(Former name, former address and former fiscal year, if changed since last report)

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 12 months (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 growth company. See definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

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 financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

As of ~~April 30,~~August 9, 2021, there were ~~42,518,653~~42,577,529 shares of registrant’s common ~~shares~~stock outstanding.

This Quarterly Report on Form 10-Q, or Quarterly Report, contains forward-looking statements, which reflect our current views with respect to, among other things, our operations and financial performance. We make such forward looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. All statements other than statements of historical facts contained in this Quarterly Report, including statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plan, objectives of management and expected market growth are forward-looking statements. You can identify these forward-looking statements by the use of words such as “outlook,” “believes,” “expects,” “potential,” “continues,” “may,” “will,” “should,” “seeks,” “approximately,” “predicts,” “intends,” “plans,” “estimates,” “anticipates” or the negative version of these words or other comparable words. Such forward-looking statements are subject to various risks and uncertainties. Accordingly, there are or will be important factors that could cause actual outcomes or results to differ materially from those indicated in these statements. We believe these factors include but are not limited to those described under “Risk Factors” and include, among other things:

All of our forward-looking statements are as of the date of this Quarterly Report only. In each case, actual results may differ materially from such forward-looking information. We can give no assurance that such expectations or forward-looking statements will prove to be correct. An occurrence of or any material adverse change in one or more of the risk factors or risks and uncertainties referred to in this Quarterly Report ~~on Form 10-Q~~ or included in our other public disclosures or our other periodic reports or other documents or filings filed with or furnished to the Securities and Exchange Commission, or the SEC, could materially and adversely affect our business, prospects, financial condition and results of operations. Except as required by law, we do not undertake or plan to update or revise any such forward-looking statements to reflect actual results, changes in plans, assumptions, estimates or projections or other circumstances affecting such forward-looking statements occurring after the date of this Quarterly Report, ~~on Form 10-Q,~~ even if such results, changes or circumstances make it clear that any forward-looking information will not be realized. Any public statements or disclosures by us following this Quarterly Report that modify or impact any of the forward-looking statements contained in this Quarterly Report will be deemed to modify or supersede such statements in this Quarterly Report.

We caution readers not to place undue reliance on any forward-looking statements made by us, which speak only as of the date they are made. We disclaim any obligation, except as specifically required by law and the rules of the SEC, to publicly update or revise any such statements to reflect any change in our expectations or in events, conditions or circumstances on which any such statements may be based, or that may affect the likelihood that actual results will differ from those set forth in the forward-looking statements.

	As of						As of
	March 31, 2021			December 31, 2020			June 30, 2021			December 31, 2020
Assets
Current assets:
Cash and cash equivalents	$	92,362		$	46,222		$	71,979		$	46,222
Prepaid expenses and other current assets		2,670			2,499			2,624			2,499
Total current assets		95,032			48,721			74,603			48,721
Property and equipment, net		7,833			8,462			7,526			8,462
Restricted cash		2,161			2,161			2,161			2,161
Total assets	$	105,026		$	59,344		$	84,290		$	59,344
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	2,412		$	5,389		$	2,695		$	5,389
Accrued expenses and other current liabilities		5,702			8,636			5,907			8,636
Current term debt, net of unamortized debt discount		4,759			2,634			3,667			2,634
Total current liabilities		12,873			16,659			12,269			16,659
Long term debt, net of unamortized debt discount		16,433			18,375			17,677			18,375
Other liabilities		3,946			3,814			4,078			3,814
Total liabilities		33,252			38,848			34,024			38,848
Commitments and contingencies (Note 7)
Stockholders’ equity:
Preferred stock, $0.001 par value, 10,000,000 authorized; 0 shares issued or outstanding		—			—			—			—
Common stock, $0.001 par value, 150,000,000 shares authorized; 42,483,171 and 36,022,811 shares issued and outstanding at March 31, 2021 and December 31, 2020, respectively		42			36
Common stock, $0.001 par value, 150,000,000 shares authorized; 42,571,380 and 36,022,811 shares issued and outstanding at June 30, 2021 and December 31, 2020, respectively								43			36
Additional paid-in capital		368,953			294,639			371,333			294,639
Accumulated deficit		(297,221	)		(274,179	)		(321,110	)		(274,179	)
Total stockholders' equity		71,774			20,496			50,266			20,496
Total liabilities and stockholders’ equity	$	105,026		$	59,344		$	84,290		$	59,344

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

	Three Months Ended March 31,						Three Months Ended June 30,						Six Months Ended June 30,
	2021			2020			2021			2020			2021			2020
Revenue:
Collaboration revenue	$	297		$	—		$	211		$	250		$	508		$	250
Operating expenses:
Research and development		17,185			13,137			17,633			12,833			34,818			25,970
General and administrative		5,460			5,917			5,785			5,559			11,245			11,476
Total operating expenses		22,645			19,054			23,418			18,392			46,063			37,446
Loss from operations		(22,348	)		(19,054	)		(23,207	)		(18,142	)		(45,555	)		(37,196	)
Other (expense) income:
Interest income		21			193			24			30			45			223
Interest expense		(709	)		(688	)		(705	)		(683	)		(1,414	)		(1,371	)
Other expense		(6	)		(2	)		(1	)		(127	)		(7	)		(129	)
Total other (expense) income, net		(694	)		(497	)		(682	)		(780	)		(1,376	)		(1,277	)
Net loss	$	(23,042	)	$	(19,551	)	$	(23,889	)	$	(18,922	)	$	(46,931	)	$	(38,473	)
Net loss per share —basic and diluted	$	(0.58	)	$	(0.64	)	$	(0.56	)	$	(0.59	)	$	(1.14	)	$	(1.24	)
Weighted-average common shares outstanding —basic and diluted		39,692,582			30,333,283			42,538,563			31,880,672			41,123,435			31,106,977

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

	Common Stock													Common Stock
	Shares		Amount		Additional Paid-In Capital			Accumulated Deficit			Stockholders’ Equity (Deficit)			Shares		Amount		Additional Paid-In Capital			Accumulated Deficit			Stockholders’ Equity
Balance at January 1, 2021		36,022,811	$	36	$	294,639		$	(274,179	)		20,496			36,022,811	$	36	$	294,639		$	(274,179	)		20,496
Issuance of common stock, net of issuance costs $4,512		6,347,156		6		69,919			—			69,925			6,347,156		6		69,919			—			69,925
Exercise of stock options		63,331		—		352			—			352			63,331		—		352			—			352
Stock-based compensation		—		—		4,229			—			4,229			—		—		4,229			—			4,229
Common stock issued upon vesting of restricted stock units, net of 21,452 shares withheld for employee taxes		49,873		—		(186	)		—			(186	)		49,873		—		(186	)		—			(186	)
Net loss		—		—		—			(23,042	)		(23,042	)		—		—		—			(23,042	)		(23,042	)
Balance at March 31, 2021		42,483,171	$	42	$	368,953		$	(297,221	)	$	71,774			42,483,171	$	42	$	368,953		$	(297,221	)	$	71,774
Exercise of stock options															52,727		1		108			—			109
Stock-based compensation															—		—		2,376			—			2,376
Common stock issued upon vesting of restricted stock units, net of 15,237 shares withheld for employee taxes															35,482		—		(104	)		—			(104	)
Net loss															—		—		—			(23,889	)		(23,889	)
Balance at June 30, 2021															42,571,380	$	43	$	371,333		$	(321,110	)	$	50,266

