Assembly Biosciences (ASMB) 10-Q 4 Nov 21 2021 Q3 Quarterly report Financial data

Document And Entity Information

Document And Entity Information - shares	9 Months Ended
	Sep. 30, 2021	Nov. 01, 2021
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Transition Report	false
Document Period End Date	Sep. 30, 2021
Entity File Number	001-35005
Entity Registrant Name	ASSEMBLY BIOSCIENCES, INC.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	20-8729264
Entity Address, Address Line One	331 Oyster Point Blvd.
Entity Address, Address Line Two	Fourth Floor
Entity Address, City or Town	South San Francisco
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94080
City Area Code	833
Local Phone Number	509-4583
Amendment Flag	false
Document Fiscal Year Focus	2021
Document Fiscal Period Focus	Q3
Entity Central Index Key	0001426800
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Trading Symbol	ASMB
Security Exchange Name	NASDAQ
Title of 12(b) Security	Common Stock, par value $0.001
Entity Common Stock, Shares Outstanding		47,861,677
Entity Shell Company	false
Entity Emerging Growth Company	false
Entity Small Business	false

CONDENSED CONSOLIDATED BALANCE

CONDENSED CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Current assets
Cash and cash equivalents	$ 70,760	$ 59,444
Marketable securities - short-term	110,142	156,969
Accounts receivable from collaborations	769	1,230
Prepaid expenses and other current assets	6,548	6,850
Total current assets	188,219	224,493
Marketable securities - long-term	9,180
Property and equipment, net	1,241	1,600
Operating lease right-of-use (ROU) assets	6,773	9,131
Other assets	1,922	6,392
Indefinite-lived intangible asset	29,000	29,000
Goodwill	12,638	12,638
Total assets	248,973	283,254
Current liabilities
Accounts payable	2,628	4,598
Accrued clinical expenses	3,744	4,444
Other accrued expenses	5,457	11,987
Operating lease liabilities - short-term	3,099	3,404
Total current liabilities	14,928	24,433
Deferred tax liabilities	2,531	2,531
Deferred revenue	2,733	8,987
Operating lease liabilities - long-term	4,136	6,725
Total liabilities	24,328	42,676
Commitments and contingencies
Stockholders' equity
Preferred stock, $0.001 par value; 5,000,000 shares authorized; no shares issued or outstanding
Common stock, $0.001 par value; 100,000,000 shares authorized as of September 30, 2021 and December 31, 2020; 47,077,052 and 34,026,680 shares issued and outstanding as of September 30, 2021 and December 31, 2020, respectively	47	34
Additional paid-in capital	796,057	742,387
Accumulated other comprehensive loss	(288)	(270)
Accumulated deficit	(571,171)	(501,573)
Total stockholders' equity	224,645	240,578
Total liabilities and stockholders' equity	$ 248,973	$ 283,254

CONDENSED CONSOLIDATED BALANC_2

CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Sep. 30, 2021	Dec. 31, 2020
Statement Of Financial Position [Abstract]
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	47,077,052	34,026,680
Common stock, shares outstanding	47,077,052	34,026,680

CONDENSED CONSOLIDATED STATEMEN

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Income Statement [Abstract]
Collaboration revenue	$ 6,254	$ 34,611	$ 6,254	$ 78,068
Operating expenses:
Research and development	18,474	26,941	53,777	73,314
General and administrative	6,655	11,689	22,276	29,888
Total operating expenses	25,129	38,630	76,053	103,202
Loss from operations	(18,875)	(4,019)	(69,799)	(25,134)
Other income:
Interest and other income, net	72	670	201	2,400
Total other income	72	670	201	2,400
Net loss	(18,803)	(3,349)	(69,598)	(22,734)
Other comprehensive (loss) income
Unrealized (loss) gain on marketable securities	(15)	(262)	(18)	43
Comprehensive loss	$ (18,818)	$ (3,611)	$ (69,616)	$ (22,691)
Net loss per share, basic and diluted	$ (0.41)	$ (0.09)	$ (1.63)	$ (0.64)
Weighted average common shares outstanding, basic and diluted	45,569,276	35,506,042	42,725,109	35,321,393

CONDENSED CONSOLIDATED STATEM_2

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Cash flows from operating activities
Net loss	$ (69,598)	$ (22,734)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	346	377
Stock-based compensation	3,292	18,106
Net accretion and amortization of investments in marketable debt securities	398	(80)
Non-cash rent expense	2,940	3,463
Loss on disposal of fixed assets	1,625	0
Changes in operating assets and liabilities:
Accounts receivable from collaboration	461	(216)
Prepaid expenses and other current assets	302	507
Other assets	4,470	(4,296)
Accounts payable	(1,970)	(120)
Accrued clinical expenses	(700)	(375)
Other accrued expenses	(6,490)	(877)
Deferred revenue	(6,254)	(28,061)
Operating lease liabilities	(2,856)	(3,382)
Net cash used in operating activities	(74,034)	(37,688)
Cash flows from investing activities
Purchases of property and equipment	(3,078)	(470)
Proceeds from sale of property and equipment	857	0
Purchases of marketable securities	(107,480)	(153,022)
Proceeds from maturities of marketable securities	132,200	165,252
Proceeds from sale of marketable securities	12,500	35,595
Net cash provided by investing activities	34,999	47,355
Cash flows from financing activities
Proceeds from the exercise of stock options	0	1,445
Proceeds from the issuance of common stock under Employee Stock Purchase Plan (ESPP)	144	467
Proceeds from sale of common stock, net of issuance costs	50,207	0
Net cash provided by financing activities	50,351	1,912
Net increase in cash and cash equivalents	11,316	11,579
Cash and cash equivalents at the beginning of the period	59,444	46,732
Cash and cash equivalents at the end of the period	70,760	58,311
Supplemental non-cash investing and financing activities
Operating lease liabilities arising from obtaining ROU assets	126	1,063
Remeasurement of lease liabilities arising from modification of ROU assets	$ (788)	$ 0

CONDENSED CONSOLIDATED STATEM_3

CONDENSED CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Balance at Dec. 31, 2019	$ 273,217	$ 32	$ 712,807	$ (201)	$ (439,421)
Balance (in shares) at Dec. 31, 2019		32,558,307
Issuance of common stock upon exercise of stock options	1,445	$ 1	1,444
Issuance of common stock upon exercise of stock options ( in shares )		172,779
Issuance of common stock under ESPP	467		467
Issuance of common stock under ESPP (in shares)		42,266
Issuance of shares of common stock for settlement of restricted stock units (RSUs) (in shares)		151,184
Unrealized gain (loss) on marketable debt securities	43			43
Stock-based compensation	18,111		18,111
Net income (loss)	(22,734)				(22,734)
Balance at Sep. 30, 2020	270,549	$ 33	732,829	(158)	(462,155)
Balance (in shares) at Sep. 30, 2020		32,924,536
Balance at Jun. 30, 2020	267,115	$ 33	725,784	104	(458,806)
Balance (in shares) at Jun. 30, 2020		32,807,519
Issuance of common stock upon exercise of stock options	843		843
Issuance of common stock upon exercise of stock options ( in shares )		81,066
Issuance of shares of common stock for settlement of restricted stock units (RSUs) (in shares)		35,951
Unrealized gain (loss) on marketable debt securities	(262)			(262)
Stock-based compensation	6,202		6,202
Net income (loss)	(3,349)				(3,349)
Balance at Sep. 30, 2020	270,549	$ 33	732,829	(158)	(462,155)
Balance (in shares) at Sep. 30, 2020		32,924,536
Balance at Dec. 31, 2020	240,578	$ 34	742,387	(270)	(501,573)
Balance (in shares) at Dec. 31, 2020		34,026,680
Issuance of common stock under at-the-market (ATM) equity offering program, net of issuance costs	$ 50,207	$ 11	50,196
Issuance of common stock under at-the-market (ATM) equity offering program, net of issuance costs (in shares)		10,399,548
Issuance of common stock upon exercise of stock options ( in shares )	0
Issuance of common stock under ESPP	$ 144		144
Issuance of common stock under ESPP (in shares)		42,803
Issuance of shares of common stock for settlement of restricted stock units (RSUs) (in shares)		184,387
Issuance of common stock upon cashless exercise of pre-funded warrants		$ 2	(2)
Issuance of common stock upon cashless exercise of pre-funded warrants (in shares)		2,423,634
Unrealized gain (loss) on marketable debt securities	(18)			(18)
Stock-based compensation	3,332		3,332
Net income (loss)	(69,598)				(69,598)
Balance at Sep. 30, 2021	224,645	$ 47	796,057	(288)	(571,171)
Balance (in shares) at Sep. 30, 2021		47,077,052
Balance at Jun. 30, 2021	231,794	$ 44	784,391	(273)	(552,368)
Balance (in shares) at Jun. 30, 2021		43,779,059
Issuance of common stock under at-the-market (ATM) equity offering program, net of issuance costs	10,055	$ 3	10,052
Issuance of common stock under at-the-market (ATM) equity offering program, net of issuance costs (in shares)		2,949,647
Issuance of shares of common stock for settlement of restricted stock units (RSUs) (in shares)		33,333
Issuance of common stock upon cashless exercise of pre-funded warrants (in shares)		315,013
Unrealized gain (loss) on marketable debt securities	(15)			(15)
Stock-based compensation	1,614		1,614
Net income (loss)	(18,803)				(18,803)
Balance at Sep. 30, 2021	$ 224,645	$ 47	$ 796,057	$ (288)	$ (571,171)
Balance (in shares) at Sep. 30, 2021		47,077,052

