Metagenomi Therapeutics, Inc.

Reorganization

We previously operated as a Delaware limited liability company under the name Metagenomi Technologies, LLC. On January 24, 2024, we completed a series of transactions pursuant to which Metagenomi Technologies, LLC merged with and into its wholly-owned subsidiary, Metagenomi, Inc., a Delaware corporation, with Metagenomi, Inc. continuing as the surviving corporation (the “Reorganization”). In connection with the Reorganization (i) all of the outstanding common unitholders of Metagenomi Technologies, LLC received shares of common stock of Metagenomi, Inc., (ii) all of the outstanding redeemable convertible preferred unitholders of Metagenomi Technologies, LLC received shares of redeemable convertible preferred stock of Metagenomi, Inc. with the same rights and privileges and (iii) certain holders of profits interests in Metagenomi Technologies, LLC received shares of common stock or unvested restricted common stock in Metagenomi, Inc. as determined by the applicable provisions of the Amended and Restated Limited Liability Company Agreement in effect immediately prior to the Reorganization. In connection with the Reorganization, by operation of law, Metagenomi, Inc. acquired all assets of the Metagenomi Technologies, LLC, and assumed all of its liabilities and obligations. The Reorganization was a non-taxable transaction to Metagenomi, Inc. for U.S. income tax purposes.

Board Composition and Structure

Our nominating and corporate governance committee’s and our Board’s priority in selecting board members is identification of persons who will further the interests of our stockholders through their established record of professional accomplishment, the ability to contribute positively to the collaborative culture among board members, knowledge of our business, understanding of the competitive landscape, professional and personal experiences and expertise relevant to our growth strategy. Our directors hold office until their successors have been elected and qualified or until their earlier resignation, removal, or death. Our amended and restated certificate of incorporation and our amended and restated bylaws also provide that our directors may be removed only for cause by the affirmative vote of at least two-thirds of the outstanding shares of common stock then entitled to vote on the election of directors, and that any vacancy on our Board, including a vacancy resulting from an enlargement of our Board, may be filled only by vote of a majority of our directors then in office.

In accordance with the terms of our amended and restated certificate of incorporation, our Board is divided into three staggered classes of directors and each director is assigned to one of the three classes. At each annual meeting of the stockholders, one class of directors is elected for a three-year term to succeed the directors of the same class whose terms are then expiring. The terms of the directors expire upon the election and qualification of successor directors at the annual meeting of stockholders to be held during the years 2025 for Class I directors, 2026 for Class II directors, and 2027 for Class III directors. Our amended and restated certificate of incorporation and our amended and restated bylaws provide that the number of our directors shall be fixed from time to time by a resolution of the majority of our Board.

On March 11, 2025, Sebastián Bernales, Ph.D., a member of the Company’s board of directors, informed the Company that he has decided not to stand for reelection at the Annual Meeting. As a result, Dr. Bernales’ service as a member of our Board will end effective as of the date of the Annual Meeting.

Board Leadership Structure

We do not have a policy on whether the roles of Chief Executive Officer and chair should be separate. Our corporate governance guidelines provide our board of directors the flexibility to determine the appropriate leadership structure to best support the dynamic demands of our business, including whether the offices of Chief Executive Officer and chair should be separate or combined. In making this determination, our board of directors considers many factors, including the needs of the business, our board of directors’ assessment of its leadership needs from time to time and the best interests of our stockholders. Brian C. Thomas, Ph.D., our Chief Executive Officer, currently serves as the chair of our board of directors. Our board of directors is of the view that the combined role of chair and Chief Executive Officer promotes united leadership and direction and provides management a clear focus to execute our strategy and business plans. As Chief Executive Officer, Dr. Thomas is best suited to ensure that critical business issues are brought before our board of directors, which enhances our board of directors’ ability to develop and implement business strategies. For these reasons and because of the strong leadership of Dr. Thomas, our board of directors has concluded that our current leadership structure is appropriate at this time.

Willard H. Dere, M.D. currently serves as our lead independent director. In sessions of our board of director meetings in which our management, including our Chief Executive Officer, does not participate, the lead independent director serves as a liaison to management on behalf of the non-employee members of our board of directors. The lead independent director’s duties and responsibilities also include serving as the liaison between the chair of our board of directors and the independent directors, reviewing meeting agendas, having the authority to call meetings of the independent directors and performing such other duties and responsibilities as may be delegated to the lead independent director by the board of directors from time to time.