	Common Stock													Common Stock
	Shares		Amount		Additional Paid-In Capital			Accumulated Deficit			Stockholders’ Equity (Deficit)			Shares		Amount		Additional Paid-In Capital			Accumulated Deficit			Stockholders’ Equity
Balance at January 1, 2020		30,127,846	$	30	$	241,412		$	(192,559	)	$	48,883			30,127,846	$	30	$	241,412		$	(192,559	)	$	48,883
Exercise of stock options		334,444		—		1,561			—			1,561			334,444		—		1,561			—			1,561
Stock-based compensation		—		—		2,725			—			2,725			—		—		2,725			—			2,725
Vesting of restricted shares		1,250		—		3			—			3			1,250		—		3			—			3
Net loss		—		—		—			(19,551	)		(19,551	)		—		—		—			(19,551	)		(19,551	)
Balance at March 31, 2020		30,463,540	$	30	$	245,701		$	(212,110	)	$	33,621			30,463,540	$	30	$	245,701		$	(212,110	)	$	33,621
Issuance of common stock, net of issuance costs $306															4,750,000		5		33,182			—			33,187
Exercise of stock options															143,089		—		620			—			620
Stock-based compensation															—		—		2,816			—			2,816
Net loss															—		—		—			(18,922	)		(18,922	)
Balance at June 30, 2020															35,356,629	$	35	$	282,319		$	(231,032	)	$	51,322

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

	Three Months Ended March 31,						Six Months Ended June 30,
	2021			2020			2021			2020
Operating activities:
Net loss	$	(23,042	)	$	(19,551	)	$	(46,931	)	$	(38,473	)
Reconciliation of net loss to net cash used in operating activities:
Depreciation and amortization		577			369			1,160			809
Stock-based compensation		4,229			2,725			6,605			5,541
Amortization of debt discount		183			173			356			263
Non-cash interest expense		181			173			175			172
Loss on disposal of fixed assets		10			—			10			114
Changes in:
Prepaid expenses and other assets		(173	)		(1,627	)		(125	)		(4,165	)
Accounts payable		(2,977	)		(792	)		(2,739	)		1,274
Accrued expense and other liabilities		(2,962	)		631			(2,568	)		710
Net cash used in operating activities		(23,974	)		(17,899	)		(44,057	)		(33,755	)
Investing activities:
Purchase of property and equipment		(30	)		(1,075	)		(262	)		(1,896	)
Net cash and restricted cash used in investing activities		(30	)		(1,075	)
Net cash used in investing activities								(262	)		(1,896	)
Financing activities:
Proceeds from exercise of stock options		352			1,561			461			2,181
Payments related to capital lease		—			(22	)		—			(45	)
Issuance of common stock, net of issuance costs		69,978			—			69,925			33,182
Net settlement of vested restricted stock units to fund related employee statutory tax withholdings		(186	)		—			(290	)		—
Payments of issuance costs related to debt								(20	)		—
Net cash provided by financing activities		70,144			1,539			70,076			35,318
Net (decrease) increase in cash, cash equivalents, and restricted cash		46,140			(17,435	)
Net increase (decrease) in cash, cash equivalents, and restricted cash								25,757			(333	)
Cash, cash equivalents, and restricted cash, beginning of period		48,383			73,526			48,383			73,526
Cash, cash equivalents, and restricted cash, end of period	$	94,523		$	56,091		$	74,140		$	73,193
Supplemental cash flow information
Interest paid	$	526		$	342		$	1,064		$	859
Supplemental disclosure of non-cash investing and financing activities
Issuance costs in accounts payable and accrued expenses	$	53		$	—
Purchases of property and equipment in accounts payable and accrued expenses							$	43		$	254
Offering costs incurred but unpaid at period end							$	—		$	277
Vesting of restricted stock	$	—		$	3		$	—		$	3

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Kaleido Biosciences, Inc. and its wholly owned subsidiaries ~~(the~~(collectively the “Company”) is a clinical-stage healthcare company that was incorporated in Delaware on January 27, 2015 and has a principal place of business in Lexington, Massachusetts. The Company was formed to use its differentiated, chemistry-driven approach to leverage the potential of the microbiome to treat disease and improve human health.

The Company is subject to risks common to companies in the biotechnology industry, including, but not limited to, successful development of technology, obtaining additional funding, protection of proprietary technology, compliance with government regulations, risks of failure of preclinical studies (including ex vivo assays), clinical studies and clinical trials, the need to obtain marketing approval for its drug candidates and if applicable, its consumer products, fluctuations in operating results, economic pressure impacting therapeutic pricing, dependence on key personnel, risks associated with changes in technologies, development by competitors of technological innovations and the ability to supply sufficient amounts of Microbiome Metabolic Therapies, (“MMT” or “MMTs”) at an acceptable quality level.

On June 4, 2020, the Company completed a public offering (the “Offering”), pursuant to which it issued and sold 4,750,000 shares of the common stock. The aggregate net proceeds received by the Company from the Offering were $33,182. On July 1, 2020, 185,000 shares were exercised under the Underwriters’ overallotment option for net proceeds of $1,260.

On August 4, 2020, the Company entered into an Equity Distribution Agreement (the “Sales Agreement”) with a sales agent for the sale of up to $50,000 of the Company’s shares of common stock, from time to time in an at-the-market public offering (the “ATM”). The sales agent is entitled to compensation at a fixed commission rate of 3.0% of the gross proceeds from the sale of the Company’s common stock pursuant to the Sales Agreement. During the year ended December 31, 2020, the Company sold 361,299 shares of its common stock under the ATM which resulted in aggregate net proceeds of $3,432 after payment of related commissions. During the quarter ended March 31, 2021, the Company sold 309,656 shares of its common stock which resulted in aggregate net proceeds of $4,860. NaN sales or common stock were made under the ATM during the quarter ended June 30, 2021. As of ~~March 31,~~June 30, 2021, there was $41,451 available under the ATM.

On February 8, 2021, the Company completed a public offering (the “2021 Offering”), pursuant to which the Company issued and sold 6,037,500 shares of common stock for net proceeds of $65,265, which included the full exercise of the Underwriters’ overallotment option.

The accompanying condensed consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and the satisfaction of liabilities in the normal course of business. As of ~~March 31,~~June 30, 2021, the Company had an accumulated deficit of ~~$297,221.~~$321,110. The Company expects to continue to generate operating losses and use cash in operations in the foreseeable future. As of ~~March 31,~~June 30, 2021, the Company had cash and cash equivalents of ~~$92,362,~~$71,979, and management expects that the cash and cash equivalents at ~~March 31,~~June 30, 2021 will be sufficient to fund its operating expenses and capital expenditure requirements into the ~~first~~second quarter of 2022. Based on its recurring losses from operations incurred since inception, expectation of continuing operating losses for the foreseeable future, and need to raise additional capital to finance its future operations, the Company has concluded that there is substantial doubt regarding the Company’s ability to continue as a going concern within one year after the date that these consolidated financial statements are issued. These financial statements do not include any adjustments that might result from the outcome of this uncertainty.

The Company will require substantial additional capital to fund its research and development and ongoing operating expenses. These capital requirements are expected to be funded through debt and equity offerings as well as possible strategic collaborations with other companies. If the Company is unable to raise additional funds when needed, it may be required to delay, reduce or eliminate its product development or future commercialization efforts, or grant rights to develop and market product candidates that the Company would otherwise prefer to develop and market itself. While there can be no assurance the Company will be able to successfully reduce operating expenses or raise additional capital, management believes ~~the~~that its historical success in managing cash flows and obtaining capital will continue in the foreseeable future.