Nature of Business

Nature of Business	9 Months Ended
	Sep. 30, 2021
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Nature of Business	Note 1 - Nature of Business Overview Assembly Biosciences, Inc. (together with its subsidiaries, Assembly or the Company), incorporated in Delaware in October 2005, is a clinical-stage biotechnology company advancing a novel class of oral therapeutic candidates for the treatment of chronic hepatitis B virus (HBV) infection. The Company operates in one segment and is headquartered in South San Francisco, California, with operations in California and China. Prior to the Company’s wind-down of its Microbiome program in January 2021, the Company also had operations in Connecticut. The Company’s research and development programs are pursuing multiple drug candidates that inhibit the HBV replication cycle and block the generation of covalently closed circular DNA (cccDNA), with the aim of discovering and developing finite and curative therapies for patients with HBV. The Company has discovered several novel core inhibitors, which are small molecules that directly target and allosterically modify the HBV core (HBc) protein in a way that affects assembly and stability of HBV nucleocapsids. Liquidity The Company has not derived any revenue from product sales to date and currently has no approved products. Once a product has been developed, it will need to be approved for sale by the U.S. Food and Drug Administration (FDA) or an applicable foreign regulatory agency. Since inception, the Company’s operations have been financed primarily through the sale of equity securities, proceeds from the exercise of warrants and stock options, issuance of debt, and upfront payments related to collaboration agreements. The Company has incurred losses from operations since inception and expects to continue to incur substantial losses for the next several years as it continues its product development efforts. Management believes the Company currently has sufficient funds to meet its operating requirements for at least the next twelve months following the date these unaudited condensed consolidated financial statements are issued. If the Company cannot generate significant cash from its operations, it intends to obtain any additional funding it requires through strategic relationships, public or private equity or debt financings, grants or other arrangements (see Note 6 for recent sales of common stock). The Company cannot assure such funding will be available on reasonable terms, if at all. Market volatility resulting from the global novel coronavirus disease (COVID-19) pandemic or other factors could also adversely impact the Company’s ability to access capital when and as needed. If the Company is unable to generate enough revenue from its collaborations, secure additional sources of funding or receive full and timely collections of amounts due, it may be necessary to significantly reduce the current rate of spending through reductions in staff and delaying, scaling back, or stopping certain research and development programs, including more costly clinical trials.

Summary of Significant Accounti

Summary of Significant Accounting Policies and Recent Accounting Pronouncements	9 Months Ended
	Sep. 30, 2021
Accounting Policies [Abstract]
Summary of Significant Accounting Policies and Recent Accounting Pronouncements	Note 2 - Summary of Significant Accounting Policies and Recent Accounting Pronouncements Basis of Presentation The accompanying unaudited condensed consolidated financial statements include the accounts of the Company and its subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (U.S. GAAP) for interim financial information and pursuant to the instructions to Form 10-Q and Rule 10-01 of Regulation S-X of the SEC. In management’s opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as the annual audited consolidated financial statements and include normal recurring adjustments necessary for the fair presentation of the Company’s financial position and its results of operations and comprehensive loss and its cash flows for the periods presented. These statements do not include all disclosures required by U.S. GAAP and should be read in conjunction with the Company’s audited consolidated financial statements and accompanying notes for the fiscal year ended December 31, 2020, which are contained in the 2020 Annual Report. The results for the three and nine months ended September 30, 2021 are not necessarily indicative of results to be expected for the entire year ending December 31, 2021 or future operating periods. Use of Estimates The preparation of the unaudited condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of expenses during the reporting period. Actual results could differ from those estimates. Estimates inherent in the preparation of the accompanying unaudited condensed consolidated financial statements include estimates for the cost-based input of revenue recognition and standalone selling price estimates for allocation of transaction price to performance obligations, revenue recognition, estimates of costs incurred but not yet invoiced for clinical trial accruals, recoverability and useful lives of our long-lived assets, the estimated fair value of our indefinite-lived intangible assets, the estimated fair value of our reporting unit for purposes of evaluating goodwill impairment, provisions for income taxes, amounts receivable under collaboration agreements, measurement of operating lease liabilities, and the fair value of stock options, stock appreciation rights, and restricted stock units (RSUs) granted to employees, directors, and consultants. The Company’s estimates could be affected by external conditions, including those unique to the Company and general economic conditions. It is reasonably possible these external factors could have an effect on the Company’s estimates and could cause actual results to differ materially from those estimates and assumptions. Other Risks and Uncertainties In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. To date, the Company’s operations have not been significantly impacted by the COVID-19 pandemic. However, the Company cannot at this time predict the specific extent, duration, or full impact the COVID-19 pandemic will have on its business, operations, strategy, prospects and financial condition and results. The impact of the COVID-19 pandemic on the Company’s financial performance will depend on future developments, including the duration of the outbreak and related governmental advisories and restrictions. These developments and the impact of the COVID-19 pandemic on the financial markets and the overall economy are highly uncertain. If the financial markets and/or the overall economy are impacted for an extended period, the Company’s results may be adversely affected. Income Taxes In March 2021, the American Rescue Plan (H.R. 1319) was signed into law. This legislation extends and enhances a number of current-law tax incentives for businesses, but also expands the definition of a “covered employee” as defined by Section 162(m)(1) of the Internal Revenue Code. The corporate tax provisions included within the bill are not expected to have a material impact on the Company. Net Loss per Share Basic net loss per share of common stock excludes dilution and is computed by dividing net loss by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock reflects the potential dilution that In December 2019, the Company sold 6,287,878 shares of common stock as well as pre-funded warrants to purchase up to 2,424,242 shares of common stock. In June 2021, 2,109,140 of the pre-funded warrants were exercised through a cashless exercise, and in July 2021, the remaining 315,102 pre-funded warrants were exercised through a cashless exercise (see Note 6). Prior to these exercises, the pre-funded warrants were exercisable for shares of common stock at an exercise price of $0.001 per share. The shares of common stock A reconciliation of the numerators and the denominators of the basic and diluted net loss per common share computations is as follows (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Numerator: Net loss $ (18,803 ) $ (3,349 ) $ (69,598 ) $ (22,734 ) Denominator: Weighted average common shares and pre-funded warrants outstanding - basic and diluted 45,569,276 35,506,042 42,725,109 35,321,393 Net loss per share - basic and diluted $ (0.41 ) $ (0.09 ) $ (1.63 ) $ (0.64 ) Securities excluded from the computation of diluted net loss per share because including them would have been antidilutive are as follows: September 30, 2021 2020 Options to purchase common stock 6,306,867 6,660,918 Common stock subject to purchase under our ESPP 49,470 25,192 Unvested RSUs 998,188 851,589 Total 7,354,525 7,537,699 Adoption of Recent Accounting Pronouncements On January 1, 2021, the Company adopted Accounting Standards Update (ASU) 2020-10, Codification Improvements – Disclosures The adoption of this standard had no material impact on the Company’s condensed consolidated financial statements and related disclosures. Recent Accounting Pronouncements In June 2016, the Financial Accounting Standards Board (the FASB) issued ASU 2016-13, Financial Instruments – Credit Losses: Measurement of Credit Losses on Financial Instruments Financial Instruments – Credit Losses (Topic 326) , Derivatives and Hedging (Topic 815) , and Leases (Topic 842): Effective Dates , The Company is currently evaluating the timing and impact of adopting ASU 2016-13 on its condensed consolidated financial statements and related disclosures. In August 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity for the derivative scope exception, which will permit more equity contracts to qualify for the scope exception and simplifies the diluted earnings per share calculation in certain areas. ASU 2020-06 is effective for interim and annual periods beginning after December 15, 2021, with early adoption permitted. Adoption of ASU 2020-06 can either be on a modified retrospective or full retrospective basis. The Company is currently evaluating the impacts of ASU 2020-06 on its condensed consolidated financial statements and related disclosures. In May 2021, the FASB issued ASU 2021-04, Issuer's Accounting for Certain Modifications or Exchanges of Freestanding Equity-Classified Written Call Options