Director Nomination Process

In considering whether to recommend any particular candidate for inclusion in our Board’s slate of recommended director nominees, our nominating and corporate governance committee takes into account the current size and composition of the Board and the needs of the Board and its committees, in addition to character, integrity, judgment, independence, skills, education, expertise, business acumen, business experience, length of service, understanding of the Company’s business and industry, conflicts of interest and other commitments. Our nominating and corporate governance committee also takes into account a candidate’s diversity, including diversity of professional experience, skills, knowledge, opinions, perspectives, social and economic background, age, and other differentiating characteristics. However, the committee does not assign any particular weight or priority to any one factor.

While we do not have a formal policy on Board diversity, the Board is committed to building a Board that consists of the optimal mix of skills, expertise, knowledge, backgrounds, personal qualities and diversity of experiences and perspectives so that the Board is capable of effectively overseeing the execution of our business and meeting the Company’s evolving needs.

The biography for each of the director nominees included herein indicates each nominee’s experience, qualifications, attributes and skills that led our nominating and corporate governance committee and our Board to conclude each such director should continue to serve as a director of our Company. Our nominating and corporate governance committee and our Board believe that each of the nominees has the individual attributes and characteristics required of each of our directors, and the nominees as a group possess the skill sets and specific experience desired of our Board as a whole.

Our amended and restated bylaws establish advance notice procedures with regard to stockholder proposals relating to the nomination of candidates for election as directors or new business to be brought before meetings of our stockholders. These procedures are described in more detail herein in the “General Matters” section under the subheading “Stockholder Proposals for 2026 Annual Meeting.” Stockholder-recommended candidates and stockholder nominees whose nominations comply with these procedures and who meet the criteria referred to above will be evaluated by the nominating and corporate governance committee in the same manner as the nominating and corporate governance committee’s nominees.

Director Composition

Our Board currently consists of six (6) members. Below is a list of the names, ages as of April 14, 2025 and classification of the individuals who currently serve as our directors.

• On March 11, 2025, Dr. Bernales informed the Company that he has decided not to stand for reelection at the Annual Meeting. As a result, Dr. Bernales’ service as a member of our Board will end effective as of the date of the Annual Meeting.

Director Nominees

Class I Directors – Present Terms Expiring at the Annual Meeting and Proposed Terms Expiring at the 2028 Annual Meeting of Stockholders

Willard H. Dere, M.D. has served on our board of directors since August 2021 and as lead independent director since November 2024. Dr. Dere currently serves as Chief Advisor and Chief Medical Officer at Angitia since July 2022, and on the board of directors of BioMarin, Seres and Mersana. From November 2014 to August 2022 he served as a director at Radius Health. He also serves on the Scientific Advisory Boards of Surrozen, AliveGen and Heranova Lifesciences. Dr. Dere served as a Professor of Internal Medicine from November 2014 to July 2022 at the University of Utah School of Medicine, and is currently Professor Emeritus, a position he has held since July 2022. Dr. Dere also served as Associate Vice President for Research, Co-Director of The Center for Genomic Medicine and Co-Director of the Utah Clinical and Translational Science Institute at the University of Utah Health Sciences Center during this time period. Before joining the University of Utah, Dr. Dere held various positions at Amgen, Inc., including Senior Vice President of Global Development and Corporate, then International Chief Medical Officer, from July 2003 to October 2014. From 1989 to 2003, Dr. Dere held multiple positions in clinical research, and regulatory affairs and safety at Eli Lilly and Company. He was also an assistant professor from 1989 to 1999 and a clinical associate professor from 1999 to 2009 at the Indiana University School of Medicine. Dr. Dere received his B.A. in history, zoology and M.D. from the University of California, Davis; he completed his postdoctoral training at the University of Utah in internal medicine, and at the University of California, San Francisco in endocrinology and metabolism.

We believe that Dr. Dere is qualified to serve on our Board of Directors because of his extensive experience in drug development, and as a board of directors member on several public companies.

Directors Continuing in Office

Class II Directors – Term Expiring at the 2026 Annual Meeting of Stockholders

Juergen Eckhardt, M.D., M.B.A. has served as our Chairman of the Board of Directors from September 2020 to February 2024. Dr. Eckhardt has served as Head of Leaps at Bayer AG since February 2019 and previously served as Head of Venture Investments from September 2016 to February 2019. He currently serves on the boards of Dewpoint Therapeutics, Khloris Biosciences, Oerth Bio, and a few other private biotechnology companies and foundations. Previously, Dr. Eckhardt served as a management consultant and Associate Partner at McKinsey & Co. and a member of McKinsey’s Healthcare Leadership Team from 1994 to 2002. Dr. Eckhardt received his M.D. from the University of Basel and his M.B.A. from INSEAD in Fontainebleau, France.

