Metagenomi Therapeutics, Inc.(Exact Name of registrant as specified in its charter) Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes☐No☒ Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act. Yes☐No☒ Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes☒No☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T(§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes☒No☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growthcompany. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. Large accelerated filer☐Accelerated filer☐Non-accelerated filer☒Smaller reporting company☒Emerging growth company☒ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financialaccounting standards provided pursuant to Section 13(a) of the Exchange Act.☒ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect thecorrection of an error to previously issued financial statements.☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of theregistrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b).☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes☐No☒ The aggregate market value of the voting and non-voting common equity held by non-affiliates, based on the closing price of the shares of common stock on The Nasdaq GlobalSelect Market on June 30, 2025 (the last business day of the registrant’s most recently completed second fiscal quarter), was $50,931,318. This calculation does not reflect adetermination that certain persons are affiliates of the registrant for any other purpose. The number of shares of registrant’s Common Stock outstanding as of March 2, 2026 was 37,620,530. DOCUMENTS INCORPORATED BY REFERENCE Part III of this Annual Report on Form 10-K incorporates certain information by reference from the registrant’s definitive proxy statement for the 2026 annual meeting ofstockholders to be filed no later than 120 days after the end of the registrant’s fiscal year ended December 31, 2025.A Table of Contents PART I Item 1........................................................................................................................................................................Business5Item 1A..................................................................................................................................................................Risk Factors34Item 1B........................................................................................................................................Unresolved Staff Comments97Item 1C...............................................................................................................................................................Cybersecurity98Item 2......................................................................................................................................................................Properties98Item 3........................................................................................................................................................Legal Proceedings99Item 4..............................................................................................................................................Mine Safety Disclosures99 PART IIItem 5. .Market forRegistrant’sCommon Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities100Item 6....................................................................................................................................................................[Reserved]100Item 7......................................Management’sDiscussion and Analysis of Financial Condition and Results of Operations101Item 7A......................................................