Fair Value Measurements and Inv

Fair Value Measurements and Investments in Marketable Securities	9 Months Ended
	Sep. 30, 2021
Investments Debt And Equity Securities [Abstract]
Fair Value Measurements and Investments in Marketable Securities	Note 3 – Fair Value Measurements and Investments in Marketable Securities The carrying amounts of cash equivalents and marketable securities approximate their fair value based upon quoted market prices. Certain of the Company’s financial instruments are not measured at fair value on a recurring basis, but are recorded at amounts that approximate their fair value due to their liquid or short-term nature, such as cash, accounts receivable, accounts payable, accrued expenses, lease liability-short term and deferred revenue-short term. The Company uses the following three-level hierarchy that maximizes the use of observable inputs and minimizes the use of unobservable inputs to value its financial instruments: Level 1: Observable inputs such as unadjusted quoted prices in active markets for identical instruments. Level 2: Quoted prices for similar instruments that are directly or indirectly observable in the marketplace. Level 3: Significant unobservable inputs that are supported by little or no market activity and that are financial instruments whose values are determined using pricing models, discounted cash flow methodologies, or similar techniques, as well as instruments for which the determination of fair value requires significant judgment or estimation. Investments in marketable securities consisted of the following (in thousands): September 30, 2021 Amortized Cost Gross Unrealized Gain Gross Unrealized Loss Fair Value Cash equivalents Money market funds $ 67,893 $ — $ — $ 67,893 Total cash equivalents 67,893 — — 67,893 Short-term marketable securities U.S. and foreign corporate debt securities 12,056 — (2 ) 12,054 Asset-backed securities 12,143 1 (6 ) 12,138 U.S. and foreign commercial paper 85,950 — — 85,950 Total short-term marketable securities 110,149 1 (8 ) 110,142 Long-term marketable securities U.S. and foreign corporate debt securities 9,188 — (8 ) 9,180 Total long-term marketable securities 9,188 — (8 ) 9,180 Total cash equivalents and marketable securities $ 187,230 $ 1 $ (16 ) $ 187,215 December 31, 2020 Amortized Cost Gross Unrealized Gain Gross Unrealized Loss Fair Value Cash equivalents Money market funds $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper 6,498 — — 6,498 Total cash equivalents 54,051 — — 54,051 Short-term marketable securities U.S. and foreign corporate debt securities 16,939 3 (3 ) 16,939 Asset-backed securities 12,674 2 (1 ) 12,675 U.S. treasury securities 23,997 2 — 23,999 U.S. and foreign commercial paper 103,356 — — 103,356 Total short-term marketable securities 156,966 7 (4 ) 156,969 Total cash equivalents and marketable securities $ 211,017 $ 7 $ (4 ) $ 211,020 All marketable securities held as of September 30, 2021 had contractual maturities of less than two years. Realized gains and losses for the three and nine months ended September 30, 2021 and 2020 were not significant. None of the Company’s investments have been in a continuous unrealized loss position for more than 12 months as of September 30, 2021. The following tables present the fair value of the Company’s financial assets measured at fair value on a recurring basis (in thousands): September 30, 2021 Level 1 Level 2 Level 3 Fair Value Cash equivalents Money market fund $ 67,893 $ — $ — $ 67,893 Total cash equivalents 67,893 — — 67,893 Short-term marketable securities U.S. and foreign corporate debt securities — 12,054 — 12,054 Asset-backed securities — 12,138 — 12,138 U.S. and foreign commercial paper — 85,950 — 85,950 Total short-term marketable securities — 110,142 — 110,142 Long-term marketable securities U.S. and foreign corporate debt securities — 9,180 — 9,180 Total long-term marketable securities — 9,180 — 9,180 Total assets measured at fair value $ 67,893 $ 119,322 $ — $ 187,215 December 31, 2020 Level 1 Level 2 Level 3 Fair Value Cash equivalents Money market fund $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper — 6,498 — 6,498 Total cash equivalents 47,553 6,498 — 54,051 Short-term marketable securities U.S. and foreign corporate debt securities — 16,939 — 16,939 Asset-backed securities — 12,675 — 12,675 U.S. treasury securities — 23,999 — 23,999 U.S. and foreign commercial paper — 103,356 — 103,356 Total short-term marketable securities — 156,969 — 156,969 Total assets measured at fair value $ 47,553 $ 163,467 $ — $ 211,020 The Company estimates the fair value of its investments in marketable securities by taking into consideration valuations obtained from third-party pricing services. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. These inputs include reported trades of and broker/dealer quotes on the same or similar securities, issuer credit spreads, benchmark securities, prepayment/default projections based on historical data, and other observable inputs. There were no transfers between Level 1, Level 2 or Level 3 during the periods presented.

Other Accrued Expenses

Other Accrued Expenses	9 Months Ended
	Sep. 30, 2021
Payables And Accruals [Abstract]
Other Accrued Expenses	Note 4 – Other Accrued Expenses Other accrued expenses consist of the following (in thousands): September 30, December 31, 2021 2020 Accrued expenses: Accrued compensation $ 4,871 $ 7,016 Accrued restructuring charges 232 4,164 Accrued professional fees and other 354 807 Total accrued expenses $ 5,457 $ 11,987

Restructurings

Restructurings	9 Months Ended
	Sep. 30, 2021
Restructuring And Related Activities [Abstract]
Restructurings	Note 5 – Restructurings Restructuring charges relate to the Company’s decision to relocate its headquarters to South San Francisco, California, which was approved by the Board of Directors in November 2019 and effective January 1, 2020 and the wind-down of the Company’s Microbiome program, which the Company and its Board of Directors determined in December 2020 was in the Company’s best interest, enabling the Company to prioritize resources and focus on the advancement of its pipeline of novel core inhibitors for chronic HBV infection. The following table summarizes the Company’s costs incurred (in thousands): Total Restructuring Cost Employee Severance and Related Benefits Asset Impairment and Other Costs Restructuring costs incurred for the nine months ended September 30, 2021 $ (1,348 ) $ (2,959 ) (1) $ 1,611 Cumulative restructuring costs incurred through September 30, 2021 $ 6,430 $ 3,240 $ 3,190 (1) The reversal of $3.0 million in employee severance and related benefits recognized during the nine months ended September 30, 2021 reflects the reversal of previously recognized stock-based compensation expense related to forfeited awards based on the Company’s policy of recognizing stock-based awards with graded vesting schedules using an accelerated attribution method on a straight-line basis over the requisite service period for each separately vesting portion of the award and to recognize forfeitures when they occur. There were no restructuring costs incurred during the three months ended September 30, 2021. The cumulative restructuring costs incurred through September 30, 2021 represents the total amount expected to be incurred. The following table presents where the restructuring charges were recognized during the nine months ended September 30, 2021 (in thousands): Research and development $ (1,625 ) General and administrative 277 Total $ (1,348 ) There were no restructuring costs incurred f or the The following table presents the activity in the accrued restructuring charges during the nine months ended September 30, 2021 (in thousands): Total Restructuring Cost Employee Severance and Related Benefits Asset Impairment and Other Costs Accrued balance as of December 31, 2020 $ 4,164 $ 4,164 $ — Costs incurred 1,611 — 1,611 Reductions for cash payments (5,543 ) (3,932 ) (1,611 ) (1) Accrued balance as of September 30, 2021 $ 232 $ 232 $ — (1) Cash payments are presented net of proceeds received from the sale of assets of $0.9 million The asset impairment and other costs includes $1.4 million for the remaining payment obligations of leased equipment the Company purchased and sold to third parties. The Company expects the accrued restructuring liability to be fully paid in 2021.