We believe that Dr. Eckhardt is qualified to serve as a director because of his extensive experience in strategy, finance, leadership and drug development.

Eric Bjerkholt, M.B.A. has served on our board of directors since January 2025. Mr. Bjerkholt has served as the Chief Financial Officer of Mirum Pharmaceuticals, Inc., a biopharmaceutical company developing treatments for orphan and rare diseases, since September 2023. Prior to that, Mr. Bjerkholt served as Chief Financial Officer of Chinook Therapeutics, Inc., a biopharmaceutical company focused on kidney diseases, from November 2020 to August 2023. In August 2023, Chinook Therapeutics was acquired by Novartis AG. Before Chinook Therapeutics, Inc., he served as the Chief Financial Officer of Aimmune Therapeutics, Inc., a biotechnology company developing treatments for food allergies, from April 2017 to November 2020, at which time, Aimmune was acquired by Nestle Health Science US Holdings, Inc. Prior to Aimmune Therapeutics, Mr. Bjerkholt spent 13 years at Sunesis Pharmaceuticals, Inc. from 2004 until 2017, where in addition to his role as Chief Financial Officer, Mr. Bjerkholt served in various capacities, including Executive Vice President of Corporate Development and Finance, Corporate Secretary and Chief Compliance Officer. Previously, Mr. Bjerkholt held senior executive finance roles at IntraBiotics Pharmaceuticals, Inc., LifeSpring Nutrition, Inc. and Age Wave, LLC and spent seven years in healthcare investment banking at J.P. Morgan & Company, Inc. He is currently a member of the board of directors of Surrozen, Inc., a publicly traded biotechnology company, and a member of the board of directors of Cerus Corporation, a publicly traded biotechnology company. Mr. Bjerkholt previously served as a member of the board of directors and Chair of the audit committee of CalciMedica, Inc., a publicly traded biotechnology company, from September 2020 until January 2025. Mr. Bjerkholt holds a Cand. Oecon degree in economics from the University of Oslo in Norway and an M.B.A. from Harvard Business School.

We believe that Mr. Bjerkholt is qualified to serve as a director because of his extensive experience in, finance, strategy, leadership, and the biotechnology industry.

Class III Directors – Terms Expiring at the 2027 Annual Meeting of Stockholders

Brian C. Thomas, Ph.D. is our founder and has served as our Chief Executive Officer since September 2016 and as our Chairman of the Board since February 2024. Since December 2022, Dr. Thomas has served as Chairman of the Board of Directors of Haya Therapeutics, Inc. Previously, from 2001 to 2017, Dr. Thomas served as a program manager at University of California, Berkeley. From 1999 to 2001, Dr. Thomas served as a lead bioinformatics scientist at EOS Biotechnology (now PDL, Inc.). Dr. Thomas received his B.Sc. in cellular biology and his Ph.D. in biochemistry from University of Kansas and completed his post-doctoral research in computational biology at University of California, Berkeley.

We believe that Dr. Thomas is qualified to serve as a director because of his considerable academic and research expertise, as well as his expansive knowledge about our Company as our founder and Chief Executive Officer.

Jian Irish, Ph.D., M.B.A. has served as our President since November 2021 and our Chief Operating Officer since January 2021. Prior to joining us, 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.

We believe that Dr. Irish is qualified to serve as a director because of her considerable academic and research expertise, as well as her expansive knowledge about our Company as our President and Chief Operating Officer.

We believe that all of our current Board members possess the professional and personal qualifications necessary for Board service and have highlighted particularly noteworthy attributes for each Board member in the individual biographies above.

