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Form 13F-HR Flagship Pioneering Inc. For: Mar 31

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May 16, 2022 3:02 PM EDT

The Securities and Exchange Commission has not necessarily reviewed the information in this filing and has not determined if it is accurate and complete.
The reader should not assume that the information is accurate and complete.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM 13F

FORM 13F COVER PAGE
OMB APPROVAL
OMB Number: 3235-0006
Expires: July 31, 2015
Estimated average burden
hours per response: 23.8
Report for the Calendar Year or Quarter Ended: 03-31-2022
Check here if Amendment   Amendment Number:
This Amendment (Check only one.):   is a restatement.
  adds new holdings entries.
Institutional Investment Manager Filing this Report:
Name: Flagship Pioneering Inc.
Address: 55 Cambridge Parkway, Suite 800E
Cambridge , MA02142
Form 13F File Number: 028-17559

The institutional investment manager filing this report and the person by whom it is signed hereby represent that the person signing the report is authorized to submit it, that all information contained herein is true, correct and complete, and that it is understood that all required items, statements, schedules, lists, and tables, are considered integral parts of this form.

Person Signing this Report on Behalf of Reporting Manager:
Name: Noubar B. Afeyan, Ph.D.
Title: Chief Executive Officer
Phone: 617-868-1888
Signature, Place, and Date of Signing:
/s/ Noubar B. Afeyan Cambridge , MA 05-16-2022
[Signature] [City, State] [Date]
Report Type (Check only one.):
X 13F HOLDINGS REPORT. (Check here if all holdings of this reporting manager are reported in this report.)
  13F NOTICE. (Check here if no holdings reported are in this report, and all holdings are reported by other reporting manager(s).)
  13F COMBINATION REPORT. (Check here if a portion of the holdings for this reporting manager are reported in this report and a portion are reported by other reporting manager(s).)
Form 13F Summary Page
Report Summary:
Number of Other Included Managers: 7
Form 13F Information Table Entry Total: 38
Form 13F Information Table Value Total: 4,258,761
(thousands)
List of Other Managers Reporting for this Manager:
[If there are no entries in this list, omit this section.]
Form 13F File Number Name
028-18466 Flagship Ventures Fund V General Partner LLC
028-17238 Flagship Ventures Fund IV General Partner LLC
028-19988 Noubar Afeyan
028-20999 Flagship Opportunities Fund I General Partner LLC
028-20997 Flagship Pioneering Special Opportunities Fund II General Partner LLC
028-21001 Nutritional Health Fund LTP General Partner LLC
028-20998 Flagship Pioneering Fund VI General Partner LLC

List of Other Included Managers:
Provide a numbered list of the name(s) and Form 13F file number(s) of all institutional investment managers with respect to which this report is filed, other than the manager filing this report.
[If there are no entries in this list, state “NONE” and omit the column headings and list entries.]
No. Form 13F File Number Name
1 028-18466 Flagship Ventures Fund V General Partner LLC
2 028-17238 Flagship Ventures Fund IV General Partner LLC
3 028-19988 Noubar Afeyan
4 028-20999 Flagship Opportunities Fund I General Partner LLC
5 028-20997 Flagship Pioneering Special Opportunities Fund II General Partner LLC
6 028-21001 Nutritional Health Fund LTP General Partner LLC
7 028-20998 Flagship Pioneering Fund VI General Partner LLC

The Securities and Exchange Commission has not necessarily reviewed the information in this filing and has not determined if it is accurate and complete.
The reader should not assume that the information is accurate and complete.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM 13F

