Schedule 13D/A

Number of

Shares

Beneficially

Owned by

Each

Reporting

Person

With

Sole Voting Power

0

Shared Voting Power

42,865

Sole Dispositive Power

0

Shared Dispositive Power

42,865

SC 13D/A 1 d13195dsc13da.htm SCHEDULE 13D/A Schedule 13D/A

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)*

Kaleido Biosciences, Inc.

(Name of Issuer)

Common Stock, par value $0.001 per share

(Title of Class of Securities)

483347100

(CUSIP Number)

Noubar B. Afeyan, Ph.D.

Flagship Ventures

55 Cambridge Parkway, Suite 800E

Cambridge, MA 02142

(617) 868-1888

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

February 8, 2021

(Date of Event Which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. ☐

*	The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934, as amended (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship VentureLabs IV, LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Fund IV, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Fund IV General Partner LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship VentureLabs V, LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship VentureLabs V Manager LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Pioneering, Inc.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Fund V, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Nutritional Health Side Fund, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Nutritional Health Disruptive Innovation Fund, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Fund V General Partner LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Nutritional Health LTP Fund, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Nutritional Health LTP General Partner LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Opportunities Fund I, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Opportunities Fund I General Partner LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures Fund 2007, L.P.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Flagship Ventures 2007 General Partner LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Cadena LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization Delaware


CUSIP No. 483347100


1.		Names of Reporting Persons. Noubar B. Afeyan, Ph.D.
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☐
3.		SEC Use Only
4.		Source of Funds (See Instructions) AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e) ☐
6.		Citizenship or Place of Organization United States of America

Item 1.

Security and Issuer

This Amendment No. 2 (this “Amendment”) amends and supplements the Schedule 13D (the “Schedule 13D”) filed by the Reporting Persons (as defined below) on March 6, 2019, as amended, with respect to the common stock, $0.001 par value per share (“Common Stock”), of Kaleido Biosciences, Inc. (the “Issuer”). Except as specifically provided herein, this Amendment does not modify any of the information previously reported in the Schedule 13D.

Item 2.

Identity and Background

Item 2 of the Schedule 13D is hereby amended and restated as follows:

This Schedule 13D is being filed by the following persons (each a “Reporting Person”):

Flagship VentureLabs IV, LLC, a Delaware limited liability company (“VentureLabs IV”). The manager of VentureLabs IV is Flagship Ventures Fund IV, L.P., a Delaware limited partnership (“Flagship Fund IV” and together with VentureLabs IV, the “Flagship Fund IV Funds”).

ii.

Flagship Fund IV. The general partner of Flagship Fund IV is Flagship Ventures Fund IV General Partner LLC (“Flagship Fund IV GP”).

iii.

Flagship Fund IV GP. Noubar B. Afeyan, Ph.D. (“Dr. Afeyan”) is the sole manager of Flagship IV GP.

iv.

Flagship VentureLabs V, LLC, a Delaware limited liability company (“VentureLabs V”). The manager of VentureLabs V is Flagship VentureLabs V Manager LLC, a Delaware limited liability company. (“VentureLabs V Manager”).

VentureLabs V Manager. The manager of VentureLabs V Manager is Flagship Pioneering, Inc. (“Flagship Pioneering”), a Delaware company.

vi.

Flagship Pioneering Dr. Afeyan is the sole director of Flagship Pioneering

vii.

Flagship Ventures Fund V, L.P., a Delaware limited partnership (“Flagship Fund V”). The general partner of Flagship Fund V is Flagship Ventures Fund V General Partner LLC, a Delaware limited liability company (“Flagship Fund V GP”).

viii.

Nutritional Health Side Fund, L.P., a Delaware limited partnership (“Nutritional Health Side Fund”). Flagship Fund V GP is the general partner of Nutritional Health Side Fund.

ix.

Nutritional Health Disruptive Innovation Fund, L.P., a Delaware limited partnership (“Nutritional Innovation Fund” and together with Flagship Fund V and Nutritional Health Side Fund, the “Flagship Fund V Funds”). Flagship Fund V GP is the general partner of Nutritional Innovation Fund.

Flagship Fund V GP. Dr. Afeyan is the sole manager of Flagship Fund V GP.

xi.

Nutritional Health LTP Fund, L.P., a Delaware limited partnership (“Nutritional LTP”). The general partner of Nutritional LTP is Nutritional Health LTP General Partner LLC, a Delaware limited liability company (“Nutritional LTP GP”).

xii.

Nutritional LTP GP. Dr. Afeyan is the sole member and manager of Nutritional LTP GP.

xiii.