A novel strain of coronavirus (COVID-19) was first identified in late 2019, and subsequently declared a global pandemic by the World Health Organization on March 11, 2020. As a result of the outbreak, many companies have experienced disruptions in their operations and in markets served. The Company has instituted some and may take additional temporary precautionary measures intended to help minimize the risk of the virus to its employees, including implementing a ~~work-at-home policy, providing flexibility for working parents,~~hybrid work environment, implementing safety measures for those employees ~~who continue to go~~currently going into the office to complete their work and ~~suspending all non-essential~~limiting business-related travel. The full extent of the future impacts of COVID-19 on our operations, including the timing and ability of the Company to complete certain clinical trials and other efforts to advance the development of our MMTs, is uncertain.

The condensed consolidated financial statements of the Company included herein have been prepared, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”). Certain information and footnote disclosures normally included in financial statements prepared in accordance with accounting principles generally accepted in the United States of America ("GAAP") have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these consolidated financial statements should be read in conjunction with the financial statements and notes thereto included in the annual report on Form 10-K for the year ended December 31, 2020 filed with the SEC on March 3, 2021.

All intercompany transactions and balances of the subsidiaries have been eliminated in consolidation. In the opinion of management, the information furnished reflects all adjustments, all of which are of a normal and recurring nature, necessary for a fair representation of the results for the reported interim periods.

The preparation of the consolidated financial statements in accordance with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of expenses during the reporting period. Actual results could differ from those estimates.

The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC Topic 808, Collaborative Arrangements (ASC 808), to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards that are dependent on the commercial success of such activities. To the extent the arrangement is within the scope of ASC 808, the Company will assess whether aspects of the arrangement between it and their collaboration partner are within the scope of other accounting literature. If the Company concludes that some or all aspects of the arrangement represent a transaction with a customer, it will account for those aspects of the arrangement within the scope of ASC 606, Revenue from Contracts with Customers, by applying the five-step model described below. If the Company concludes that some or all aspects of the arrangement are within the scope of ASC 808 and do not represent a transaction with a customer, the Company will recognize its allocation of the shared costs incurred with respect to the jointly conducted activities as a component of the related expense in the period incurred.

If a contract is determined to be within the scope of ASC 606 at inception, the Company assesses the goods or services promised within such contract, determines which of those goods and services are performance obligations, and assesses whether each promised good or service is distinct. Promised goods and services are considered distinct provided that: (i) the customer can benefit from the good or service either on its own or together with other resources that are readily available to the customer (that is, the good or service is capable of being distinct) and (ii) the entity’s promise to transfer the good or service to the customer is separately identifiable from other promises in the contract (that is, the promise to transfer the good or service is distinct within the context of the contract). In assessing whether a promised good or service is distinct, the Company considers factors such as the research, manufacturing and commercialization capabilities of the collaboration partner and the availability of the associated expertise in the general marketplace. The Company also considers the intended benefit of the contract in assessing whether a promised good or service is separately identifiable from other promises in the contract. If a promised good or service is not distinct, an entity is required to combine that good or service with other promised goods or services until it identifies a bundle of goods or services that is distinct.

The Company may provide options to additional goods or services in such arrangements exercisable at a customer’s discretion. The Company assesses if these options provide a material right to the customer and if so, they are considered performance obligations. The identification of material rights requires judgments related to the determination of the value of the underlying good and services to the option exercise price.

The Company determines transaction price based on the amount of consideration the Company expects to receive for transferring the promised goods or services in the contract. Consideration may be fixed, variable, or a combination of both. The Company then allocates the transaction price to each performance obligation based on the relative standalone selling prices (“SSP”). SSP is determined at contract inception and is not updated to reflect changes between contract inception and when the performance obligations are satisfied. In developing the SSP for a performance obligation, the Company considers applicable market conditions and relevant entity-specific factors, including factors that were contemplated in negotiating the agreement with the customer and estimated costs.

If the consideration promised in a contract includes a variable amount, the Company estimates the amount of consideration to which it will be entitled by using the expected value method or the most likely amount method. The Company includes the unconstrained amount of estimated variable consideration in the transaction price. The amount included in the transaction price is constrained to the amount for which it is probable that a significant reversal of cumulative revenue recognized will not occur. At the end of each subsequent reporting period, the Company re-evaluates the estimated variable consideration included in the transaction price and any related constraint, and if necessary, adjusts its estimate of the overall transaction price.

The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligation when (or as) the performance obligation is satisfied, either at a point in time or over time, and if over time recognition is based on the use of an output or input method.

Amounts received prior to satisfying the revenue recognition criteria are recorded as deferred revenue in the Company’s condensed consolidated balance sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to receipt are recorded as other current assets in the Company's balance sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in other current assets.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which applies to all leases and will require the Company to record most leases on the balance sheet. The Company will use a modified retrospective approach of adoption for ASU 2016-02. As an emerging growth company, this standard is required to be adopted on January 1, 2022, and the Company is evaluating the impact that the adoption of ASU 2016-02 will have on its consolidated financial statements. The Company expects to recognize a significant lease obligation and right to use asset upon adoption.

The following tables set forth by level, within the fair value hierarchy, the assets carried at fair value on a recurring basis:

	Fair Value Measurements as of March 31, 2021								Fair Value Measurements as of June 30, 2021
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets:
Money market funds included within cash and cash equivalents	$	25,412		—		—	$	25,412	$	25,413		—		—	$	25,413
Total	$	25,412		—		—	$	25,412	$	25,413		—		—	$	25,413

The fair value of money market funds was measured by the Company based on quoted market prices.

Financial Instruments Not Recorded at Fair Value – The carrying value of cash, cash equivalents, restricted cash, accounts payable and accrued expenses that are reported on the condensed consolidated balance sheets approximate their fair value due to the short-term nature of these assets and liabilities. The carrying value of the long-term debt approximates fair value as evidenced by the recent refinancings.

	As of						As of
	March 31, 2021			December 31, 2020			June 30, 2021			December 31, 2020
Laboratory equipment	$	7,302		$	6,843		$	7,374		$	6,843
Office and computer equipment		1,590			1,590			1,590			1,590
Leasehold improvements		1,910			1,910			1,910			1,910
Construction in process		1,087			1,612			1,291			1,612
Property and equipment – at cost		11,889			11,955			12,165			11,955
Less accumulated depreciation and amortization		(4,056	)		(3,493	)		(4,639	)		(3,493	)
Property and equipment – net	$	7,833		$	8,462		$	7,526		$	8,462

Depreciation and amortization expense for the three months ended ~~March 31,~~June 30, 2021 and 2020 was ~~$577~~$583 and ~~$369,~~$388, respectively. Depreciation and amortization expense for the six months ended June 30, 2021 and 2020 was $1,160 and $809, respectively. During the ~~quarter~~six months ended ~~March 31,~~June 30, 2021, the Company recorded gross fixed asset disposal of $24 and related accumulated depreciation of $14. During the six months ended June 30, 2020, the Company recorded gross fixed asset disposal of $1,036 and related accumulated depreciation of $922.

