target a general competitive position, based on independent third-party benchmark analytics to inform the mix of compensation of base salary, bonus and long-term incentives. Our compensation committee typically reviews and discusses management’s proposed compensation with our Chief Executive Officer for all executives other than the Chief Executive Officer. Based on those discussions and its discretion, taking into account the factors noted above, the compensation committee then sets the compensation for each executive officer other than the Chief Executive Officer. For the Chief Executive Officer, our compensation committee recommends our Chief Executive Officer’s compensation for approval by our Board of Directors. Our compensation committee may delegate certain authorities to an officer of the Company, as described above in “Corporate Governance - Compensation Committee.”

Our compensation committee has the authority to engage the services of a consulting firm or other outside advisor to assist it in designing our executive compensation programs and in making compensation decisions.

During the fiscal year ended December 31, 2024, our compensation committee engaged the Prior Compensation Consultant, and in November 2024, engaged Aon to assist it in evaluating the Company’s executive and director compensation practices, including program design, identification of an appropriate peer group for compensation comparison purposes and providing pay benchmarking data. The Prior Compensation Consultant and Aon also provided (i) analysis and recommendations to our compensation committee regarding trends and emerging topics with respect to executive compensation; (ii) compensation programs for executives, directors and our employees generally; and (iii) stock utilization and related metrics.

2024 Base Salary

Our NEOs each receive a base salary to compensate them for services rendered to our Company. The base salary payable to each named executive officer is intended to provide a fixed component of compensation reflecting the executive’s skill set, experience, role and responsibilities. Base salaries may be adjusted from time to time to realign salaries with market levels after taking into account individual responsibilities, performance and experience. Effective March 1, 2024, our Board approved increases to our NEO’s base salaries as follows:

2024 Annual Bonus

For the fiscal year ended December 31, 2024, each of the NEOs was eligible to earn an annual cash bonus determined by our board of directors in its sole discretion, based on achievement of certain individual and corporate performance goals, relating primarily to research and development goals, business development and organizational goals. The target annual bonus for each of our named executive officers for the fiscal years ended December 31, 2023 and 2024 was equal to the percentage of the executive’s respective annual base salary specified below:

With respect to the fiscal year ended December 31, 2024, our compensation committee approved a payout of cash bonuses in an amount of 68% of target for each of Dr. Thomas, Dr. Irish and Ms. Wapnick.

Equity-Based Compensation

We believe that equity grants provide our executives with a strong link to our long-term performance, create an ownership culture and help to align the interests of our executives and our stockholders. These equity awards are a key aspect of our compensation philosophy and serve to align the interests of our executive officers with our stockholders, as they are tied to future increases in the value of our stock. Further, we believe that equity awards with a time-based vesting feature promote retention because this feature incentivizes our named executive officers to remain in our employment during the vesting period. Accordingly, our compensation committee periodically reviews the equity incentive compensation of our NEOs and may recommend or approve, as applicable, equity incentive awards to them from time to time. In furtherance of these goals, in 2024, each of our NEOs was granted awards of restricted stock units and stock options.

Prior to our IPO, we historically granted our executives, including our NEOs, profits interests under our 2019 Equity Incentive Plan (the “2019 Plan”). In connection with the Reorganization, these profits interests were exchanged for shares of common stock and restricted common stock of Metagenomi, Inc.

For additional information regarding outstanding equity awards held by our NEOs as of December 31, 2024, see the “Outstanding Equity Awards at 2024 Fiscal Year-End Table” below.

Perquisites/Personal Benefits

Perquisites or other personal benefits are not a significant component of our executive compensation program. Accordingly, we do not provide significant perquisites or other personal benefits to our executive officers, including our NEOs.

Equity Grant Timing

Prior to our public offering in February 2024, we did not have a formal policy regarding the grant of equity. In connection with our public offering in February 2024, we adopted an equity grant policy pursuant to which anyannual equity awards will be made by the board or compensation committee and effective on the first trading day of the month following such approval. In addition, new hires receive equity awards at the time their hiring effective on the first day of the month following approval of such awards. During 2024, our compensation committee did not take into account any material nonpublic information when determining the timing and terms of equity incentive awards, andwe did not time the disclosure of material nonpublic information for the purpose of affecting the value of executive compensation. During 2024, we did not grant stock options to our NEOs during any period beginning four business days before and ending one business day after the filing or furnishing of a Form 10-Q, 10-K or 8-K that discloses material nonpublic information.