Flagship Ventures Opportunities Fund I, L.P., a Delaware limited partnership (“Flagship Opportunities I).The general partner of Flagship Opportunities I is Flagship Ventures Opportunities Fund I General Partner LLC, a Delaware limited liability company (“Flagship Opportunities GP”).

xiv.

Flagship Opportunities GP. Dr. Afeyan is the sole manager of Flagship Opportunities GP.

xv.

Flagship Ventures Fund 2007, L.P., a Delaware limited partnership (“Flagship Fund 2007”). The general partner of Flagship Fund 2007 is Flagship Ventures 2007 General Partner LLC (“Flagship Fund 2007 GP”).

xvi.

Flagship Fund 2007 GP. Dr. Afeyan is the sole manager of Flagship Fund 2007 GP.

xvii.

Cadena LLC, a Delaware limited liability company (“Cadena” and together with the Flagship IV Funds, VentureLabs V, the Flagship V Funds, Nutritional LTP, Flagship Opportunities I and Flagship Fund 2007, the “Flagship Funds”). Dr. Afeyan is the sole manager of Cadena LLC.

xviii.

Dr. Afeyan, a citizen of the United States of America.

The principal business of each Reporting Person is the venture capital investment business. The principal business address of each Reporting Person is 55 Cambridge Parkway, Suite 800E, Cambridge, Massachusetts 02142.

During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

During the last five years, none of the Reporting Persons has been party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding were or are subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Item 4.

Purpose of Transaction

Item 4 is hereby amended to include the following:

On February 8, 2021, Flagship Fund IV, Flagship Opportunities I, and Nutritional LTP purchased an additional 71,666 shares, 71,667 shares, and 71,667 shares, respectively, of the Issuer’s Common Stock in an underwritten public offering (the “February 2021 Public Offering”) at a price per share of $11.50.

Item 5.

Interest in Securities of the Issuer

Item 5(a)-(c) is hereby amended and restated as follows:

(a)-(b) The information set forth in rows 7 through 13 of the cover pages to this Schedule 13D is incorporated by reference. The percentage set forth in row 13 is based on 41,079,506 outstanding shares of Common Stock immediately following the February 2021 Public Offering, as reported in the Issuer’s prospectus supplement filed on February 5, 2021, which does not include shares of Common Stock that may be issued if the underwriters exercise their option to purchase additional shares in the offering.

VentureLabs IV and Flagship Fund IV directly hold 42,865 shares and 1,685,444 shares of Common Stock, respectively. Flagship Fund IV, as the manager of VentureLabs IV, may be deemed to beneficially own the shares directly held by VentureLabs IV. Flagship Fund IV GP, as the general partner of the Flagship Fund IV Funds, may be deemed to beneficially own the shares directly held by the Flagship Fund IV Funds.

VentureLabs V, Flagship Fund V, Nutritional Health Side Fund and Nutritional Innovation Fund directly hold 2,500,000 shares, 2,560,096 shares, 639,360 shares and 6,560,523 shares of Common Stock, respectively. VentureLabs V Manager, as the manager of VentureLabs V, and Flagship Pioneering as the manager of VentureLabs V Manager, may be deemed to beneficially own the shares directly held by VentureLabs V. Flagship Fund V GP, as the general partner of the Flagship Fund V Funds, may be deemed to beneficially own the shares directly held by the Flagship Fund V Funds.

Nutritional LTP directly holds 738,333 shares of Common Stock. Nutritional LTP GP, as the general partner of Nutritional LTP, may be deemed to beneficially own the shares directly held by Nutritional LTP.

Flagship Opportunities I directly holds 2,982,639 shares of Common Stock. Flagship Opportunities GP, as the general partner of Flagship Opportunities I, may be deemed to beneficially own the shares directly held by Flagship Opportunities I.

Flagship Fund 2007 directly holds 216,451 shares of Common Stock. Flagship Fund 2007 GP, as the general partner of Flagship Fund 2007, may be deemed to beneficially own the shares directly held by Flagship Fund 2007.

Cadena LLC directly holds 1,649,999 shares of Common Stock.

Dr. Afeyan, as the sole manager of Flagship Fund IV GP, Flagship Fund 2007 GP, Flagship Fund V GP, Nutritional LTP GP, Flagship Opportunities GP and Cadena LLC and as the sole director of Flagship Pioneering, Inc., may be deemed to beneficially own the shares directly held by the Flagship Fund IV Funds, Flagship Fund 2007, Flagship Fund V Funds, Nutritional LTP, VentureLabs V, Flagship Opportunities I and Cadena LLC.