Director Independence

Our common stock is listed on the Nasdaq Global Select Market. Under the Nasdaq listing rules, independent directors must comprise a majority of a listed company’s board of directors within twelve months from the date of listing. In addition, the Nasdaq listing rules require that, subject to specified exceptions, each member of a listed company’s audit, compensation and nominating and corporate governance committees be independent within twelve months from the date of listing. Audit committee members must also satisfy additional independence criteria, including those set forth in Rule 10A-3 under the Exchange Act and compensation committee members must also satisfy the independence criteria set forth in Rule 10C-1 under the Exchange Act. Under Nasdaq listing rules, a director will only qualify as an “independent director” if, in the opinion of that company’s board of directors, that person does not have a relationship that would interfere with the exercise of independent judgment in carrying out the responsibilities of a director. In order to be considered independent for purposes of Rule 10A-3 under the Exchange Act, a member of an audit committee of a listed company may not, other than in his or her capacity as a member of the audit committee, the board of directors or any other board committee: (i) accept, directly or indirectly, any consulting, advisory or other compensatory fee from the listed company or any of its subsidiaries, other than compensation for board service; or (ii) be an affiliated person of the listed company or any of its subsidiaries. In order to be considered independent for purposes of Rule 10C-1, the board of directors must consider, for each member of a compensation committee of a listed company, all factors specifically relevant to determining whether a director has a relationship to such company which is material to that director’s ability to be independent from management in connection with the duties of a compensation committee member, including, but not limited to: the source of compensation of the director, including any consulting advisory or other compensatory fee paid by such company to the director, and whether the director is affiliated with the company or any of its subsidiaries or affiliates.

In March of 2025, our board of directors undertook a review of the composition of our board of directors and its committees and the independence of each director. Based upon information requested from and provided by each director concerning his or her background, employment and affiliations, including family relationships, our board of directors has determined that all current members of our board of directors, except Brian C. Thomas and Jian Irish, and each former director who served as a member of the Board during the last fiscal year, are independent directors, including for purposes of Nasdaq and the SEC rules. Dr. Thomas and Dr. Irish are not independent under the Nasdaq Rules as a result of their positions as our Chief Executive Officer and Chief Operating Officer, respectively. In making these determinations, our Board considered the current and prior relationships that each non-employee director has with our company and all other facts and circumstances our Board deemed relevant in determining their independence, including the beneficial ownership of our shares by each non-employee director and the transactions described herein. We believe that the composition and functioning of our board of directors and each of our committees comply with all applicable requirements of Nasdaq and the rules and regulations of the SEC. There are no family relationships among any of our executive officers and directors.

Role of Board in Risk Oversight Process and Board Leadership Structure

Our Board has an active role, as a whole and also at the committee level, in overseeing the management of our risks. Our Board is responsible for general oversight of risks and regular review of information regarding our risks, including credit risks, liquidity risks, operational risks and cybersecurity. The compensation committee is responsible for overseeing the management of risks relating to our executive compensation plans and arrangements. The audit committee is responsible for overseeing the management of risks relating to accounting, cybersecurity, and financial reporting matters. The nominating and corporate governance committee is responsible for overseeing the management of risks associated with the independence of our Board and potential conflicts of interest. Although each committee is responsible for evaluating certain risks and overseeing the management of such risks, the entire Board is regularly informed through discussions from committee members about such risks. Our Board believes its administration of its risk oversight function has not negatively affected our Board’s leadership structure.

Board Committees

Our Board has established an audit committee, a compensation committee and a nominating and corporate governance committee, each of which operates pursuant to a charter adopted by our Board. We believe that the composition and functioning of all of our committees comply with the applicable requirements of Nasdaq, the Sarbanes-Oxley Act of 2002 and SEC rules and regulations that are applicable to us. We intend to comply with future requirements to the extent they become applicable to us.

The full text of our audit committee charter, compensation committee charter and nominating and corporate governance committee charter are posted on the “Corporate Governance” portion of our website athttps://ir.metagenomi.co/. We do not incorporate the information contained on, or accessible through, our corporate website into this proxy statement, and you should not consider it a part of this proxy statement.

The following table describes which directors serve on each of our Board’s committees as of April 14, 2025.

Audit Committee

Among other things, our audit committee’s responsibilities include:

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appointing, approving the compensation of, and assessing the independence of our independent registered public accounting firm;

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pre-approving auditing and permissible non-audit services, and the terms of such services, to be provided by our independent registered public accounting firm;

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reviewing the overall audit plan with our independent registered public accounting firm and members of management responsible for preparing our financial statements;

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reviewing and discussing with management and our independent registered public accounting firm our annual and quarterly financial statements and related disclosures as well as critical accounting policies and practices used by us;

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coordinating the oversight and reviewing the adequacy of our internal control over financial reporting;

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establishing policies and procedures for the receipt and retention of accounting-related complaints and concerns;