Stockholders' Equity

Stockholders' Equity	9 Months Ended
	Sep. 30, 2021
Equity [Abstract]
Stockholders' Equity	Note 6 – Stockholders’ Equity The Company was authorized to issue 5,000,000 shares of preferred stock as of September 30, 2021 and December 31, 2020, respectively. As of September 30, 2021 and December 31, Sale of Common Stock In August 2020, the Company filed a shelf registration statement on Form S-3 with the SEC, File No. 333-248469, that became effective on September 4, 2020 (the 2020 Registration Statement). The Company may from time to time sell any combination of the securities described in the 2020 Registration Statement in one or more offerings up to an aggregate offering price of $300.0 million. In connection with the filing of the 2020 Registration Statement, the Company entered into a sales agreement under which the Company may offer and sell shares of its common stock having an aggregate offering price of up to $100.0 million through “at-the-market” offerings (2020 ATM), which shares are included in the $300.0 million of securities registered pursuant to the 2020 Registration Statement. During the nine months ended September 30, 2021, the Company sold 10,399,548 shares of common stock under the 2020 ATM, for which the Company received net proceeds of $50.2 million, after deducting commissions, fees and expenses. Common Stock Warrants The following warrants to purchase shares of the Company’s common stock were issued and outstanding: Issue date Expiration date Exercise Price per Share September 30, 2021 December 31, 2020 December 16, 2019 None $ 0.001 — 2,424,242 During the three and nine months ended September 30, 2021, 315,102 and 2,424,242 warrants were exercised through a cashless exercise, respectively, resulting in the issuance of 2,423,634 shares of the Company’s common stock. three and nine months ended September 30, 2020

Stock Plans and Stock-Based Com

Stock Plans and Stock-Based Compensation	9 Months Ended
	Sep. 30, 2021
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Stock Plans and Stock-Based Compensation	Note 7 – Stock Plans and Stock-Based Compensation Equity Incentive Plans In May 2018, the Company’s stockholders approved (1) the Assembly Biosciences, Inc. 2018 Stock Incentive Plan (the 2018 Plan) pursuant to which the Company reserved 1,900,000 shares of its common stock for issuance in connection with equity incentive awards and (2) the Assembly Biosciences Inc. Employee Stock Purchase Plan pursuant to which the Company reserved 400,000 shares of its common stock for issuance in connection with purchases by employees pursuant to this plan. In May 2019, the Company’s stockholders approved an amendment to the 2018 Plan that increased the aggregate number of shares of common stock reserved under the 2018 Plan to In June 2020, the Company’s stockholders approved an amendment to the 2018 Plan that increased the aggregate number of shares of common stock reserved under the 2018 Plan to 4,600,000. In May 2021, the Company’s stockholders approved an amendment to the 2018 Plan that increased the aggregate number of shares of common stock reserved under the 2018 Plan to 6,600,000 and an Amended and Restated Assembly Biosciences, Inc. 2018 Employee Stock Purchase Plan (the 2018 ESPP) that, among other things, increased the number of shares of common stock reserved to an aggregate of 1,300,000. As of September 30, 2021, the Company had awards outstanding under the following shareholder-approved plans: the 2010 Equity Incentive Plan (the 2010 Plan), which has been frozen; the Amended and Restated 2014 Stock Incentive Plan (the 2014 Plan); and the 2018 Plan. The Company issues new shares of common stock to settle options exercised and vested RSUs. The Company also issues new shares of common stock in connection with purchases of shares of common stock by eligible employees under the Company’s 2018 ESPP. Stock Plan Activity Stock Options A summary of the Company’s option activity and related information for the nine months ended September 30, 2021 is as follows: Number of Shares Weighted Average Exercise Price Per Share Weighted Average Remaining Contractual Term (Years) Total Intrinsic Value (in thousands) Outstanding as of December 31, 2020 6,696,592 $ 15.70 6.9 $ 1,856 Granted 1,484,370 4.28 Forfeited (1,864,895 ) 18.70 Expired (9,200 ) 30.00 Outstanding as of September 30, 2021 6,306,867 $ 12.10 6.7 $ 588 Options vested and exercisable as of September 30, 2021 3,767,464 $ 13.77 5.2 $ 587 The weighted-average grant-date fair value of options granted was $3.08 and $11.01 during the nine months ended September 30, 2021 and 2020, respectively. The total intrinsic value of options exercised during the nine months ended September 30, 2020 was $2.0 million. There were no options exercised during the nine months ended September 30, 2021. RSUs A summary of the Company’s RSUs and related information for the nine months ended September 30, 2021 is as follows: Number of RSUs Weighted Average Fair Value Per RSU at Grant Price Nonvested as of December 31, 2020 886,868 $ 20.36 Granted 721,341 3.78 Vested (184,387 ) 18.27 Forfeited (285,634 ) 14.51 Nonvested as of September 30, 2021 1,138,188 (1) $ 17.03 (1) Includes 140,000 RSUs that have vested but are subject to deferred settlement, which have a weighted average remaining contractual term of 0.1 years. The total fair value of RSUs vested and settled during the nine months ended September 30, 2021 and 2020 was $3.5 million and $6.2 million, respectively. The total intrinsic value of RSUs vested and settled during the nine months ended September 30, 2021 and 2020 was $0.8 million and $3.9 million, respectively. In September 2019, the Company granted 100,000 RSUs with performance-based vesting conditions to its chief executive officer. On March 31, 2021, 25,000 of these awards were forfeited back to the Company due to the expiration of the time period to complete one of the performance conditions. On July 31, 2021, an additional 25,000 of these awards were forfeited back to the Company due to the expiration of the time period to complete one of the performance conditions. The outstanding 50,000 awards with an aggregate fair value of $0.4 million vest upon performance conditions not yet deemed probable. Accordingly, no stock-based compensation expense has been recognized as of September 30, 2021. In July 2021, the Company granted a total of 324,214 RSUs with performance-based vesting conditions upon the achievement of clinical milestones to the majority of employees, including our executive officers. The awards had a grant date fair value of $1.2 million and vest upon performance conditions not yet deemed probable. Accordingly, no stock-based compensation expense has been recognized as of September 30, 2021. ESPP Employees purchased 42,803 and 42,266 shares of common stock under the 2018 ESPP during the nine months ended September 30, 2021 and 2020, respectively. Valuation Assumptions The fair value of the stock options granted or modified during the periods indicated was estimated using the Black-Scholes option pricing model, based on the following assumptions: Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Exercise price $3.47 - $3.90 $20.14 - $23.30 $3.47 - $5.79 $14.45 - $23.30 Expected volatility 79.7% - 88.9% 68.9% - 81.6% 79.7% - 91.2% 66.4% - 82.2% Risk-free rate 0.73% - 1.24% 0.26% - 0.52% 0.50% - 1.37% 0.26% - 1.44% Expected term (years) 5.5 - 7.5 5.5 - 7.0 5.5 - 7.5 5.5 - 7.5 Expected dividend yield 0% 0% 0% 0% The fair value of RSUs granted is determined based on the price of the Company’s common stock on the date of grant. The fair value of ESPP purchase rights were not material for any period presented. Stock-Based Compensation Expense The following table summarizes the components of total stock-based compensation expense included in the condensed consolidated statements of operations and comprehensive loss (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Research and development $ 1,108 $ 2,759 $ (240 ) (1) $ 8,310 General and administrative 484 3,289 3,532 9,796 Total stock-based compensation expense $ 1,592 $ 6,048 $ 3,292 $ 18,106 (1) Includes the reversal of previously recognized stock-based compensation expense of $4.1 million related to forfeited awards of terminated employees, $2.7 million of which resulted from the wind-down of the Company’s Microbiome program (see Note 5). As of September 30, 2021, there was $12.0 million of total unrecognized stock-based compensation related to outstanding equity awards, which is expected to be recognized over a weighted average remaining amortization period of 1.7 years.