	As of				As of
	March 31, 2021		December 31, 2020		June 30, 2021		December 31, 2020
Payroll and benefits	$	834	$	2,943	$	1,710	$	2,943
Consulting service		513		1,049		218		1,049
Legal service		133		173		96		173
Research and development		2,742		3,010		2,815		3,010
Interest		181		181		175		181
Deferred revenue		281		498		189		498
Other		1,018		782		704		782
Accrued expenses and other current liabilities	$	5,702	$	8,636	$	5,907	$	8,636

On December 31, 2019, the Company entered into a Credit Agreement (the “Credit Agreement”) with Hercules Capital, Inc. (the “Lender”). Under the Credit Agreement, the Company borrowed $22,500, and the Company has the option to draw down an additional $12,500 if certain milestones and conditions are met. The Company incurred fees of $410, which was paid to the Lender on the closing date. These amounts were recorded as a debt discount and are being amortized as interest expense using the effective interest method over the life of the Credit Agreement. The Credit Agreement also includes an end of term charge equal to 7.55% of the aggregate principal amount of all advances. The end of term charge, totaling $1,698 at ~~March 31,~~June 30, 2021, was recognized as a debt discount and is reflected as a reduction in the carrying value of the debt and recorded in other long-term liabilities. The debt discount created by the end of term charge is being accreted and will be recognized as additional interest expense over the term of the Credit Agreement using the effective interest method.

The Credit Agreement contains customary representations and warranties, events of default and affirmative and negative covenants, including, among others, covenants that limit or restrict the Company’s ability to, among other things, incur additional indebtedness, merge or consolidate, make acquisitions, pay dividends or other distributions or repurchase equity, make investments, dispose of assets and enter into certain transactions with affiliates, in each case subject to certain exceptions. As security for its obligations under the Credit Agreement, the Company granted the Lender a first priority security interest on substantially all of the Company’s assets (other than intellectual property), and subject to certain exceptions.

The outstanding principal under the Credit Agreement has a 48-month term with interest only payments for the first 15 months, which period can be extended to up to 24 months, depending on the achievement of certain performance milestones. The principal bears interest at a rate equal to the greater of (i) 8.95% plus the prime rate minus 4.75% and (ii) 8.95%. The Credit Agreement includes mandatory prepayment provisions that require prepayment upon the occurrence of a change in control event.

On June 15, 2020, the Company entered into a Second Amendment to Loan and Security Agreement (the ~~“Amendment”~~“Second Amendment”). The Second Amendment was entered into for the primary purpose of amending the Credit Agreement as follows: (i) the second tranche of the term loan (the “Term Loan”) iswas terminated; (ii) amounts available under Tranche 3 of the Term Loan iswas increased to $12,500 from the previous $7,500 availability amount and its availability period is extended through December 15, 2021, subject to future approval by the ~~Agent’s~~Lender’s investment committee; (iii) the interest-only period iswas extended through July 31, 2021; (iv) the interest rate on borrowings is increased by 0.4%, such that the per annum interest rate on outstanding borrowings will be the greater of (a) 9.35% and (b) 9.35% plus the Wall Street Journal prime rate minus 3.25%; and (v) the variable amount and duration of a minimum cash covenant in the Agreement ~~are~~were amended. The Second Amendment has been accounted for as a modification and the Company incurred fees of $79, which was paid to the ~~lender~~Lender on the closing date and were recorded as a debt discount, which will be amortized as interest expense using the effective interest method.

~~Future principal payments under the Credit Agreement as of March 31, 2021 are as follows (in thousands):~~

On April 30, 2021, the Company entered into a Third Amendment to Loan and Security Agreement (the ~~“Amendment”~~“Third Amendment”). The Third Amendment was entered into for the primary ~~ppickurpose~~purpose of amending the Credit Agreement as follows: (i) the interest-only period was extended through January 31, 2022; (ii) the second tranche of the term loan (the “Term Loan”) was reinstated and the related $5,000 is available to be drawn at the Company’s option on or before June 1, 2021; and (iii) the Minimum Cash Covenant was reduced from $22,500 to $15,000. The Company incurred fees of $20, which was paid to the ~~lender~~Lender on the closing ~~date.~~date and were recorded as a debt discount, which will be amortized as interest expense using the effective interest method.

Future principal payments under the Credit Agreement as of June 30, 2021 are as follows (in thousands):

In March 2018, the Company entered into a non-cancelable ten-year lease agreement for laboratory and office space in Lexington, Massachusetts. In March 2019, the Company exercised its option to lease additional space in the building. The lease expires in 2029, subject to one option to extend the lease for 10 years.

Rent expense for the three months ended ~~March 31,~~June 30, 2021 and 2020 totaled ~~$1,623~~$1,629 and ~~$1,779,~~$1,871, respectively. Rent expense for the six months ended June 30, 2021 and 2020 totaled $3,252 and $3,650. Future minimum lease payments under the non-cancelable operating leases consisted of the following as of ~~March 31,~~June 30, 2021:

Year Ending December 31,
2021	$	4,532	$	3,038
2022		6,207		6,207
2023		6,393		6,393
2024		6,584		6,584
2025		6,782		6,782
Thereafter		25,502		25,502
	$	56,000	$	54,506

On January 20, 2021, the Company entered into a separation agreement with the former Chief Medical Officer and Head of Research and Development of the Company, which amended an existing employment agreement and provided for changes in the term of service and compensation under the agreement. The outstanding options and restricted stock units held by the former Chief Medical Officer were modified to accelerate certain vesting provisions and the period of exercisability. As a result, the Company recorded stock-based compensation expense of $1,968 related to the incremental fair value of the modified awards during the ~~three months~~first quarter of 2021. There

Basic and diluted net loss per common share is determined by dividing net loss by the weighted-average common shares outstanding during the period. The Company has computed diluted net loss per common share after giving consideration to all potentially dilutive

common shares, including options to purchase common stock and unvested restricted common stock, outstanding during the period determined using the treasury stock method, except where the effect of including such securities would be anti-dilutive. Because the Company has reported net losses since inception, these potential common shares have been anti-dilutive and therefore basic and diluted net loss per share have been equivalent.

The following table presents securities that have been excluded from the computations of diluted weighted-average shares outstanding as they would be anti-dilutive:

	As of March 31,				As of June 30,
	2021		2020		2021		2020
Options to purchase common stock		6,206,765		6,644,275		6,979,895		6,913,830
Restricted stock units		272,296		50,000		195,516		235,767
		6,479,061		6,694,275		7,175,411		7,149,597

In December 2019, the Company entered into a research collaboration agreement with Janssen’s World Without Disease Accelerator (“Janssen”), part of the Janssen Pharmaceutical Companies of Johnson & Johnson, to explore the potential for MMT to prevent the onset of childhood allergy and other atopic, immune and metabolic conditions.

The collaboration includes 3 milestones of research and development with deliverables due to Janssen at end of the milestone at which point Janssen will have 60 days to decide to proceed with the next milestone.

The Company assessed the Janssen collaboration agreement in accordance with ASC 808 and ASC 606 and concluded that it represents a contract with a customer and is within the scope of ASC 606. The promised goods and services represent one combined performance obligation and the entire transaction price will be allocated to that single combined performance obligation. In addition, the Company concluded the right to proceed with the following milestones does not provide any discounts to Janssen if it decides to proceed with the next milestones. As such, the Company concluded the milestone is not considered to be a material right. Each milestone is considered a separate contract and will reflect applicable standalone selling prices.

Under the Janssen collaboration agreement, Janssen is obligated to reimburse the Company for the costs incurred under an agreed upon research plan. Costs incurred are billed by the Company to Janssen at completion of each milestone. The Company recognizes revenue over the research period and as the performance obligation is satisfied using total estimated hours to be incurred throughout each milestone. For the quarter ended ~~March 31,~~June 30, 2021, the Company recognized ~~$297~~$211 as collaboration revenue under the collaboration agreement with ~~Janssen. Additionally, as~~Janssen, of ~~March 31, 2021, the Company recognized $218 of~~which $92 was previously recorded deferred revenue within current liabilities on the Company’s condensed consolidated balance sheets ~~related~~relates to the Janssen collaboration ~~agreement~~.agreement. The June 30, 2021 deferred revenue balance of $189 is comprised of $79 for amounts received prior to satisfying the revenue recognition criteria and $110 for work performed to be recognized upon completion of a milestone. The expected research term of this arrangement is expected to be completed during 2021, and the aggregate consideration to be received by the Company is not expected to be ~~material.~~material.