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recommending based upon the audit committee’s review and discussions with management and our independent registered public accounting firm whether our audited financial statements shall be included in our Annual Report on Form 10-K;

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monitoring the integrity of our financial statements and our compliance with legal and regulatory requirements as they relate to our financial statements and accounting matters;

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preparing the audit committee report required by SEC rules to be included in our annual proxy statement;

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reviewing all related person transactions for potential conflict of interest situations and approving all such transactions;

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discussing and reviewing items of enterprise risk management and considering major risk exposures, including financial, operational, privacy, security, cybersecurity, competition, legal, regulatory, hedging and accounting risk exposures;

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evaluating the performance, responsibilities, budget and staffing of our internal audit function and reviewing the internal audit plan; and

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reviewing quarterly earnings releases.

All audit services and all permitted non-audit services to be provided to us by our independent registered public accounting firm must be approved in advance by our audit committee.

The members of our audit committee are Eric Bjerkholt, M.B.A, Juergen Eckhardt, M.D., M.B.A., and Willard H. Dere, M.D. Mr. Bjerkholt chairs the audit committee. All members of our audit committee meet the requirements for financial literacy under the applicable rules and regulations of the SEC and the Nasdaq listing rules. Our Board has determined that each of Dr. Eckhardt and Mr. Bjerkholt qualify as an “audit committee financial expert” within the meaning of applicable SEC regulations. Our Board has determined that all current members of our audit committee, and Dr. Bernales, who served on the audit committee during the fiscal year ended December 31, 2024, satisfy the relevant independence requirements for service on the audit committee set forth in the rules of the SEC and the Nasdaq listing rules. Both our independent registered public accounting firm and management periodically meet privately with our audit committee. Our audit committee charter, which has been adopted by our Board, is available on our website.

During the fiscal year ended December 31, 2024, our audit committee met four times. The report of our audit committee is included in this proxy statement below under “Audit Committee Report.”

Compensation Committee

Among other things, our compensation committee’s responsibilities include:

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reviewing and reassessing periodically our processes and procedures for the consideration and determination of director and executive officer compensation;

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annually reviewing and recommending to the board of directors the corporate goals and objectives relevant to the compensation of our Chief Executive Officer;

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evaluating the performance of our Chief Executive Officer in light of such corporate goals and objectives and based on such evaluation (i) recommending the cash compensation of our Chief Executive Officer and (ii) recommending long-term incentive awards to our Chief Executive Officer under equity-based plans;

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reviewing and approving the compensation of our other executive officers;

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overseeing and administering our compensation and similar plans;

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evaluating and assessing potential and current compensation advisors in accordance with the independence standards identified in the applicable Nasdaq listing rules;

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reviewing and approving our policies and procedures for the grant of equity-based awards;

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reviewing and recommending to the board of directors the compensation of our non-employee directors;

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preparing our compensation committee report if and when required by SEC rules;

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reviewing and discussing annually with management our “Compensation Discussion and Analysis,” if and when required, to be included in our annual proxy statement; and

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reviewing and approving the retention or termination of any consulting firm or outside advisor to assist in the evaluation of compensation matters.

The members of our compensation committee are Eric Bjerkholt, M.B.A, Willard H. Dere, M.D., and Juergen Eckhardt, M.D., M.B.A. Dr. Dere chairs the compensation committee. Each member of our compensation committee is a non-employee director, as defined in Rule 16b-3 promulgated under the Exchange Act. Our Board has determined that each current member of our compensation committee, and Dr. Bernales, who served on the compensation committee during the fiscal year ended December 31, 2024, satisfies the applicable rules and regulations of the SEC and the Nasdaq listing rules. Our compensation committee may delegate any of the responsibilities of the full committee to subcommittees and may delegate certain responsibilities of the full committee to executive officers of the Company and other persons as may be permitted by applicable laws, rules or regulations and in accordance with the listing standards set forth by Nasdaq. Our compensation committee charter, which has been adopted by our Board, is available on our website.

During the fiscal year ended December 31, 2024, our compensation committee met three times.

Compensation Consultant

Our compensation committee previously engaged Mercer (the “Prior Compensation Consultant”) as its independent compensation consultant. In November 2024, after a competitive bid process pursuant to which several compensation consultants were considered, our compensation committee selected Aon plc (“Aon”) as its new independent compensation consultant. When requested, Aon consultants attend meetings of our compensation committee, including executive sessions in which executive compensation-related matters are discussed without the presence of our management. Aon reports to our compensation committee and not to our management, although Aon meets with our management for purposes of gathering information for its analyses and recommendations.