Collaboration Agreements

Collaboration Agreements	9 Months Ended
	Sep. 30, 2021
Collaboration Agreement [Abstract]
Collaboration Agreements	Note 8 - Collaboration Agreements Allergan Agreement In January 2017, the Company and Allergan Pharmaceuticals International Limited (Allergan) entered into the Research, Development, Collaboration and License Agreement (the Allergan Agreement) to develop and commercialize select microbiome gastrointestinal disease therapies. In June 2020, following its acquisition of Allergan, AbbVie Inc. (AbbVie), on behalf of Allergan, gave written notice of termination of the Allergan Agreement, which subsequently became effective on October 10, 2020. Upon termination, the licenses granted by the Company and its know-how reverted to the Company. For the three and nine months ended September 30, 2020, the Company recognized $3.6 million and $47.1 million, respectively, in revenue associated with the Allergan Agreement. A contract asset balance of $1.0 million was recorded as of December 31, 2020. There were no deferred revenue contract liabilities as of December 31, 2020 and no revenue, contract assets or contract liabilities recognized as of and for the three and nine months ended September 30, 2021 due to the termination of the Allergan Agreement in 2020. BeiGene Agreement In July 2020, the Company and BeiGene, Ltd. (BeiGene) entered into a Collaboration Agreement (the BeiGene Agreement) to develop and commercialize the Company’s novel core inhibitor product candidates VBR, ABI-H2158 and ABI-H3733 for chronic HBV infection (the Licensed Product Candidates) in the People’s Republic of China, Hong Kong, Taiwan and Macau (the Territory). Under the agreement, the Company and BeiGene will collaborate on certain global clinical studies and both the Company and BeiGene will independently conduct other clinical studies in their own respective territories. BeiGene agreed to pay all development and regulatory costs for the Licensed Product Candidates in the Territory up to an aggregate of $45.0 million. Development and regulatory costs for the Licensed Product Candidates for the Territory in excess of $45.0 million will be shared equally by the Company and BeiGene. If the Company conducts certain ancillary studies outside of the plan to develop these candidates in the Territory, BeiGene may elect to obtain access to the know-how and clinical data resulting for such ancillary studies and shall reimburse the Company proportionally for the Territory costs of such studies. Activities under the BeiGene Agreement will be governed by a joint steering committee (JSC) consisting of equal representatives from each party to the agreement. All decisions of the JSC are to be made by consensus with final decision-making authority granted to each party based on key areas of the collaboration for which they are responsible. During the term of the BeiGene Agreement, neither party will commercialize any competing products in the Territory. The Company will be responsible for manufacturing and supply of the candidates to be used in and outside of the Territory, although the parties may approve BeiGene to take on some or all of the commercial supply activities of the applicable Licensed Products in the Territory. The Company is not obligated to perform pre-Phase 3 clinical study development work outside the Territory on ABI-H2158 and ABI-H3733 but must provide BeiGene pre-Phase 3 clinical study know-how and development results if and when such development efforts are completed. If, after ABI-H2158 and ABI-H3733 reach the end of Phase 2 clinical studies, the Company and BeiGene are unable to mutually agree on the terms of a Phase 3 global study, BeiGene may elect to terminate the BeiGene Agreement solely as it relates to that compound, as applicable. Such a termination would result in Assembly regaining all rights to the applicable compound in the Territory. In addition, BeiGene may terminate the BeiGene Agreement for convenience at any time upon 90 days’ advance written notice to Assembly. The BeiGene Agreement also contains customary provisions for termination by either party, including in the event of breach of the BeiGene Agreement, subject to cure. Pursuant to the terms of the BeiGene Agreement, the Company received an upfront cash payment of $40.0 million from BeiGene for the delivery of exclusive, royalty-bearing licenses to develop and commercialize the Licensed Product Candidates in the Territory, and the Company is eligible to receive up to approximately $500.0 million in cash milestone payments, comprised of up to $113.8 million for development and regulatory milestones and up to $385.0 million in net sales milestones. In addition, the Company is eligible to receive tiered royalties at percentages ranging from the mid-teens to the low thirties of net sales. The collaborative arrangements guidance as both parties are active participants and are exposed to significant risks and rewards dependent on the success of commercializing the Licensed Product Candidates in the Territory. However, the unit of account related to the delivery of Licensed Product Candidates is within the scope of the contract with customers guidance. The remaining units of account related to participation on the JSC and subcommittees, supply and other in Territory and global development activities (the Collaboration Activities) are within the scope of the collaborative arrangements guidance. Commercial supply will be evaluated as a separate contract when the agreement is executed and a purchase order is received from BeiGene. The Company identified the following material promises related to the contract with customers unit of account under the BeiGene Agreement ABI-H2158 and (3) the transfer of the ABI-H3733 License. The Company concluded each of these licenses to be functional BeiGene date . The ABI-H2158 and ABI-H3733 Licenses have a The agreed upon prices for the clinical and commercial supply of the Licensed Product Candidates to BeiGene do not represent material rights, and therefore are not performance obligations, and such pricing on an aggregate basis represents the standalone selling price an entity would typically pay for such a product in that region or market. There are also no minimum purchase commitments. The Company estimated the standalone selling price (SSP) of the Licenses using an income-based valuation approach for the estimated The transaction price at the inception of the agreement was limited to the $40.0 million upfront payment. The variable consideration related to the remaining development and commercialization milestone payments has not been included in the transaction price Upon entering into the BeiGene Agreement in July 2020, the Company recognized $31.0 million as collaboration revenue for the amount allocated to the VBR License as substantial completion of the license technology transfer had occurred. The remaining transaction price allocated to the ABI-H2158 and ABI-H3733 Licenses of $9.0 million was recorded as long-term deferred revenue contract liability as of December 31, 2020. In September 2021, the Company discontinued development of ABI-H2158 following the observation of elevated alanine transaminase levels in the Phase 2 clinical stud y consistent with drug-induced hepatotoxicity . The obligation related to the technology transfer associated with the license of ABI-H2158 was considered to be completed upon the Company's discontinuation of the development of this compound. Accordingly, t he Company recognized $ 6.3 million as collaboration revenue for the amount allocated to ABI-H2158 during the three months ended September 30, 2021 . The remaining transaction price allocated to the ABI-H3733 License of $ 2.7 million was recorded as a long-term deferred revenue contract liability on the unaudited condensed consolidated balance sheet as of September 30, 2021 . Revenue for the remaining performance obligation will be recognized when the Company provides pre-Phase 3 clinical study know-how and development results for ABI-H3733 to BeiGene or a termination of the BeiGene Agreement for ABI-H3733 . Payments to, or reimbursements from, BeiGene related to the Collaboration Activities will be accounted for as an increase to or reduction of research and development expenses when incurred or realized, respectively. During the three and nine months ended September 30, 2021, the Company did not recognize any increase or reduction of research and development expense under the BeiGene Agreement. The Company incurred $3.5 million in incremental costs of obtaining the BeiGene Agreement. These contract costs have been capitalized and are being recognized consistent with the pattern of recognition of revenue associated with the Licensed Product Candidates. As of September 30, 2021 and December 31, 2020, the remaining unamortized contract costs are $0.2 million and $0.8 million, respectively, and are included in other assets on the condensed consolidated balance sheet. Arbutus Biopharma Agreement In August 2020, the Company and Arbutus Biopharma Corporation (Arbutus Biopharma) entered into a Clinical Trial Collaboration Agreement (the Arbutus Biopharma Agreement) to conduct a randomized, multi-center, open-label Phase 2 clinical study to explore the safety, PK and antiviral activity of the triple combination of VBR, AB-729 and a nucleos(t)ide reverse transcriptase inhibitor (NrtI) compared to the double combinations of VBR plus NrtI and AB-729 plus NrtI. The Arbutus Biopharma Agreement is within the scope of the collaborative arrangements guidance as both parties are active participants and are exposed to significant risks and rewards dependent on the success of the collaborative activity. Arbutus Biopharma is not a customer as it does not obtain an output from the collaborative activities as they were not provided an exclusive license to VBR or the ability to manufacture VBR, and the Company does not consider performing such collaborative activities to be a part of its ongoing activities. The revenue from contracts with customers guidance was considered by analogy in determining the unit of account, and the recognition and measurement of such unit of account for collaborative activities under the Agreement and concluded there is one activity, to run an open-label Phase 2 clinical study, which is akin to a performance obligation related to collaborative activities. Reimbursements and cost-sharing portions of this performance obligation will be reflected as a reduction of research and development expense when realized in the Company’s condensed consolidated statements of operations, as the Company does not consider performing research and development services for reimbursement to be a part of its ongoing major or central operations. During the three and nine months ended September 30, 2021, the Company recognized a reduction of research and development expenses of $0.5 million and $1.3 million, respectively under the Arbutus Agreement. Antios Agreement In July 2021, the Company and Antios Therapeutics, Inc. (Antios) entered into a Clinical Trial Collaboration Agreement (the Antios Agreement) to collaborate on a clinical trial of a combination therapy using either or both of the Company’s core inhibitors, VBR and ABI-H2158, and Antios’s active site polymerase inhibitor nucleotide ATI-2173 for the treatment of HBV. Assembly and Antios will share responsibility for the costs of the study equally, excluding manufacturing supply, which each company will need to supply their respective drugs. The Antios Agreement does not bind either party to conducting a collaboration trial or collaboration trial cohort unless and until a Joint Development Committee (the JDC) formed by both parties decides to initiate a collaboration trial or collaboration trial cohort. Due to the discontinuation of development of ABH-H2158 in September 2021, any study under the Antios Agreement would be with VBR. The Antios Agreement is within the scope of the collaborative arrangements guidance as both parties are active participants and are exposed to significant risks and rewards dependent on the success of the collaborative activity. Antios is not a customer as it does not obtain an output from the collaborative activities as they were not provided an exclusive license to ABI-H2158 or VBR or the ability to manufacture ABI-H2158 or VBR, and the Company does not consider performing such collaborative activities to be a part of its ongoing activities. In October 2021, the JDC agreed to initiate a collaboration trial cohort to evaluate a triple combination treatment in patients with chronic HBV infection. There were no costs incurred during the three and nine months ended September 30, 2021 . Contract Liabilities The following table presents changes in the Company’s contract liabilities (in thousands): Balance at Beginning of Period Additions Deductions Balance at End of Period Nine Months Ended September 30, 2021 Contract liabilities: Deferred revenue $ 8,987 $ — $ (6,254 ) $ 2,733 Balance at Beginning of Period Additions Deductions Balance at End of Period Nine Months Ended September 30, 2020 Contract liabilities: Deferred revenue $ 37,048 $ 40,000 $ (68,061 ) $ 8,987