401(k) Plan

We maintain a retirement savings plan (“401(k) plan”) that is intended to qualify for favorable tax treatment under Section 401(a) of the Internal Revenue Code (the “Code”) and contains a cash or deferred feature that is intended to meet the requirements of Section 401(k) of the Code. U.S. employees are generally eligible to participate in the 401(k) plan, subject to certain criteria. Participants may make pre-tax and certain after-tax (Roth) salary deferral contributions to the plan from their eligible earnings up to the statutorily prescribed annual limit under the Code. Participants who are 50 years of age or older may contribute additional amounts based on the statutory limits for catch-up contributions. Participant contributions are held in trust as required by law. We provide employer matching contributions of 100% on the first 5% of participant’s compensation contributed to our 401(k) plan.

Outstanding Equity Awards at 2024 Fiscal Year-End Table

The following table lists all outstanding equity awards held by our NEOs as of December 31, 2024.

(1)

Represent stock option awards granted under our 2024 Stock Option and Incentive Plan which vest as follows: 25% of the shares subject to each option vested or will vest on the one year anniversary of the vesting commencement date, with the remainder vesting in 36 equal monthly installments thereafter, subject to continued service through each vesting date.

(2)

The fair market value is based on the closing price of our common stock on December 31, 2024, the last trading date of 2024, of $3.61.

(3)

Represent unvested restricted common stock our NEOs received in exchange for profits interests units upon conversion of the Company from a limited liability company to a C corporation. The unvested restricted common stock vest as follows: 25% vest on the one year anniversary of the vesting commencement date; and then the remaining 75% of the total vest in substantially equal amounts on each monthly anniversary of the vesting commencement date thereafter, until fully vested on the fourth anniversary of the vesting commencement date, subject to continued service through each vesting date.

(4)

Represents unvested restricted stock units granted under our 2024 Stock Option and Incentive Plan which vest as follows: 25% vest on June 5, 2025, with the remainder vesting in 12 equal quarterly installments thereafter, subject to continued service through each vesting date.

(5)

Represents unvested restricted stock units granted under our 2024 Stock Option and Incentive Plan which vest as follows: 25% vested on September 5, 2024, with the remainder vested or will vest in 12 equal quarterly installments thereafter, subject to continued service through each vesting date.

Current Employment Agreements with our NEOs

We have entered into offer letters and/or employment agreements with each of our named executive officers. Each offer letter or employment agreement provides for “at-will” employment and the compensation and benefits described below.

Brian C. Thomas, Ph.D.

On March 20, 2023, the Company executed an executive employment agreement with Dr. Thomas (the “Thomas Employment Agreement”), for the position of Chief Executive Officer. The Thomas Employment Agreement provides for Dr. Thomas’s at-will employment. The base salary for Dr. Thomas was increased from $520,000 to $650,000, effective March 1, 2024 and his target annual bonus amount was increased for 2024 from 50% to 60% of his annual base salary. In February 2025, the compensation committee recommended, and our board of directors approved, an increase to Dr. Thomas’ 2025 base salary to $666,000. Dr. Thomas is eligible to participate in the employee benefit plans available to our employees, subject to the terms of such plans.

Dr. Thomas entered into an Employee Invention Assignment and Confidentiality Agreement that contains various restrictive covenants, including non-solicitation provisions that apply during his employment and for a period of twelve months thereafter.

Upon termination of Dr. Thomas’s employment by us without Cause or his resignation for Good Reason outside of the Change in Control Period, as such terms are defined in the Thomas Employment Agreement, subject to (i) Dr. Thomas resigning from all positions, (ii) signing a general release of claims in favor of the Company and (iii) not breaching any of the post-employment covenants and contractual obligations to the Company, Dr. Thomas shall be entitled to (A) a lump sum payment equal to nine (9) months of his then current base salary and pro-rated target bonus, based on the number of days he was employed in such year, divided by 365, payable within sixty (60) days following his termination, and (B) if Dr. Thomas 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 Dr. Thomas’s and his eligible dependents monthly COBRA premium. In addition, and subject to the same conditions, upon a termination by us without Cause or his resignation for Good Reason during the Change in Control Period, he shall be entitled to (A) a lump sum payment equal to twelve (12) months of his then current base salary and pro-rated target bonus, based on the number of days he was employed in such year, divided by 365, payable within sixty (60) days following his termination, (B) if Dr. Thomas 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. Thomas’s and his eligible dependents monthly COBRA premium, and (C) full acceleration of his then outstanding and unvested equity awards. The foregoing benefits would not apply in the event Dr. Thomas receives benefits under the Company’s Severance Policy (as defined below).

Jian Irish, Ph.D., M.B.A.