Our compensation committee assessed the independence of Aon from management, taking into consideration relevant factors, including the absence of other services provided to our Company by Aon, the amount of fees our Company paid to Aon as a percentage of Aon’s total revenue, the policies and procedures of Aon that are designed to prevent conflicts of interest, any business or personal relationship of the individual compensation advisors employed by Aon with any executive officer of the Company, any business or personal relationship the individual compensation advisors employed by Aon have with any member of our compensation committee and any stock of our Company owned by Aon or the individual compensation advisors employed by Aon. On the basis of that assessment and taking into consideration the independence factors that are required to be considered under applicable stock exchange rules, our compensation committee determined that no relationships existed that would create a conflict of interest or that would compromise Aon’s independence, and that Aon is independent pursuant to the independence standards set forth in the Nasdaq listing standards promulgated pursuant to Section 10C of the Exchange Act.

Nominating and Corporate Governance Committee

Among other things, our nominating and corporate governance committee’s responsibilities include:

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developing, recommending to the board of directors criteria for board and committee membership;

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establishing procedures for identifying and evaluating board of director candidates, including nominees recommended by stockholders;

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to the extent deemed appropriate, retaining third-party search firms or other advisors to identify and evaluate director nominee candidates;

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reviewing the composition of the board of directors to ensure that it is composed of members containing the appropriate skills and expertise to advise us;

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identifying individuals qualified to become members of the board of directors;

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recommending to the board of directors the persons to be nominated for election as directors and to each of the board’s committees;

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developing, recommending to the board of directors and periodically assessing the adequacy of a set of corporate governance guidelines;

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overseeing the evaluation of our board of directors; and

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reviewing and discussing with the board of directors corporate succession plans for our Chief Executive Officer and our other key officers.

The members of our nominating and corporate governance committee are Eric Bjerkholt, M.B.A, Willard H. Dere, M.D, and Juergen Eckhardt, M.D., M.B.A. Dr. Dere chairs our nominating and corporate governance committee. Our Board has determined that each current member of our nominating and corporate governance committee, and Dr. Bernales, who served on the nominating and corporate governance committee during the fiscal year ended December 31, 2024, satisfies the independence standards of the applicable rules of Nasdaq. Our nominating and corporate governance committee charter, which has been adopted by our Board, is available on our website.

During the fiscal year ended December 31, 2024, our nominating and corporate governance committee met three times.

Board Meetings and Attendance

Our full Board held eleven meetings during the year ended December 31, 2024. Each of our incumbent directors, attended in person or participated via teleconference at least 75% of the aggregate meetings of our Board and the committees of our Board on which he or she served during the year ended December 31, 2024 (in each case, which were held during the period for which he or she was a director and/or a member of the applicable committee and excluding any meetings in which a director was an interested party). Our non-employee directors met in executive session during each of the regularly scheduled Board meetings during the year ended December 31, 2024.

Our Corporate Governance Guidelines provide that each member of the Board is expected to make reasonable efforts to attend meetings of the Board, whether regular or special. Attendance and participation at meetings is an important component of the directors’ duties and, as such, attendance rates are taken into account by the nominating and corporate governance committee in assessing directors for renomination as directors.

Director Attendance at Annual Meeting of Stockholders

Directors are encouraged, but not required, to attend our annual meetings of stockholders.

Environmental, Social and Governance Highlights

We believe corporate responsibility is essential for good governance because it strengthens the accountability of our board of directors and management team. We view Environmental, Social and Governance (“ESG”) initiatives as long-term value drivers for the Company and our stockholders. Our focus on, and commitment to ESG initiatives, is tied to our belief that achieving and sustaining business excellence goes hand-in-hand with strong corporate leadership and stewardship. Our board of directors is primarily responsible for overseeing our corporate strategy, which includes the oversight of ESG matters that impact our business and related risks.

The following is a summary of our current ESG policies and practices:

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Lead Independent Director: We appointed a Lead Independent Director to ensure the Board’s independent oversight of management.

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Independent Committees: Each of our committees consist entirely of independent directors.

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Regularly Held Executive Sessions: The independent directors of our Board meet separately in executive session on a regular basis to discuss matters relating to the Company and the Board, without members of the management team present.