Milestones and Research Agreeme

Milestones and Research Agreements	9 Months Ended
	Sep. 30, 2021
Milestones And Research Agreements [Abstract]
Milestones and Research Agreements	Note 9 - Milestones and Research Agreements HBV Research Agreement with Indiana University Since September 2013, the Company has been party to an exclusive License Agreement dated September 3, 2013 with Indiana University Research and Technology Corporation (IURTC) from whom it has licensed aspects of the Company’s HBV program held by IURTC. The license agreement requires the Company to make milestone payments based upon the successful accomplishment of clinical and regulatory milestones. The aggregate amount of all performance milestone payments under the IURTC license agreement, should all milestones through development be met, is $0.8 million, with a portion related to the first performance milestone having been paid. The Company is obligated to pay IURTC royalty payments based on net sales of the licensed technology as well as a portion of any sublicensing revenue Assembly receives. The Company is also required to pay diligence maintenance fees each year to the extent that the royalty, sublicensing, and milestone payments to IURTC are less than such fees for that year. No amounts were paid in the nine months ended September 30, 2021. Amounts paid in the nine months ended September 30, 2020 were insignificant. Microbiome Targeted Colonic Delivery Platform In November 2013, the Company entered into a License and Collaboration Agreement with Therabiome, LLC (Therabiome), for all intellectual property and know-how owned or controlled by Therabiome relating to the oral delivery of pharmaceutical drugs to specific sites in the intestine, using a pH sensitive controlled release capsule-in-capsule technology. The Company was solely responsible for all research and development activities with respect to any product it developed under the license. The Company was obligated to pay Therabiome clinical and regulatory milestones for each product or therapy advanced from the platform for U.S. regulatory milestones. In addition, the Company was obligated to pay Therabiome lesser amounts for foreign regulatory milestones, which varied by country and region. The Company was also required to pay Therabiome royalties on annual net sales of a product in the low to mid-single digit percentages plus, once annual net sales exceeded certain thresholds, a one-time cash payment upon reaching such thresholds. Therabiome was obligated to pay the Company royalties on annual net sales of any product Therabiome was permitted to develop using the intellectual property in the low double to mid-double-digit percentages, depending on the level of development or involvement the Company had in the product. No amounts were accrued for this agreement as of and for the nine months ended September 30, 2021 or 2020. Door Pharma Agreement In November 2020, the Company and Door Pharmaceuticals, LLC (Door Pharma) entered into an exclusive, two-year For the three and nine months ended September 30, 2021, the Company incurred $0.5 million and $1.3 million, respectively, of research and development funding. Under the consolidation accounting standard, the Company determined that Door Pharma is a variable interest entity. The Company does not have the power to direct the activities that most significantly affect the economic performance of Door Pharma and as such the Company is not the primary beneficiary and consolidation is not required. As of September 30, 2021, the Company has not provided financial or other support to Door Pharma that was not contractually required.

Leases

Leases	9 Months Ended
	Sep. 30, 2021
Lease Cost [Abstract]
Leases	Note 10 – Leases The Company leases office and laboratory space in South San Francisco, California under a sub-sublease that expires in December 2023. The sub-sublease contains scheduled rent increases over the lease term. The Company also leases office space in Carmel, Indiana under a lease agreement that expires in August 2023. When the Company cannot determine the implicit rate in its leasing arrangements , the Company uses its incremental borrowing rate as the discount rate when measuring operating lease liabilities. The incremental borrowing rate represents an estimate of the interest rate the Company would incur at lease commencement to borrow an amount equal to the lease payments on a collateralized basis over the term of a lease within a particular currency environment. At September 30, 2021, the Company had operating lease liabilities of $7.2 million and ROU assets of $6.8 million. The following summarizes quantitative information about the Company’s operating leases (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Lease cost Operating lease cost $ 902 $ 1,164 $ 2,940 $ 3,463 Short-term lease cost 32 101 227 301 Variable lease cost 312 409 1,063 1,101 Sublease income (38 ) — (104 ) — Total lease cost $ 1,208 $ 1,674 $ 4,126 $ 4,865 Nine Months Ended September 30, 2021 2020 Operating cash flows from operating leases $ 2,856 $ 3,382 ROU assets exchanged for new operating lease liabilities $ 126 $ 1,063 As of September 30, 2021 and December 31, 2020, the weighted-average remaining lease term for operating leases was 2.2 years and 2.7 years, respectively. As of September 30, 2021 and December 31, 2020, the weighted-average discount rate for operating leases was 9.7% and 9.2%, respectively. As of September 30, 2021, the maturities of the Company’s operating lease liabilities were as follows (in thousands): Three months ending December 31, 2021 $ 927 Year Ending December 31, 2022 3,643 Year Ending December 31, 2023 3,491 Year Ended December 31, 2024 13 Total 8,074 Less: present value discount (839 ) Operating lease liabilities $ 7,235

Summary of Significant Accoun_2

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	9 Months Ended
	Sep. 30, 2021
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying unaudited condensed consolidated financial statements include the accounts of the Company and its subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (U.S. GAAP) for interim financial information and pursuant to the instructions to Form 10-Q and Rule 10-01 of Regulation S-X of the SEC. In management’s opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as the annual audited consolidated financial statements and include normal recurring adjustments necessary for the fair presentation of the Company’s financial position and its results of operations and comprehensive loss and its cash flows for the periods presented. These statements do not include all disclosures required by U.S. GAAP and should be read in conjunction with the Company’s audited consolidated financial statements and accompanying notes for the fiscal year ended December 31, 2020, which are contained in the 2020 Annual Report. The results for the three and nine months ended September 30, 2021 are not necessarily indicative of results to be expected for the entire year ending December 31, 2021 or future operating periods.
Use of Estimates	Use of Estimates The preparation of the unaudited condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of expenses during the reporting period. Actual results could differ from those estimates. Estimates inherent in the preparation of the accompanying unaudited condensed consolidated financial statements include estimates for the cost-based input of revenue recognition and standalone selling price estimates for allocation of transaction price to performance obligations, revenue recognition, estimates of costs incurred but not yet invoiced for clinical trial accruals, recoverability and useful lives of our long-lived assets, the estimated fair value of our indefinite-lived intangible assets, the estimated fair value of our reporting unit for purposes of evaluating goodwill impairment, provisions for income taxes, amounts receivable under collaboration agreements, measurement of operating lease liabilities, and the fair value of stock options, stock appreciation rights, and restricted stock units (RSUs) granted to employees, directors, and consultants. The Company’s estimates could be affected by external conditions, including those unique to the Company and general economic conditions. It is reasonably possible these external factors could have an effect on the Company’s estimates and could cause actual results to differ materially from those estimates and assumptions.
Other Risks and Uncertainties	Other Risks and Uncertainties In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. To date, the Company’s operations have not been significantly impacted by the COVID-19 pandemic. However, the Company cannot at this time predict the specific extent, duration, or full impact the COVID-19 pandemic will have on its business, operations, strategy, prospects and financial condition and results. The impact of the COVID-19 pandemic on the Company’s financial performance will depend on future developments, including the duration of the outbreak and related governmental advisories and restrictions. These developments and the impact of the COVID-19 pandemic on the financial markets and the overall economy are highly uncertain. If the financial markets and/or the overall economy are impacted for an extended period, the Company’s results may be adversely affected.
Income Taxes	Income Taxes In March 2021, the American Rescue Plan (H.R. 1319) was signed into law. This legislation extends and enhances a number of current-law tax incentives for businesses, but also expands the definition of a “covered employee” as defined by Section 162(m)(1) of the Internal Revenue Code. The corporate tax provisions included within the bill are not expected to have a material impact on the Company.
Net Loss per Share	Net Loss per Share Basic net loss per share of common stock excludes dilution and is computed by dividing net loss by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock reflects the potential dilution that In December 2019, the Company sold 6,287,878 shares of common stock as well as pre-funded warrants to purchase up to 2,424,242 shares of common stock. In June 2021, 2,109,140 of the pre-funded warrants were exercised through a cashless exercise, and in July 2021, the remaining 315,102 pre-funded warrants were exercised through a cashless exercise (see Note 6). Prior to these exercises, the pre-funded warrants were exercisable for shares of common stock at an exercise price of $0.001 per share. The shares of common stock A reconciliation of the numerators and the denominators of the basic and diluted net loss per common share computations is as follows (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Numerator: Net loss $ (18,803 ) $ (3,349 ) $ (69,598 ) $ (22,734 ) Denominator: Weighted average common shares and pre-funded warrants outstanding - basic and diluted 45,569,276 35,506,042 42,725,109 35,321,393 Net loss per share - basic and diluted $ (0.41 ) $ (0.09 ) $ (1.63 ) $ (0.64 ) Securities excluded from the computation of diluted net loss per share because including them would have been antidilutive are as follows: September 30, 2021 2020 Options to purchase common stock 6,306,867 6,660,918 Common stock subject to purchase under our ESPP 49,470 25,192 Unvested RSUs 998,188 851,589 Total 7,354,525 7,537,699
Recent Accounting Pronouncements	Adoption of Recent Accounting Pronouncements On January 1, 2021, the Company adopted Accounting Standards Update (ASU) 2020-10, Codification Improvements – Disclosures The adoption of this standard had no material impact on the Company’s condensed consolidated financial statements and related disclosures. Recent Accounting Pronouncements In June 2016, the Financial Accounting Standards Board (the FASB) issued ASU 2016-13, Financial Instruments – Credit Losses: Measurement of Credit Losses on Financial Instruments Financial Instruments – Credit Losses (Topic 326) , Derivatives and Hedging (Topic 815) , and Leases (Topic 842): Effective Dates , The Company is currently evaluating the timing and impact of adopting ASU 2016-13 on its condensed consolidated financial statements and related disclosures. In August 2020, the FASB issued ASU 2020-06, Debt—Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging—Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity for the derivative scope exception, which will permit more equity contracts to qualify for the scope exception and simplifies the diluted earnings per share calculation in certain areas. ASU 2020-06 is effective for interim and annual periods beginning after December 15, 2021, with early adoption permitted. Adoption of ASU 2020-06 can either be on a modified retrospective or full retrospective basis. The Company is currently evaluating the impacts of ASU 2020-06 on its condensed consolidated financial statements and related disclosures. In May 2021, the FASB issued ASU 2021-04, Issuer's Accounting for Certain Modifications or Exchanges of Freestanding Equity-Classified Written Call Options