On January 19, 2021, the Company executed an offer letter with Dr. Irish (the “Irish Offer Letter”), for the position of Chief Operations Officer. The Irish Offer Letter provides for Dr. Irish’s at-will employment. Dr. Irish was promoted to President and Chief Operating Officer effective November 1, 2021. The base salary for Dr. Irish was increased from $468,000 to $550,000 effective March 1, 2024 and her target annual bonus amount was increased from 45% to 50% of her annual base salary. In February 2025, the compensation committee approved an increase to Dr. Irish’s 2025 base salary to $564,000. Dr. Irish is eligible to participate in the employee benefit plans available to our employees, subject to the terms of such plans.

Upon a termination of Dr. Irish’s agreement by us without Cause, or her resignation for Good Reason, as such terms are defined in the Irish Offer Letter, she will be eligible to receive six (6) months of base salary, pro-rated annual bonus, and six (6) months vesting acceleration. The foregoing benefits would not apply in the event Dr. Irish receives benefits under the Company’s Severance Policy.

Dr. Irish entered into an Employee Invention Assignment and Confidentiality Agreement that contains various restrictive covenants, including non-solicitation provisions that apply during her employment and for a period of twelve months thereafter.

Pamela Wapnick, M.B.A.

On September 1, 2023, the Company executed an offer letter with Ms. Wapnick (the “Wapnick Offer Letter”), for the position of Chief Financial Officer. The Wapnick Offer Letter provides for Ms. Wapnick’s at-will employment. The base salary for Ms. Wapnick was increased from $420,000 to $450,000 effective March 1, 2024 and her target annual bonus amount is 40% of her annual base salary. In February 2025, the compensation committee approved an increase to Ms. Wapnick’s 2025 base salary to $461,000. Ms. Wapnick is eligible to participate in the employee benefit plans available to our employees, subject to the terms of such plans. In addition, Ms. Wapnick is also eligible to receive severance benefits upon a qualifying termination pursuant to our Severance Policy (as described below).

Ms. Wapnick entered into an Employee Invention Assignment and Confidentiality Agreement that contains various restrictive covenants, including non-solicitation provisions that apply during her employment and for a period of twelve months thereafter.

Employee Benefit and Equity Compensation Plans

2019 Equity Incentive Plan

The 2019 Plan was initially approved by the board of managers of the Company in March 2019. The 2019 Plan provided for the grant of profits interests, restricted common units, options to purchase common units and restricted equity units to selected employees, officers, directors and consultants of the Company. The 2019 Plan was terminated in connection with the Reorganization.

2024 Stock Option and Incentive Plan

The 2024 Stock Option and Incentive Plan (as amended from time to time, the “2024 Plan”) replaced the 2019 Plan. The 2024 Plan provides flexibility to our compensation committee to use various equity-based incentive awards as compensation tools to motivate our workforce.

2024 Employee Stock Purchase Plan

The 2024 Employee Stock Purchase Plan (the “ESPP”) includes two components: a Code Section 423 Component (the “423 Component”), and a non-Code Section 423 Component, or the Non-423 Component. The 423 Component is intended to qualify as an “employee stock purchase plan” under Section 423 of the Code. Under the Non-423 Component, which does not qualify as an “employee stock purchase plan” within the meaning of Section 423 of the Code, options will be granted pursuant to rules adopted by the administrator of the ESPP designed to achieve tax or securities laws, or other objectives for eligible employees.

Senior Executive Cash Incentive Bonus Plan

Our Senior Executive Cash Incentive Bonus Plan, provides for cash bonus payments based upon Company and individual performance targets established by our compensation committee. The payment targets will be related to financial and operational measures or objectives with respect to our company, or the corporate performance goals, as well as individual performance objectives.

Executive Severance and Change in Control Policy

Our board of directors adopted an Executive Severance and Change in Control Policy (the “Severance Policy”) in which our named executive officers, and certain other executives, participate. The benefits provided in the Severance Policy replaced any severance for which our executive officers may be eligible under their existing severance and change in control agreements; provided that, in the event an executive is party to an agreement or other arrangement that provides greater benefits than set forth in the Severance Policy, such executive will be entitled to receive the payments and benefits under such other agreement or arrangement and will not be eligible to receive any payments or benefits under the Severance Policy.

The Severance Policy provides that upon a termination due to death, “disability”, as defined in the Severance Policy, or “retirement” (as defined in the Severance Policy), an eligible executive will be entitled to receive, subject in the case of a termination due to retirement to the execution and delivery of an effective and irrevocable release of claims in favor of the Company and continued compliance with all applicable restrictive covenants, (i) a lump sum amount equal to the eligible executive’s annual target bonus in effect immediately prior to such termination, pro-rated for the number of days of service provided by the participant during the year of the termination, and (ii) for all outstanding and unvested equity awards of the company that are subject to time-based vesting held by the participant, full accelerated vesting of such awards; provided, that the performance conditions applicable to any outstanding and unvested equity awards subject to performance-based vesting will be deemed satisfied in accordance with the terms of the applicable award agreement.