FORM 13F INFORMATION TABLE
OMB APPROVAL
OMB Number: 3235-0006
Expires: July 31, 2015
Estimated average burden
hours per response: 23.8
COLUMN 1 COLUMN 2 COLUMN 3 COLUMN 4 COLUMN 5 COLUMN 6 COLUMN 7 COLUMN 8
VALUE SHRS OR SH/ PUT/ INVESTMENT OTHER VOTING AUTHORITY
NAME OF ISSUER TITLE OF CLASS CUSIP (x$1000) PRN AMT PRN CALL DISCRETION MANAGER SOLE SHARED NONE
Axcella Health Inc COM 05454B105 32,487 12,640,890 SH DFND 2,3 0 12,640,890 0
Axcella Health Inc COM 05454B105 11,477 4,465,866 SH DFND 3,4 0 4,465,866 0
Axcella Health Inc COM 05454B105 4,526 1,761,029 SH DFND 3 0 1,761,029 0
Codiak Biosciences Inc COM 192010106 13,301 2,121,354 SH DFND 1,3 0 2,121,354 0
Codiak Biosciences Inc COM 192010106 3,047 485,949 SH DFND 3 0 485,949 0
Denali Therapeutics Inc COM 24823R105 84,284 2,619,968 SH DFND 1,3 0 2,619,968 0
Evelo Biosciences Inc COM 299734103 34,596 10,205,282 SH DFND 1,3 0 10,205,282 0
Evelo Biosciences Inc COM 299734103 15,876 4,683,213 SH DFND 2,3 0 4,683,213 0
Evelo Biosciences Inc COM 299734103 13,985 4,125,461 SH DFND 3,4 0 4,125,461 0
Evelo Biosciences Inc COM 299734103 4,646 1,370,476 SH DFND 3,6 0 1,370,476 0
Evelo Biosciences Inc COM 299734103 8,969 2,645,637 SH DFND 3 0 2,645,637 0
Foghorn Therapeutics Inc COM 344174107 142,109 9,330,878 SH DFND 1,3 0 9,330,878 0
Foghorn Therapeutics Inc COM 344174107 22,715 1,491,441 SH DFND 3,4 0 1,491,441 0
Foghorn Therapeutics Inc COM 344174107 28,203 1,851,801 SH DFND 3,5 0 1,851,801 0
Kaleido Biosciences Inc COM 483347100 16,104 9,759,979 SH DFND 1,3 0 9,759,979 0
Kaleido Biosciences Inc COM 483347100 2,852 1,728,309 SH DFND 2,3 0 1,728,309 0
Kaleido Biosciences Inc COM 483347100 4,921 2,982,639 SH DFND 3,4 0 2,982,639 0
Kaleido Biosciences Inc COM 483347100 1,218 738,333 SH DFND 3,6 0 738,333 0
Kaleido Biosciences Inc COM 483347100 7,205 4,366,450 SH DFND 3 0 4,366,450 0
Moderna Inc COM 60770K107 3,027,830 17,577,092 SH DFND 2,3 0 17,577,092 0
Moderna Inc COM 60770K107 676 3,924 SH DFND 3 0 3,924 0
Omega Therapeutics Inc COM 68217N105 43,586 6,984,856 SH DFND 1,3 0 6,984,856 0
Omega Therapeutics Inc COM 68217N105 34,412 5,514,707 SH DFND 3,5 0 5,514,707 0
Omega Therapeutics Inc COM 68217N105 6,056 970,588 SH DFND 3,6 0 970,588 0
Omega Therapeutics Inc COM 68217N105 53,773 8,617,413 SH DFND 3,7 0 8,617,413 0
Omega Therapeutics Inc COM 68217N105 23,804 3,814,705 SH DFND 3 0 3,814,705 0
Rubius Therapeutics Inc COM 78116T103 64,185 11,648,828 SH DFND 1,3 0 11,648,828 0
Rubius Therapeutics Inc COM 78116T103 133,474 24,223,995 SH DFND 2,3 0 24,223,995 0
Rubius Therapeutics Inc COM 78116T103 14,512 2,633,703 SH DFND 3,4 0 2,633,703 0
Sana Biotechnology Inc COM 799566104 107,979 13,072,570 SH DFND 1,3 0 13,072,570 0
Sana Biotechnology Inc COM 799566104 80,330 9,725,122 SH DFND 3,7 0 9,725,122 0
Sana Biotechnology Inc COM 799566104 94,505 11,441,326 SH DFND 3 0 11,441,326 0
Seres Therapeutics Inc COM 81750R102 60,184 8,452,876 SH DFND 2,3 0 8,452,876 0
Seres Therapeutics Inc COM 81750R102 21,096 2,962,963 SH DFND 3,7 0 2,962,963 0
Seres Therapeutics Inc COM 81750R102 21,096 2,962,963 SH DFND 3,6 0 2,962,963 0
Sigilon Therapeutics Inc COM 82657L107 13,067 8,888,888 SH DFND 1,3 0 8,888,888 0
Sigilon Therapeutics Inc COM 82657L107 2,178 1,481,481 SH DFND 3,5 0 1,481,481 0
Syros Pharmaceuticals Inc COM 87184Q107 3,497 2,938,494 SH DFND 2,3 0 2,938,494 0

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