Summary of Significant Accoun_3

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Tables)	9 Months Ended
	Sep. 30, 2021
Accounting Policies [Abstract]
Schedule of Earnings Per Share, Basic and Diluted	A reconciliation of the numerators and the denominators of the basic and diluted net loss per common share computations is as follows (in thousands, except per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Numerator: Net loss $ (18,803 ) $ (3,349 ) $ (69,598 ) $ (22,734 ) Denominator: Weighted average common shares and pre-funded warrants outstanding - basic and diluted 45,569,276 35,506,042 42,725,109 35,321,393 Net loss per share - basic and diluted $ (0.41 ) $ (0.09 ) $ (1.63 ) $ (0.64 )
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share	Securities excluded from the computation of diluted net loss per share because including them would have been antidilutive are as follows: September 30, 2021 2020 Options to purchase common stock 6,306,867 6,660,918 Common stock subject to purchase under our ESPP 49,470 25,192 Unvested RSUs 998,188 851,589 Total 7,354,525 7,537,699

Fair Value Measurements and I_2

Fair Value Measurements and Investments in Marketable Securities (Tables)	9 Months Ended
	Sep. 30, 2021
Investments Debt And Equity Securities [Abstract]
Schedule of Investments in Marketable Securities	Investments in marketable securities consisted of the following (in thousands): September 30, 2021 Amortized Cost Gross Unrealized Gain Gross Unrealized Loss Fair Value Cash equivalents Money market funds $ 67,893 $ — $ — $ 67,893 Total cash equivalents 67,893 — — 67,893 Short-term marketable securities U.S. and foreign corporate debt securities 12,056 — (2 ) 12,054 Asset-backed securities 12,143 1 (6 ) 12,138 U.S. and foreign commercial paper 85,950 — — 85,950 Total short-term marketable securities 110,149 1 (8 ) 110,142 Long-term marketable securities U.S. and foreign corporate debt securities 9,188 — (8 ) 9,180 Total long-term marketable securities 9,188 — (8 ) 9,180 Total cash equivalents and marketable securities $ 187,230 $ 1 $ (16 ) $ 187,215 December 31, 2020 Amortized Cost Gross Unrealized Gain Gross Unrealized Loss Fair Value Cash equivalents Money market funds $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper 6,498 — — 6,498 Total cash equivalents 54,051 — — 54,051 Short-term marketable securities U.S. and foreign corporate debt securities 16,939 3 (3 ) 16,939 Asset-backed securities 12,674 2 (1 ) 12,675 U.S. treasury securities 23,997 2 — 23,999 U.S. and foreign commercial paper 103,356 — — 103,356 Total short-term marketable securities 156,966 7 (4 ) 156,969 Total cash equivalents and marketable securities $ 211,017 $ 7 $ (4 ) $ 211,020
Schedule of Fair Value of Financial Assets	The following tables present the fair value of the Company’s financial assets measured at fair value on a recurring basis (in thousands): September 30, 2021 Level 1 Level 2 Level 3 Fair Value Cash equivalents Money market fund $ 67,893 $ — $ — $ 67,893 Total cash equivalents 67,893 — — 67,893 Short-term marketable securities U.S. and foreign corporate debt securities — 12,054 — 12,054 Asset-backed securities — 12,138 — 12,138 U.S. and foreign commercial paper — 85,950 — 85,950 Total short-term marketable securities — 110,142 — 110,142 Long-term marketable securities U.S. and foreign corporate debt securities — 9,180 — 9,180 Total long-term marketable securities — 9,180 — 9,180 Total assets measured at fair value $ 67,893 $ 119,322 $ — $ 187,215 December 31, 2020 Level 1 Level 2 Level 3 Fair Value Cash equivalents Money market fund $ 47,553 $ — $ — $ 47,553 U.S. and foreign commercial paper — 6,498 — 6,498 Total cash equivalents 47,553 6,498 — 54,051 Short-term marketable securities U.S. and foreign corporate debt securities — 16,939 — 16,939 Asset-backed securities — 12,675 — 12,675 U.S. treasury securities — 23,999 — 23,999 U.S. and foreign commercial paper — 103,356 — 103,356 Total short-term marketable securities — 156,969 — 156,969 Total assets measured at fair value $ 47,553 $ 163,467 $ — $ 211,020

Other Accrued Expenses (Tables)

Other Accrued Expenses (Tables)	9 Months Ended
	Sep. 30, 2021
Payables And Accruals [Abstract]
Schedule of Other Accrued Expenses	Other accrued expenses consist of the following (in thousands): September 30, December 31, 2021 2020 Accrued expenses: Accrued compensation $ 4,871 $ 7,016 Accrued restructuring charges 232 4,164 Accrued professional fees and other 354 807 Total accrued expenses $ 5,457 $ 11,987

Restructurings (Tables)

Restructurings (Tables)	9 Months Ended
	Sep. 30, 2021
Restructuring And Related Activities [Abstract]
Summary of Restructuring Costs	The following table summarizes the Company’s costs incurred (in thousands): Total Restructuring Cost Employee Severance and Related Benefits Asset Impairment and Other Costs Restructuring costs incurred for the nine months ended September 30, 2021 $ (1,348 ) $ (2,959 ) (1) $ 1,611 Cumulative restructuring costs incurred through September 30, 2021 $ 6,430 $ 3,240 $ 3,190 (1) The reversal of $3.0 million in employee severance and related benefits recognized during the nine months ended September 30, 2021 reflects the reversal of previously recognized stock-based compensation expense related to forfeited awards based on the Company’s policy of recognizing stock-based awards with graded vesting schedules using an accelerated attribution method on a straight-line basis over the requisite service period for each separately vesting portion of the award and to recognize forfeitures when they occur.
Schedule of Restructuring Charges	The following table presents where the restructuring charges were recognized during the nine months ended September 30, 2021 (in thousands): Research and development $ (1,625 ) General and administrative 277 Total $ (1,348 )
Schedule of Accrued Restructuring Charges	The following table presents the activity in the accrued restructuring charges during the nine months ended September 30, 2021 (in thousands): Total Restructuring Cost Employee Severance and Related Benefits Asset Impairment and Other Costs Accrued balance as of December 31, 2020 $ 4,164 $ 4,164 $ — Costs incurred 1,611 — 1,611 Reductions for cash payments (5,543 ) (3,932 ) (1,611 ) (1) Accrued balance as of September 30, 2021 $ 232 $ 232 $ — (1) Cash payments are presented net of proceeds received from the sale of assets of $0.9 million

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	9 Months Ended
	Sep. 30, 2021
Equity [Abstract]
Summary of Warrants to Purchase Shares of Company's Common Stock	The following warrants to purchase shares of the Company’s common stock were issued and outstanding: Issue date Expiration date Exercise Price per Share September 30, 2021 December 31, 2020 December 16, 2019 None $ 0.001 — 2,424,242