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with (i) our condensed consolidated financial statements and related notes appearing elsewhere in this Quarterly Report and audited financial statements the notes thereto contained in our current report on Form 10-K filed with the Securities and Exchange Commission (the “SEC”), on March 3, 2021.

Investors and others should note that we announce material financial information to our investors using our investor relations website ( https://investors.kaleido.com/ ), SEC filings, press releases, public conference calls and webcasts. We use these channels as well as social media to communicate with the public about our company, our business, our product candidates, and other matters. It is possible that the information we post on social media could be deemed to be material information. Therefore, we encourage investors, the media, and others interested in our company to review the information we post on the social media channels listed on our investor relations website.

We are a clinical-stage healthcare company with a differentiated, chemistry-driven approach focused on targeting the microbiome to treat disease and improve human health. We have built a proprietary product platform for discovery and development that we believe will enable the rapid advancement of a broad portfolio of novel product candidates into human clinical studies under regulations supporting research with food. Our product candidates are Microbiome Metabolic Therapies (“MMT” or “MMTs”), which are designed to modulate the metabolic output and profile of the microbiome by driving the function and distribution of the gut’s existing microbes. We have an industrialized approach to the discovery and development of MMTs, and our initial MMTs are targeted glycans. Each targeted glycan is an ensemble of complex carbohydrates that is intended to modulate microbial metabolism and community composition to drive a specific biological response. We believe our MMTs have the potential to be novel treatments across a variety of diseases and conditions.

The human microbiome is generally a community of more than 30 trillion microbes, organisms that include bacteria, viruses, archaea and fungi, which reside on and inside the human body. By evolving together over thousands of years, microbes and humans have developed an intricate and mutually beneficial relationship. Given the profound impact that microbes have on human health, this highly complex microbial ecosystem has been referred to as a “newly discovered organ.” There is a growing body of research that links a healthy microbiome with overall human health, while dysbiosis, or imbalance, in the microbiome has been correlated with numerous human conditions, including those that can cause significant morbidity and mortality. Some of these conditions include irritable bowel syndrome, Parkinson’s disease, diabetes, metabolic syndrome, cancer, allergies and ulcerative colitis. The gut microbiome remains a largely untapped frontier in healthcare, and we believe that we are uniquely positioned to succeed in translating its promise into solutions for human health.

To date, therapeutic approaches to the microbiome have focused primarily on adding or subtracting bacteria, either through fecal microbiota transplant, the introduction of a consortia of bacteria, single strain approaches or antibiotics. We believe our approach is novel in that we seek to deliver MMTs that drive the function and distribution of the gut microbiome’s existing microbes, enabling an industrialized approach to treat disease and improve human health.

We have developed proprietary synthetic chemistry technologies that allow us to create MMT candidates. We believe the key characteristics of our MMT candidates include that they are orally administered, have limited systemic exposure and are selectively metabolized, structurally diverse, readily scalable, novel and proprietary. We believe that each of our MMT candidates works through one or more mechanisms of action, including decreasing production of metabolites, such as ammonia and trimethylamine generated by bacteria in the microbiome; increasing production of metabolites, such as short chain fatty acids generated by bacteria in the microbiome; and advantaging or disadvantaging certain existing species in the microbiome community (such as decreasing pathogenic bacteria).

Utilizing our proprietary product platform, we have created a library of more than 1,500 MMT candidates to probe the structure-activity relationships of our MMTs. Our MMT library is continuously growing as we continue to invest in techniques and technologies for chemical synthesis. Our MMT candidates and aspects of the proprietary product platform are supported by our expanding intellectual property portfolio, that includes ~~twelve~~14 U.S. patents, ~~two~~4 European Patent Office, or EPO, patents and more than ~~125~~130 non-provisional applications pending ~~worldwide.~~worldwide as of July 23, 2021

Through the use of our proprietary product platform, the effect of MMTs is first tested ex vivo using a highly multiplexed advanced screening platform with microbiome communities from both healthy and patient populations. To establish how MMTs impact therapeutically relevant pathways, a broad range of bioanalytical technologies are used to analyze metabolites, effector molecules and host responses, while sequencing determines key microbial community changes. A candidate MMT may then either undergo further testing in animal models or go straight into clinical evaluation in humans.

Abbreviated development may be possible because in some cases MMTs are synthesized from naturally occurring carbohydrate monomers, are orally administered with limited systemic exposure and can be designated as Generally Recognized as Safe (GRAS).

This enables us to gain valuable insights into our MMT candidates’ effects on the microbiome and human health before choosing to allocate additional time and capital to proceed to develop a drug product candidate under an IND or regulatory equivalent outside the United States.

In our human clinical studies, we are able to measure safety, tolerability and potential markers of effect, which allows us to assess the potential use of our MMT candidates in humans. Furthermore, we initiated our first Phase 2 clinical trial under an IND approximately two years after conducting our first ex vivo screening. We believe that this provides support for our belief that our approach is more expeditious and cost efficient than traditional drug development.

Since our inception in 2015, we have devoted substantially all of our resources to building our proprietary product platform, developing our pipeline of MMT candidates, building our intellectual property portfolio and process development and manufacturing function, business planning, raising capital and providing general and administrative support for these operations. To date, we have primarily financed our operations through public offering of our equity securities, private placement of our convertible preferred stock and borrowings of long-term debt.

We have incurred significant net losses since inception and expect to continue to incur net operating losses for the foreseeable future. We expect to continue to incur significant expenses and increasing operating losses for at least the next several years. We expect that our expenses and capital requirements will increase substantially in connection with our ongoing activities, particularly if and as we:

We will not generate revenue from product sales unless and until we successfully complete clinical development and obtain regulatory approval for or identify alternate non-drug pathways for our product candidates. If we obtain regulatory approval for or otherwise commercialize any of our product candidates, we expect to incur significant expenses related to developing our commercialization capability to support product sales, marketing and distribution.

As of ~~March 31,~~June 30, 2021, we had ~~$92.4~~$72.0 million in cash and cash equivalents and an accumulated deficit of ~~$297.2~~$321.1 million. Based on our current operating plans, ~~and net proceeds from the 2021 Offering,~~ we have sufficient cash and cash equivalents to fund our operating expenses and capital expenditures into the ~~first~~second quarter of 2022. We will require substantial additional capital to sustain our operations and pursue our growth strategy, including the development of our MMT candidates. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through equity or debt financings or other capital sources, which may include collaborations with other companies or other strategic transactions. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on favorable terms, or at all. If we fail to raise capital or enter into such agreements as and when needed, we may have to significantly delay, reduce or eliminate the development and commercialization of one or more of our product candidates or delay our pursuit of potential in-licenses or acquisitions. See “Liquidity and capital resources.”

Because of the numerous risks and uncertainties associated with product development, we are unable to predict the timing or amount of increased expenses or when or if we will be able to achieve or maintain profitability. Even if we are able to generate product sales,

we may not become profitable. If we fail to become profitable or are unable to sustain profitability on a continuing basis, then we may be unable to continue our operations at planned levels and be forced to reduce or terminate our operations.