(c) On February 8, 2021, Flagship Fund IV, Flagship Opportunities I, and Nutritional LTP purchased an additional 71,666 shares, 71,667 shares, and 71,667 shares, respectively, of the Issuer’s Common Stock in connection with the June 2020 Public Offering. The purchase price was $11.50 per share.

Item 6.

Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer

Item 6 is hereby amended to include the following:

In connection with the February 2021 Public Offering, the Flagship funds entered into a lock-up agreement (the “Lock-Up Agreement”) with Morgan Stanley & Co., LLC and Piper Sandler & Co. Pursuant to the terms of the Lock-Up Agreement, the Flagship Funds have agreed, with certain exceptions, during the period ending 90 days after February 3, 2021, not to

•

offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, or otherwise transfer or dispose of, directly or indirectly, any shares of the Issuer’s common stock or any securities convertible into or exercisable or exchangeable for our common stock (including without limitation, common stock or such other securities which may be deemed to be beneficially owned by the undersigned in accordance with the rules and regulations of the Securities and Exchange Commission and securities which may be issued upon exercise of a stock option or warrant), or publicly disclose the intention to make any offer, sale, pledge or disposition, or

•

enter into any swap or other agreement that transfers, in whole or in part, any of the economic consequences of ownership of our common stock or such other securities, or publicly disclose the intention to enter into any such swap or other agreement.

The foregoing description of the Lock-Up Agreement is qualified in its entirety by reference to the full text of the Form of Lock-Up Agreement, a copy of which is filed as Exhibit 2 hereto, and is incorporated by reference into this Item 6.

Item 7.

Material to be Filed as Exhibits


Exhibit 1		Joint Filing Agreement (filed herewith).

Exhibit 2		Lock-Up Agreement (incorporated by reference to ExhibitA-1 to Exhibit 1.1 to the Issuer’s Form 8-K filed on February 8, 2021).

SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.


Dated: February 10, 2021	FLAGSHIP VENTURELABS IV, LLC

	By:	Flagship Ventures Fund IV, L.P.

	By:	Flagship Ventures Fund IV General Partner LLC

		By:	/s/ Noubar B. Afeyan, Ph.D.
		Name:	Noubar B. Afeyan, Ph.D.
		Title:	Manager

	FLAGSHIP VENTURES FUND IV, L.P.

	By:	Flagship Ventures Fund IV General Partner LLC

		By:	/s/ Noubar B. Afeyan, Ph.D.
		Name:	Noubar B. Afeyan, Ph.D.
		Title:	Manager

	FLAGSHIP VENTURES FUND IV GENERAL PARTNER LLC

		By:	/s/ Noubar B. Afeyan, Ph.D.
		Name:	Noubar B. Afeyan, Ph.D.
		Title:	Manager

	FLAGSHIP VENTURELABS V, LLC

	By:	Flagship VentureLabs V Manager LLC

	By:	Flagship Pioneering, Inc.

		By:	/s/ Noubar B. Afeyan, Ph.D.
		Name:	Noubar B. Afeyan, Ph.D.
		Title:	Director

	FLAGSHIP VENTURELABS V MANAGER LLC

	By:	Flagship Pioneering, Inc.

		By:	/s/ Noubar B. Afeyan, Ph.D.
		Name:	Noubar B. Afeyan, Ph.D.
		Title:	Director



FLAGSHIP PIONEERING, INC.

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Director

FLAGSHIP VENTURES FUND V, L.P.

By:	Flagship Ventures Fund V General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

NUTRITIONAL HEALTH SIDE FUND, L.P.

By:	Flagship Ventures Fund V General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

NUTRITIONAL HEALTH DISRUPTIVE INNOVATION FUND, L.P.

By:	Flagship Ventures Fund V General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

FLAGSHIP VENTURES FUND V GENERAL PARTNER LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

NUTRITIONAL HEALTH LTP FUND, L.P.

By:	Nutritional Health LTP Fund General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager



NUTRITIONAL HEALTH LTP FUND GENERAL PARTNER LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

FLAGSHIP VENTURES OPPORTUNITIES FUND I, L.P.

By:	Flagship Ventures Opportunities Fund I General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

FLAGSHIP VENTURES OPPORTUNITIES FUND I GENERAL PARTNER LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

FLAGSHIP VENTURES FUND 2007, L.P.

By:	Flagship Ventures 2007 General Partner LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

FLAGSHIP VENTURES 2007 GENERAL PARTNER LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

CADENA LLC

	By:	/s/ Noubar B. Afeyan, Ph.D.
	Name:	Noubar B. Afeyan, Ph.D.
	Title:	Manager

/s/ Noubar B. Afeyan, Ph.D.
NOUBAR B. AFEYAN, PH.D.

SEC Form SC 13D/A filed