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(Mark One)☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 OR ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 Metagenomi, Inc.(Exact Name of Registrant as Specified in its Charter) Delaware(State or other jurisdiction ofincorporation or organization)5959 Horton Street,7th FloorEmeryville,California(Address of principal executive offices) (510)871-4880(Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the SecuritiesExchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) hasbeen 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 toRule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was requiredto submit such files).Yes☒No☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reportingcompany, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and“emerging growth company” in Rule 12b-2 of the Exchange Act. Accelerated filer☐Smaller reporting company☒Emerging growth company☒ Large accelerated filer☐Non-accelerated filer☒ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period forcomplying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☒ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).Yes☐No☒As of May 7, 2025, the registrant had37,381,495shares of common stock, $0.0001 par value per share, outstanding. Table of Contents PART I.FINANCIAL INFORMATION Item 1.Financial Statements (Unaudited)4Condensed Balance Sheets4Condensed Statements of Operations and Comprehensive Loss5Condensed Statements of Redeemable Convertible Preferred Stock and Stockholders’ Equity6Condensed Statements of Cash Flows7Notes to Unaudited Condensed Financial Statements8Item 2.Management’s Discussion and Analysis of Financial Condition and Results of Operations21Item 3.Quantitative and Qualitative Disclosures About Market Risk30Item 4.Controls and Procedures30 PART II.OTHER INFORMATION Item 1.Legal ProceedingsItem 1A.Risk FactorsItem 2.Unregistered Sales of Equity Securities and Use of ProceedsItem 3.Defaults Upon Senior SecuritiesItem 4.Mine Safety DisclosuresItem 5.Other InformationItem 6.ExhibitsSignatures SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS This Quarterly Report on Form 10-Q contains express or implied forward-looking statements that are based on our management’sbelief and assumptions and on information currently available to our management and which are made pursuant to the safe harborprovisions of Section 27A of the Securities Act of 1933, as amended (the “Securities Act”), and Section 21E of the SecuritiesExchange Act of 1934, as amended (the “Exchange Act”). Although we believe that the expectations reflected in these forward-looking statements are reasonable, these statements relate to future events or our future operational or financial performance, andinvolve known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievementsto be materially different from any future results, performance or achievements expressed or implied by these forward-lookingstatements. Forward-looking statements in this Quarterly Report on Form 10-Q include, but are not limited to, statements about: •the initiation, timing, progress and results of our research and development programs, preclinical studies and future clinicaltrials;•our ability to demonstrate, and the timing of, preclinical proof-of-conceptin vivoandex vivofor multiple programs;•our ability to advance any product candidates that we may identify and successfully complete any clinical studies, includingthe manufacture of any such product candidates;•our ability to quickly leverage programs within our initial target indications and to progress additional programs to furtherdevelop our pipeline;•the timing of our Investigational New Drug (“IND”) applications submissions;•the implementation of our strategic plans for our business, programs and technology;•the scope of protection we are able to establish and maintain for intellectual property rights covering our genome editingtechnology and platform;•developments related to our competitors and our industry;•our ability to leverage the clinical, r