We have recently begun to generate collaboration revenue but have not generated and do not expect to generate any revenue from the sale of products in the near future, if at all. If our development efforts for our current product candidates or additional product candidates that we may develop in the future are successful and can be commercialized, or if we enter into future collaboration or license agreements with third parties, we may generate revenue in the future from a combination of product sales or payments from such collaboration or license agreements.

The collaboration revenue recognized in 2021 relates to a research collaboration with Janssen’s World Without Disease Accelerator, part of the Janssen Pharmaceutical Companies of Johnson & Johnson. The collaboration explores the potential for Kaleido’s Microbiome Metabolic Therapies (MMT™) to prevent the onset of childhood allergy and other atopic, immune and metabolic conditions by driving specific microbiome features which support an appropriate maturation of the infant immune system. We do not expect the total revenue under this arrangement to be material in the aggregate.

Research and development expenses consist primarily of costs incurred in connection with the discovery and development of our product candidates. These expenses include:

We expense research and development costs as incurred. Advance payments that we make for goods or services to be received in the future for use in research and development activities are recorded as prepaid expenses. The prepaid amounts are expensed as the related goods are delivered or the services are performed.

Our direct external research and development expenses are tracked on a program-by-program basis and consist of costs that include fees, reimbursed materials and other costs paid to consultants, contractors, CMOs and CROs in connection with our preclinical and clinical development and manufacturing activities. We do not allocate employee costs, costs associated with our discovery efforts, laboratory supplies and facilities expenses, including depreciation or other indirect costs, to specific product development programs because these costs are deployed across multiple programs and our platform technology and, as such, are not separately classified.

Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. At this time, we cannot accurately estimate or know the nature, timing and costs of the efforts that will be necessary to complete the preclinical and clinical development of any of our product candidates. The successful development and commercialization of our product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with product development and commercialization, including the following:

A change in the outcome of any of these variables with respect to the development of our product candidates could significantly change the costs and timing associated with the development of that product candidate. We may never succeed in obtaining regulatory approval or commercialization for any of our product candidates.

General and administrative expenses consist primarily of salaries and related costs, including stock-based compensation, for personnel in executive, finance, corporate and business development and administrative functions. General and administrative expenses also include legal fees relating to patent and corporate matters; professional fees for accounting, auditing, tax and administrative consulting services; insurance costs; administrative travel expenses; and facility-related expenses, which include direct depreciation costs and allocated expenses for rent and maintenance of facilities and other operating costs.

We anticipate that our general and administrative expenses will increase in the future as we increase our headcount to support our continued research activities and development of our product candidates.

The following table summarizes our results of operations for the three months ended ~~March~~June 30, 2021 and 2020:

	Three Months Ended March 31,									Three Months Ended June 30,
	2021			2020			Change			2021			2020			Change
	(in thousands)									(in thousands)
Revenue:	$	297		$	—		$	297		$	211		$	250		$	(39	)
Collaboration revenue
Operating expenses:
Research and development		17,185			13,137			4,048			17,633			12,833			4,800
General and administrative		5,460			5,917			(457	)		5,785			5,559			226
Total operating expenses		22,645			19,054			3,591			23,418			18,392			5,026
Loss from operations		(22,348	)		(19,054	)		(3,294	)		(23,207	)		(18,142	)		(5,065	)
Other income (expense)
Interest income		21			193			(172	)		24			30			(6	)
Interest expense		(709	)		(688	)		(21	)		(705	)		(683	)		(22	)
Other expense		(6	)		(2	)		(4	)		(1	)		(127	)		126
Total other expense, net		(694	)		(497	)		(197	)		(682	)		(780	)		98
Net loss	$	(23,042	)	$	(19,551	)	$	(3,491	)	$	(23,889	)	$	(18,922	)	$	(4,967	)

	Three Months Ended March 31,						Three Months Ended June 30,
	2021		2020		Change		2021		2020		Change
	(in thousands)						(in thousands)
Personnel-related	$	4,985	$	4,716	$	269	$	4,064	$	4,060	$	4
Stock-based compensation expense		2,511		940		1,571		677		990		(313	)
External manufacturing and research		3,729		3,556		173		6,758		2,540		4,218
Laboratory supplies and research materials		576		372		204		767		394		373
Professional and consulting fees		2,644		1,123		1,521		2,354		1,941		413
Facility-related and other		2,740		2,430		310		3,013		2,908		105
Total research and development expenses	$	17,185	$	13,137	$	4,048	$	17,633	$	12,833	$	4,800

Research and development expenses ~~increased~~increased by ~~$4.0~~$4.8 million for the three months ended ~~March 31,~~June 30, 2021 as compared to the three months ended ~~March 31,~~June 30, 2020. The increase in external manufacturing and research of $4.2 million was primarily due to an increase in production of material for use in our clinical studies.

General and administrative expenses increased by $0.2 million for the three months ended June 30, 2021 as compared to the period ended June 30, 2020. The increase in facility-related and other expenses of $0.4 million was primarily due to increased facility operating costs that were attributed to general and administrative functions.

The following table summarizes our results of operations for the six months ended June 30, 2021 and 2020:

	Six Months Ended June 30,
	2021			2020			Change
	(in thousands)
Revenue:	$	508		$	250		$	258
Collaboration revenue
Operating expenses:
Research and development		34,818			25,970			8,848
General and administrative		11,245			11,476			(231	)
Total operating expenses		46,063			37,446			8,617
Loss from operations		(45,555	)		(37,196	)		(8,359	)
Other income (expense)
Interest income		45			223			(178	)
Interest expense		(1,414	)		(1,371	)		(43	)
Other expense		(7	)		(129	)		122
Total other expense, net		(1,376	)		(1,277	)		(99	)
Net loss	$	(46,931	)	$	(38,473	)	$	(8,458	)

Research and development expenses increased by $8.8 million for the six months ended June 30, 2021 as compared to the six months ended June 30, 2020. The increase in stock-based compensation expense of ~~$1.6~~$1.3 million was primarily due to the modification of the vesting provisions of stock options and restricted stock units related to the resignation of our former Chief Medical Officer. The increase in external manufacturing and research of $4.4 million was primarily due to an increase in production of material for use in our clinical studies. The increase in professional and consulting fees of ~~$1.5~~$1.9 million was primarily the result of increased spend relating to our two COVID-19 ~~studies.~~studies during the first quarter of 2021.

	Three Months Ended March 31,							Six Months Ended June 30,
	2021		2020		Change			2021		2020		Change
	(in thousands)							(in thousands)
Personnel-related	$	1,534	$	1,758	$	(224	)	$	2,884	$	3,378	$	(494	)
Stock-based compensation expense		1,718		1,785		(67	)		3,417		3,611		(194	)
Professional and consulting fees		756		956		(200	)		1,902		1,837		65
Facility-related and other		1,452		1,418		34			3,042		2,650		392
Total general and administrative expenses	$	5,460	$	5,917	$	(457	)	$	11,245	$	11,476	$	(231	)

General and administrative expenses decreased by ~~$0.5~~$0.2 million for the ~~three~~six months ended ~~March 31,~~June 30, 2021 as compared to the period ended ~~March 31,~~June 30, 2020. The decrease in personnel-related cost of ~~$0.2~~$0.5 million was primarily due to reduced headcount in our general and administrative functions. The ~~decrease~~increase in ~~professional~~facility-related and ~~consulting fees~~other expenses of ~~$0.2~~$0.4 million was primarily due to ~~lower utilization of outside contractors.~~