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Code of Conduct: All of our employees, officers, agents and representatives, including directors and consultants, are subject to the Code of Business Conduct and Ethics, which is available on our website athttps://metagenomi.co/ under the heading “Investors – Corporate Governance – Documents & Charters.”

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Human Capital Management: We are committed to the health and welfare of our employees. We support the development of our employees with a competitive compensation and benefits package, health and wellness programs, internal advancement, and individualized development opportunities.

Code of Business Conduct and Ethics

Our Board adopted a Code of Business Conduct and Ethics, which applies to all of our employees, officers (including our principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions), agents and representatives, including directors and consultants.

We intend to disclose future amendments, if any, to certain provisions of our Code of Business Conduct and Ethics on our website identified below. The full text of our Code of Business Conduct and Ethics is posted on our website athttps://metagenomi.co under the heading “Investors – Corporate Governance.” The inclusion of our website address in this proxy statement does not include or incorporate by reference the information on our website into this proxy statement, and you should not consider that information a part of this proxy statement.

Policy on Trading, Pledging and Hedging of Company Stock

Certain transactions in our securities (such as purchases and sales of publicly traded put and call options, and short sales) create a heightened compliance risk or could create the appearance of misalignment between management and stockholders. In addition, securities held in a margin account or pledged as collateral may be sold without consent if the owner fails to meet a margin call or defaults on the loan, thus creating the risk that a sale may occur at a time when an officer or director is aware of material, non-public information or otherwise is not permitted to trade in Company securities. Our insider trading policy expressly prohibits short sales, derivative, and hedging transactions of our stock and purchases or sales of puts, calls, or other derivative securities of the Company or any derivative securities that provide the economic equivalent of ownership of any of the Company’s securities or an opportunity, direct or indirect, to profit from any change in the value of the Company’s securities or engage in any other hedging transaction with respect to the Company’s securities, or pledge of the Company’s securities as collateral for a loan, at any time, by our executive officers, directors and employees.

Rule 10b5-1 Trading Plan Policy

We have adopted a Rule 10b5-1 trading plan policy, which permits our officers, directors, employees and certain other persons to enter into trading plans complying with Rule 10b5-1 under the Exchange Act. Generally, under these trading plans, the individual relinquishes control over the transactions once the trading plan is put into place and can only put such plans into place while the individual is not in possession of material nonpublic information. Accordingly, sales under these plans may occur at any time, including possibly before, simultaneously with, or immediately after significant events involving our company.

Insider Trading Policy

We have adopted insider trading policies and procedures governing the purchase, sale, and other dispositions of our securities by directors, officers, and employees that we believe are reasonably designed to promote compliance with insider trading laws, rules and regulations, and applicable Nasdaq listing standards. Our insider trading policy states, among other things, that our directors, officers, and employees are prohibited from trading in such securities while in possession of material, nonpublic information. The foregoing summary of our insider trading policies and procedures does not purport to be complete and is qualified by reference to our Insider Trading Policy filed as an exhibit to our 2024 Annual Report. In addition, with regard to the Company's trading in its own securities, it is our policy to comply with the federal securities laws and the applicable exchange listing requirements.

Compensation Recovery Policy

In accordance with the requirements of the SEC and Nasdaq listing rules, our Board adopted a compensation recovery policy on January 26, 2024, effective as of January 5, 2024. The compensation recovery policy provides that in the event of a material restatement of our financial results, the compensation committee of our Board will review all incentive-based compensation that was paid to our executive officers on the basis of having met or exceeded specific performance targets for performance periods. If the bonuses paid pursuant to such incentive-based compensation would have been lower had the bonuses been calculated based on such restated results, the Company will recoup the portion of the excess compensation that was received unless recovery would be impractical and either the third-party costs associated with recovery would exceed the amount to be recovered or recovery would cause a tax qualified plan to fail to remain tax qualified.

Communication with Directors

Any stockholders desiring to communicate with our Board, or one or more of our directors, may send a letter addressed to the Board of Directors of Metagenomi, Inc, 5959 Horton Street, 7th Floor, Emeryville, CA 94608. Communications intended for a specific director or directors should be addressed to their attention at the address provided above. All such letters will be promptly forwarded to the appropriate members of our Board or individual directors, as applicable. The board of directors has authorized the Secretary, in his or her discretion, to exclude a communication if it is illegal, unduly hostile or threatening, or similarly inappropriate. Advertisements, solicitations for periodical or other subscriptions, and other similar communications generally will not be forwarded to the directors.