The Severance Policy provides that upon a termination by us without “cause,” as defined in the Severance Policy, or a resignation by the executive for “good reason,” as defined in the Severance Policy, in each case outside of the change in control period (i.e., the period of one year after a “sale event,” as defined in the Severance Policy), an eligible executive will be entitled to receive, subject to the execution and delivery of an effective and irrevocable release of claims in favor of the company and continued compliance with all applicable restrictive covenants, (i) base salary continuation for 12 months for our Chief Executive Officer, 9 months for Tier 2 officers (which is determined by the plan administrator and includes the named executive officers other than the Chief Executive Officer) and 6 months for Tier 3 officers (which is determined by the Policy administrator but generally includes vice presidents and above) and (ii) an amount equal to the monthly employer contribution, based on the premiums as of the date of termination, that we would have made to provide health insurance for the applicable executive if he or she had remained employed by us for up to 12 months for our Chief Executive Officer, 9 months for Tier 2 officers and 6 months for Tier 3 officers. The payments under (i) and (ii) will be paid in substantially equal installments in accordance with our payroll practice over 12 months for our Chief Executive Officer, 9 months for Tier 2 officers and 6 months for Tier 3 officers. The Severance Policy will also provide that upon a (A) termination by us without cause or (B) resignation for good reason, in each case within the change in control period, an eligible executive will be entitled to receive, in lieu of the payments and benefits above and subject to the execution and delivery of an effective and irrevocable release of claims in favor of the company and continued compliance with all applicable restrictive covenants, (I) a lump sum amount equal to the executive’s base salary for a period of 18 months for our Chief Executive Officer, 12 months for our Tier 2 officers and 10 months for our Tier 3 officers, (II) a lump sum payment equal to 100% of the executive’s annual target bonus in effect immediately prior to the date of termination, pro-rated for the number of days of service provided by the executive during the year of the termination, (III) a lump sum amount equal to the monthly employer contribution, based on the premiums as of the date of termination, that we would have made to provide health insurance for the applicable executive if he or she had remained employed by us for 18 months for our Chief Executive Officer, 12 months for our Tier 2 officers and 10 months for our Tier 3 officers, and (IV) for all outstanding and unvested equity awards of the company that are subject to time-based vesting held by the participant, full accelerated vesting of such awards; provided, that the performance conditions applicable to any outstanding and unvested equity awards subject to performance-based vesting will be deemed satisfied in accordance with the terms of the applicable award agreement.

The payments and benefits provided under the Severance Policy in connection with a change in control may not be eligible for a federal income tax deduction by us pursuant to Section 280G of the Code. These payments and benefits may also subject an eligible executive, including the named executive officers, to an excise tax under Section 4999 of the Code. If the payments or benefits payable in connection with a change in control would be subject to the excise tax imposed under Section 4999 of the Code, then those payments or benefits will be reduced if such reduction would result in a higher net after-tax benefit to the participant.

Equity Compensation Plan Information

The following table provides information as of December 31, 2024 with respect to the shares of our common stock that may be issued under our existing equity compensation plans:

(1)

The weighted-average exercise price does not reflect the shares of our common stock that will be issued in connection with the settlement of restricted stock unit awards, which have no exercise price.

(2)

The 2024 Plan contains an “evergreen” provision, pursuant to which, on or about January 1, 2025 and each anniversary of such date thereafter until the expiration of the plan, the maximum number of shares reserved for issuance under the 2024 Plan is increased by a number equal to the lesser of (i) 5% of the number of shares of common stock issued and outstanding on December 31 of the immediately preceding fiscal year or (ii) such lesser number of shares as determined by our compensation committee or board of directors. Pursuant to the terms of the 2024 Plan, an additional 1,870,923 shares were added to the number of available shares, effective January 1, 2025.

(3)

The ESPP has an evergreen provision that allows for an annual increase in the number of shares available for issuance under the ESPP to be added on or about January 1, 2025 and on each anniversary of such date thereafter prior to the termination of the plan, in an amount equal to the lesser of (i) 750,000 shares of common stock, (ii) 1% of the number of shares of our common stock issued and outstanding on December 31 of the immediately preceding fiscal year, or (iii) such number of shares of common stock as determined by our compensation committee or board of directors. Pursuant to the terms of the ESPP, an additional 374,184 shares were added to the number of available shares, effective January 1, 2025.

(4)

Does not include purchase rights accruing under the ESPP because the purchase price (and therefore the number of shares to be purchased) will not be determined until the end of the applicable purchase period.