Since our inception, we have incurred significant operating losses. We have not yet commercialized any of our product candidates and we do not expect to generate revenue from sales of any product candidates for several years, if at all. To date, we have primarily financed our operations through the public offering of our equity securities, private placement of our convertible preferred stock and borrowings of long-term debt. As of ~~March 31,~~June 30, 2021, $22.5 million was outstanding under the debt facility and $12.5 million was available for borrowing contingent upon successful completion of financing and operational milestones. On June 4, 2020, ~~the Company~~we completed a public offering (the “Offering”), pursuant to which itwe issued and sold 4,750,000 shares of the common stock. The aggregate net proceeds received by ~~the Company~~us from the Offering were $34.5 million, including 185,000 shares exercised on July 1, 2020 for the Underwriters’ option. On August 4, 2020, the Company entered into an Equity Distribution Agreement (the “Sales Agreement”) with a sales agent for the sale of up to $50.0 million of ~~the Company’s~~our shares of common stock, from time to time in an at-the-market public offering (the “ATM”). The sales agent is entitled to compensation at a fixed commission rate of 3.0% of the gross proceeds from the sale of ~~the Company’s~~our common stock pursuant to the Sales Agreement. During the year ended December 31, 2020, ~~the Company~~we sold 361,299 shares of ~~its~~our common stock under the ATM which resulted in aggregate net proceeds of $3.4 million after payment of related commissions.

In January and February 2021, ~~the Company~~we sold 309,656 shares of ~~its~~our common stock under the ATM which resulted in aggregate net proceeds of $4.9 million after payment of commissions. As of ~~March 31,~~June 30, 2021, there was $41.5 million available under the ATM. On February 8, 2021, we completed the ~~Company completed a public offering (the “2021 Offering”),~~2021 Offering, pursuant to which itwe issued and sold 6,037,500 shares our common stock for aggregate net proceeds of $65.3 million, which included the full exercise of the Underwriters’ overallotment option. As of ~~March 31,~~June 30, 2021, we had ~~$92.4~~$72.0 million in cash and cash equivalents and an accumulated deficit of ~~$297.2~~$321.1 million. Based on our current operating plans, we have sufficient cash and cash equivalents to fund our operating expenses and capital expenditures into the ~~first~~second quarter of 2022. We will require substantial additional capital to sustain our operations and pursue our growth strategy, including the development of our MMT candidates. If we fail to raise capital or enter into such agreements as and when needed, we may have to significantly delay, reduce or eliminate the development and commercialization of one or more of our product candidates or delay our pursuit of potential in-licenses or acquisitions. These factors raise substantial doubt about our ability to continue as a going concern.

The following table summarizes our sources and uses of cash for each of the periods presented:

	Three Months Ended March 31,						Six Months Ended June 30,
	2021			2020			2021			2020
	(in thousands)						(in thousands)
Net cash used in operating activities	$	(23,974	)	$	(17,899	)	$	(44,057	)	$	(33,755	)
Net cash used in investing activities		(30	)		(1,075	)		(262	)		(1,896	)
Net cash provided by financing activities		70,144			1,539			70,076			35,318
Net (decrease) increase in cash, cash equivalents and restricted cash	$	46,140		$	(17,435	)
Net increase (decrease) in cash, cash equivalents, and restricted cash							$	25,757		$	(333	)

During the ~~three~~six months ended ~~March 31,~~June 30, 2021, operating activities used ~~$24.0~~$44.1 million of cash, due to our net loss of ~~$23.0~~$46.9 million and net cash used as a result of changes in our operating assets and liabilities of ~~$6.1~~$5.4 million, partially offset by non-cash charges of ~~$5.2~~$8.3 million. Net cash used as a result of changes in our operating assets and liabilities consisted of a ~~$6.0~~$5.3 million decrease in accounts payable, accrued expenses and other liabilities and a ~~$0.2~~$0.1 million increase in prepaid expenses and other assets.

~~During~~During the ~~three~~six months ended ~~March 31,~~June 30, 2020, operating activities used ~~$17.9~~$33.8 million of cash, due to our net loss of ~~$19.6~~$38.5 million and net cash used as a result of changes in our operating assets and liabilities of ~~$1.8~~$2.2 million, partially offset by non-cash charges of ~~$3.4~~$6.9 million. Net cash used as a result of changes in our operating assets and liabilities ~~primarily~~ consisted of a ~~$1.6~~$4.2 million increase in prepaid expenses and other assets, ~~arising from reimbursable tenant improvements and a $0.8 million decrease in accounts payable,~~ partially offset by a $1.3 million increase in accounts payable and a $0.7 million increase in accrued expenses and other liabilities.

Changes in prepaid expenses and other current assets, accounts payable and accrued expenses and other liabilities were generally due to the advancement of our research programs and the timing of vendor ~~invoices and~~ payments.

During the ~~three~~six months ended ~~March 31,~~June 30, 2021 and 2020, net cash used in investing activities ~~was~~resulted from property and equipment purchases of $0.3 million and ~~$1.1~~$1.9 million, ~~respectively, due to purchases of property and equipment.~~respectively.

During the ~~three~~six months ended ~~March 31,~~June 30, 2021, net cash provided by financing activities was $70.1 million, consisting primarily of proceeds from the 2021 Offering in February 2021, ATM, and proceeds from the exercise of stock options.

During the ~~three~~six months ended ~~March 31,~~June 30, 2020, net cash provided by financing activities was ~~$1.5~~$35.3 million, consisting primarily of proceeds from the Offering in June 2020 and proceeds from the exercise of stock options.

In December 2019, we entered into a Credit Agreement (“the Credit Agreement”) with Hercules Capital, Inc. (the “Lender”). Under the Credit Agreement, and we borrowed $22.5 million to us, with the option to drawn down an additional $12.5 million if certain milestones and conditions are met.

The Credit Agreement contains customary representations and warranties, events of default and affirmative and negative covenants, including, among others, covenants that limit or restrict our ability to, amount other things, incur additional indebtedness, merge or consolidate, make acquisitions, pay dividends or other distributions or repurchase equity, make investment, dispose of assets and entered into certain transactions with affiliates, in each case subject to certain exceptions. As security under the Credit Agreement, we granted the Lender a first priority security interest on substantially all of our assets (other than intellectual property), subject to certain exceptions.

Following the entry into a Third Amendment to Loan and Security Agreement, the facility has a 48-month term with interest only payments ~~has~~that have been extended to January 31, 2022. The Term Loan will mature in January 2024 and bears an interest rate of equal to the greater of (a) 9.35% and (b) 9.35% plus the Wall Street Journal prime rate minus 3.25%. The Term Loan is subject to mandatory prepayment provisions that require prepayment upon the occurrence of a Change in Control event (as defined in the Credit Agreement).

Over the next several quarters, we are focusing our activities on key exploratory and clinical studies and clinical trials which we expect will reduce our overall expense rate. In the periods that follow, assuming the success of our clinical studies and clinical trials, we anticipate our expenses to increase as we progress towards larger and more pivotal clinical studies and clinical trials of our product candidates, with the potential for larger clinical studies, clinical trials and associated manufacturing. The timing and amount of our operating expenditures will depend largely on:

We believe that our existing cash and cash equivalents will enable us to fund our operating expenses, capital expenditure requirements and debt service into the ~~first~~second quarter of 2022. We have based this estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect.