Director Compensation

The following table presents the total compensation for each person who served as a non-employee member of our Board during the fiscal year ended December 31, 2024. Other than as set forth in the table and described more above, we did not pay any compensation, make any equity awards or non-equity awards to, or pay any other compensation to any of the non-employee members of our Board during the fiscal year ended December 31, 2024. We reimburse members of our Board for reasonable travel and out-of-pocket expenses incurred in attending meetings of our Board and committees of our Board. Dr. Thomas, who is our Chief Executive Officer, and Dr. Irish, who is our President and Chief Operating Officer, did not receive any additional compensation for their service as directors. The compensation received by Dr. Thomas and Dr. Irish, as NEOs of the Company, is presented in the “2024 Summary Compensation Table” below.

(1)

Amounts represent annual cash compensation earned for services rendered by independent members of our Board and the committees thereof during the fiscal year ended December 31, 2024. The fees earned by Dr. Bernales and Dr. Eckhardt were pro-rated based on the number of days during the fiscal year ended December 31, 2024 following the closing of our IPO.

(2)

Amounts reflect the aggregate grant date fair value of option awards granted during 2024 in accordance with our Non-Employee Director Compensation Policy, described below, calculated in accordance with Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Topic 718. Such grant date fair values do not take into account any estimated forfeitures. See Note 11 – Stock-Based Compensation to our audited consolidated financial statements appearing in our 2024 Annual Report for assumptions underlying the valuation of equity awards. The amounts reported in this column reflect the accounting cost for these options and do not correspond to the actual economic value that may be received by our directors upon the exercise of the options or any sale of the underlying shares of common stock.

(3)

As of December 31, 2024, Drs. Dere, Bernales and Eckhardt each held options to purchase an aggregate of 78,636 shares of common stock.

(4)

Dr. Palani’s service on our Board ended on January 17, 2024. Accordingly, Dr. Palani did not receive any compensation during the 2024 fiscal year. As of December 31, 2024, Dr. Palani did not hold any equity awards.

(5)

Dr. Stack’s service on our Board ended on February 8, 2024. Accordingly, Dr. Stack did not receive any compensation during the 2024 fiscal year. As of December 31, 2024, Dr. Stack did not hold any equity awards.

On January 13, 2025, our board approved an increase in the size of our board from five directors to six directors, and appointed Eric Bjerkholt, M.B.A. to serve as a director of our board effective January 27, 2025. Accordingly, Mr. Bjerkholt did not receive any compensation during the 2024 fiscal year.

Non-Employee Director Compensation Policy

We have adopted a non-employee director compensation policy designed to enable us to attract and retain, on a long-term basis, highly qualified non-employee directors. Under the policy, our non-employee directors are eligible to receive annual cash retainers (which are payable quarterly in arrears and prorated for partial years of service) and equity awards as set forth below:

In addition, our policy provided that, upon initial election or appointment to our board of directors, each new non-employee director was granted a one-time grant of a non-statutory stock option to purchase shares of our common stock equivalent to $600,000 in value on the date of such director’s election or appointment to the board of directors (the “Director Initial Grant”). The Director Initial Grant will vest over three years, with 33% vesting on the first anniversary of the grant date and the remaining 67% vesting in 24 equal monthly installments thereafter, subject to the non-employee director’s continued services to us. On the date of each annual meeting of stockholders of our company, each non-employee director who will continue as a non-employee director following such meeting will be granted an annual award of a non-statutory stock option to purchase shares of common stock equivalent to $300,000 in value (the “Director Annual Grant”). The Director Annual Grant will vest in full on the earlier of the one-year anniversary of the grant date or on the date of our next annual meeting of stockholders, subject to the non-employee director’s continued services to us. Such awards are subject to full acceleration vesting upon the sale of our company. The aggregate amount of compensation, including both equity compensation and cash compensation, paid to any non-employee director for service as a non-employee director in a calendar year period will not exceed $1,000,000 in the first calendar year such individual becomes a non-employee director and $800,000 in any other calendar year.

In January 2025, our board of directors approved an amendment to our policy that provides that the Director Initial Award will be an award of 42,000 stock options; provided, however that the award shall be reduced so that the grant date fair value of the option is no greater than $600,000, and the Director Annual Grant will be an award of 21,000 stock options; provided that the award shall be reduced so that the grant date fair value of the option is no greater than $300,000.