Until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through a combination of equity offerings, debt financings, collaborations, strategic alliances, and marketing, distribution or licensing arrangements with third parties. To the extent that we raise additional capital through the sale of equity or convertible debt securities, your ownership interest may be materially diluted, and the terms of such securities could include liquidation or other preferences that adversely affect your rights as a common stockholder. Debt financing and preferred equity financing, if available, may involve agreements that include restrictive covenants that limit our ability to take specified actions, such as incurring additional debt, making capital expenditures or declaring dividends. If we raise funds through collaborations, strategic alliances or marketing, distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings or other arrangements when needed, we may be required to delay, reduce or eliminate our product development or future commercialization efforts, or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

During the three months ended ~~March 31,~~June 30, 2021, there were no material changes to our contractual obligations and commitments.

As of ~~March 31,~~June 30, 2021, we did not have any off-balance sheet arrangements as defined under applicable SEC rules.

Our condensed consolidated financial statements are prepared in accordance with generally accepted accounting principles. The preparation of our condensed consolidated financial statements and related disclosures requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, costs and expenses, and the disclosure of contingent assets and liabilities in our financial statements. We base our estimates on historical experience, known trends and events and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and assumptions on an ongoing basis. Our actual results may differ from these estimates under different assumptions or conditions.

There have been no significant changes to our critical accounting policies from those described in our Annual Report on Form 10-K filed with the SEC on March 3, 2021.

Refer to Note 2, “Summary of Significant Accounting Policies,” in the accompanying notes to the consolidated financial statements for a discussion of recent accounting pronouncements.

The Jumpstart Our Business Startups Act of 2012 permits an “emerging growth company” such as us to take advantage of an extended transition period to comply with new or revised accounting standards applicable to public companies until those standards would otherwise apply to private companies. We have elected to not “opt out” of this provision and, as a result, we will adopt new or revised accounting standards at the time private companies adopt the new or revised accounting standard and will do so until such time that we either (i) irrevocably elect to “opt out” of such extended transition period or (ii) no longer qualify as an emerging growth company.

We are also a “smaller reporting company” meaning that the market value of our stock held by non-affiliates is less than $700 million and our annual revenue was less than $100 million during the most recently completed fiscal year. We may continue to be a smaller reporting company if either (i) the market value of our stock held by non-affiliates is less than $250 million or (ii) our annual revenue was less than $100 million during the most recently completed fiscal year and the market value of our stock held by non-affiliates is less than $700 million. If we are a smaller reporting company at the time we cease to be an emerging growth company, we may continue to rely on exemptions from certain disclosure requirements that are available to smaller reporting companies. Specifically, as a smaller reporting company we may choose to present only the two most recent fiscal years of audited financial statements in our Annual Report and, similar to emerging growth companies, smaller reporting companies have reduced disclosure obligations regarding executive compensation.

We are a smaller reporting company as define by Rule 12b-2 of the Exchange Act and are no require to provide the information under this item.

We have established disclosure controls and procedures designed to ensure that information required to be disclosed in the reports that we file or submits under the Securities Exchange Act of 1934, as amended, (the "Exchange Act"), is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms and is accumulated and communicated to management, including the principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure.

Our management, with the participation of our Principal Executive Officer and Principal Financial Officer, evaluated the effectiveness of our disclosure controls and procedures as of ~~March 31,~~June 30, 2021. The term “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by the company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the ~~Securities and Exchange Commission’s~~SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, or persons performing similar functions, as appropriate to allow timely decisions regarding required disclosure. Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of ~~March 31,~~June 30, 2021, our Principal Executive Officer and Principal Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

There was no change in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15(d)-15(f) under the Exchange Act) that occurred during the period covered by this Quarterly Report ~~on Form 10-Q~~ that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

From time to time, we may become involved in legal proceedings arising in the ordinary course of our business. We are not currently a party to any material legal proceedings.

We operate in a changing environment that involves numerous known and unknown risks and uncertainties that could materially adversely affect our operations. You should carefully consider the following discussion of risk factors, in its entirety, in addition to the other information contained in this Quarterly Report, ~~on Form 10-Q,~~ our Annual Report on Form 10-K for the year ended December 31, 2020 and the other filings we make with the SEC. Factors that have affected our Company are described in Part I, Item 1A of our Annual Report on Form 10-K filed with the SEC for the year ended December 31, 2020 as filed with the SEC on March 3, 2021, and are incorporated by reference herein.

† This certification will not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liability of that section. Such certification will not be deemed to be incorporated by reference into any filing under the Securities Act of 1933, as amended, or the Exchange Act, except to the extent specifically incorporated by reference into such filing.

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

Delaware	47-3048279
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

65 Hayden Avenue, Lexington, MA	02421
(Address of principal executive offices)	(Zip Code)

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, $0.001 Par Value	KLDO	NASDAQ Global Select Market

		Page Number
PART I: FINANCIAL INFORMATION
Item 1.	Condensed Consolidated Financial Statements (Unaudited)	2
	Condensed Consolidated Balance Sheets	2
	Condensed Consolidated Statements of Operations	3
	Condensed Consolidated Statements of Stockholders' Equity	4
	Condensed Consolidated Statements of Cash Flows	5
	Notes to Condensed Consolidated Financial Statements	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	12
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	2021
Item 4.	Controls and Procedures	2021
PART II: OTHER INFORMATION
Item 1.	Legal Proceedings	2122
Item 1A.	Risk Factors	2122
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	2122
Item 3.	Defaults Upon Senior Securities	2122
Item 4.	Mine Safety Disclosures	2122
Item 5.	Other Information	2122
Item 6.	Exhibits	2223
Signatures		2324


	1)	Identification of the contract, or contracts, with a customer,
	2)	Identification of the performance obligations in the contract, including whether they are distinct within the context of the contract
	3)	Determination of the transaction price, including the constraint on variable consideration
	4)	Allocation of the transaction price to the performance obligations in the contract
	5)	Recognition of revenue when, or as, performance obligations are satisfied

2021		3,379
2022		8,686
2023		9,547
2024		888
Total future principal payments		22,500
Less unamortized debt discount		1,308
Total balance	$	21,192

Large accelerated filer	☐	Accelerated filer	☐
Non-accelerated filer	☒	Smaller reporting company	☒
		Emerging growth company	☒

	Fair Value Measurements as of December 31, 2020
	Level 1		Level 2		Level 3		Total
Assets:
Money market funds included within cash and cash equivalents	$	45,410		—		—	$	45,410
Total	$	45,410		—		—	$	45,410

2021		—
2022		9,776
2023		11,671
2024		1,053
Total future principal payments		22,500
Less unamortized debt discount		1,156
Total balance	$	21,344


Exhibit No.		Exhibit Index


10.1		~~Separation~~Third Amendment to Loan and Security Agreement, dated ~~January 25,~~April 30, 2021, by and ~~between~~among Kaleido Biosciences, Inc. and ~~Katharine Knobil~~each of its Qualified Subsidiaries (including Cadena Bio, Inc.), the several banks and other financial institutions or entities from time to time parties to the Loan Agreement and Hercules Capital, Inc. (Incorporated by reference to Exhibit ~~10.1.~~10.1 to the Registrant’s ~~Current Report on~~Registration Form 8-K (File No. 001-38822) filed on ~~January 25,~~May 4, 2021.


31.1*		Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

31.2*		Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

32.1†		Certification of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

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	KALEIDO BIOSCIENCES, INC.
Date: ~~May 4,~~August 11, 2021	By:	/s/ Daniel L. Menichella
		Daniel L. Menichella
		President and Chief Executive Officer
		(Principal Executive Officer)

Date: ~~May 4,~~August 11, 2021	By:	/s/ William Duke, Jr.
		William Duke, Jr.
		Chief Financial Officer
		(Principal Financial and Accounting Officer)