Stock Plans and Stock-Based C_2

Stock Plans and Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2021
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Summary of Stock Option Activity and Related Information	A summary of the Company’s option activity and related information for the nine months ended September 30, 2021 is as follows: Number of Shares Weighted Average Exercise Price Per Share Weighted Average Remaining Contractual Term (Years) Total Intrinsic Value (in thousands) Outstanding as of December 31, 2020 6,696,592 $ 15.70 6.9 $ 1,856 Granted 1,484,370 4.28 Forfeited (1,864,895 ) 18.70 Expired (9,200 ) 30.00 Outstanding as of September 30, 2021 6,306,867 $ 12.10 6.7 $ 588 Options vested and exercisable as of September 30, 2021 3,767,464 $ 13.77 5.2 $ 587
Summary of Restricted Stock Units and Related Information	A summary of the Company’s RSUs and related information for the nine months ended September 30, 2021 is as follows: Number of RSUs Weighted Average Fair Value Per RSU at Grant Price Nonvested as of December 31, 2020 886,868 $ 20.36 Granted 721,341 3.78 Vested (184,387 ) 18.27 Forfeited (285,634 ) 14.51 Nonvested as of September 30, 2021 1,138,188 (1) $ 17.03 (1) Includes 140,000 RSUs that have vested but are subject to deferred settlement, which have a weighted average remaining contractual term of 0.1 years.
Summary of Assumptions Used to Estimate Fair Values of Stock Options Grants	The fair value of the stock options granted or modified during the periods indicated was estimated using the Black-Scholes option pricing model, based on the following assumptions: Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Exercise price $3.47 - $3.90 $20.14 - $23.30 $3.47 - $5.79 $14.45 - $23.30 Expected volatility 79.7% - 88.9% 68.9% - 81.6% 79.7% - 91.2% 66.4% - 82.2% Risk-free rate 0.73% - 1.24% 0.26% - 0.52% 0.50% - 1.37% 0.26% - 1.44% Expected term (years) 5.5 - 7.5 5.5 - 7.0 5.5 - 7.5 5.5 - 7.5 Expected dividend yield 0% 0% 0% 0%
Schedule of Recognized Stock-Based Compensation Expense	The following table summarizes the components of total stock-based compensation expense included in the condensed consolidated statements of operations and comprehensive loss (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Research and development $ 1,108 $ 2,759 $ (240 ) (1) $ 8,310 General and administrative 484 3,289 3,532 9,796 Total stock-based compensation expense $ 1,592 $ 6,048 $ 3,292 $ 18,106 (1) Includes the reversal of previously recognized stock-based compensation expense of $4.1 million related to forfeited awards of terminated employees, $2.7 million of which resulted from the wind-down of the Company’s Microbiome program (see Note 5).

Collaboration Agreements (Table

Collaboration Agreements (Tables)	9 Months Ended
	Sep. 30, 2021
Collaboration Agreement [Abstract]
Schedule of Changes in Contract Liabilities	The following table presents changes in the Company’s contract liabilities (in thousands): Balance at Beginning of Period Additions Deductions Balance at End of Period Nine Months Ended September 30, 2021 Contract liabilities: Deferred revenue $ 8,987 $ — $ (6,254 ) $ 2,733

Leases (Tables)

Leases (Tables)	9 Months Ended
	Sep. 30, 2021
Lease Cost [Abstract]
Schedule of Quantitative Information of Operating Leases	The following summarizes quantitative information about the Company’s operating leases (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2021 2020 2021 2020 Lease cost Operating lease cost $ 902 $ 1,164 $ 2,940 $ 3,463 Short-term lease cost 32 101 227 301 Variable lease cost 312 409 1,063 1,101 Sublease income (38 ) — (104 ) — Total lease cost $ 1,208 $ 1,674 $ 4,126 $ 4,865 Nine Months Ended September 30, 2021 2020 Operating cash flows from operating leases $ 2,856 $ 3,382 ROU assets exchanged for new operating lease liabilities $ 126 $ 1,063
Schedule of Maturities Operating Lease Liabilities	As of September 30, 2021, the maturities of the Company’s operating lease liabilities were as follows (in thousands): Three months ending December 31, 2021 $ 927 Year Ending December 31, 2022 3,643 Year Ending December 31, 2023 3,491 Year Ended December 31, 2024 13 Total 8,074 Less: present value discount (839 ) Operating lease liabilities $ 7,235

Nature of Business - Additional

Nature of Business - Additional Information (Details)	9 Months Ended
	Sep. 30, 2021segmentproduct
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Operating segments (in segments) | segment	1
FDA approved products (in products) | product	0

Summary of Significant Accoun_4

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Additional Information (Details) - $ / shares	1 Months Ended			3 Months Ended		9 Months Ended
	Jul. 31, 2021	Jun. 30, 2021	Dec. 31, 2019	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Significant Accounting Policies [Line Items]
Number of pre-funded warrants sold to purchase of common stock				2,423,634		2,423,634
Number of warrants exercised	315,102	2,109,140		315,102	0	2,424,242	0
ASU 2020-10
Significant Accounting Policies [Line Items]
Change in Accounting Principle, Accounting Standards Update, Adoption Date				Jan. 1, 2021		Jan. 1, 2021
Change in Accounting Principle, Accounting Standards Update, Adopted [true false]				true		true
Change in Accounting Principle, Accounting Standards Update, Immaterial Effect [true false]				true		true
Common Stock
Significant Accounting Policies [Line Items]
Number of shares sold				2,949,647		10,399,548
Public Offering
Significant Accounting Policies [Line Items]
Number of pre-funded warrants sold to purchase of common stock			2,424,242
Pre-funded warrants exercisable price per share			$ 0.001
Public Offering | Common Stock
Significant Accounting Policies [Line Items]
Number of shares sold			6,287,878

Summary of Significant Accoun_5

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Schedule of Earnings Per Share, Basic and Diluted (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Numerator:
Net income (loss)	$ (18,803)	$ (3,349)	$ (69,598)	$ (22,734)
Denominator:
Weighted average common shares outstanding, basic and diluted	45,569,276	35,506,042	42,725,109	35,321,393
Net loss per share, basic and diluted	$ (0.41)	$ (0.09)	$ (1.63)	$ (0.64)

Summary of Significant Accoun_6

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share (Details) - shares	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of loss per share	7,354,525	7,537,699
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of loss per share	6,306,867	6,660,918
Common stock subject to purchase under ESPP
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of loss per share	49,470	25,192
RSUs
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of loss per share	998,188	851,589

Fair Value Measurements and I_3

Fair Value Measurements and Investments in Marketable Securities - Schedule of Investments in Marketable Securities (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Investments in marketable securities:
Amortized Cost	$ 70,760	$ 59,444
Fair Value	110,142	156,969
Amortized Cost	187,230	211,017
Gross Unrealized Gain	1	7
Gross Unrealized Loss	(16)	(4)
Fair Value	187,215	211,020
Cash equivalents
Investments in marketable securities:
Amortized Cost	67,893	54,051
Gross Unrealized Gain	0	0
Gross Unrealized Loss	0	0
Fair Value	67,893	54,051
Cash equivalents | Money market fund
Investments in marketable securities:
Amortized Cost	67,893	47,553
Gross Unrealized Gain	0	0
Gross Unrealized Loss	0	0
Fair Value	67,893	47,553
Short-term marketable securities
Investments in marketable securities:
Amortized Cost	110,149	156,966
Gross Unrealized Gain	1	7
Gross Unrealized Loss	(8)	(4)
Fair Value	110,142	156,969
Long Term Marketable Securities
Investments in marketable securities:
Amortized Cost	9,188
Gross Unrealized Gain	0
Gross Unrealized Loss	(8)
Fair Value	9,180
U.S and foreign corporate debt securities | Short-term marketable securities
Investments in marketable securities:
Amortized Cost	12,056	16,939
Gross Unrealized Gain	0	3
Gross Unrealized Loss	(2)	(3)
Fair Value	12,054	16,939
U.S and foreign corporate debt securities | Long Term Marketable Securities
Investments in marketable securities:
Amortized Cost	9,188
Gross Unrealized Gain	0
Gross Unrealized Loss	(8)
Fair Value	9,180
U.S. and foreign commercial paper | Cash equivalents
Investments in marketable securities:
Amortized Cost		6,498
Gross Unrealized Gain		0
Gross Unrealized Loss		0
Fair Value		6,498
U.S. and foreign commercial paper | Short-term marketable securities
Investments in marketable securities:
Amortized Cost	85,950	103,356
Gross Unrealized Gain	0	0
Gross Unrealized Loss	0	0
Fair Value	85,950	103,356
Asset-backed securities | Short-term marketable securities
Investments in marketable securities:
Amortized Cost	12,143	12,674
Gross Unrealized Gain	1	2
Gross Unrealized Loss	(6)	(1)
Fair Value	$ 12,138	12,675
U.S. treasury securities | Short-term marketable securities
Investments in marketable securities:
Amortized Cost		23,997
Gross Unrealized Gain		2
Gross Unrealized Loss		0
Fair Value		$ 23,999

Fair Value Measurements and I_4

Fair Value Measurements and Investments in Marketable Securities - Additional Information (Details) - USD ($)	9 Months Ended
	Sep. 30, 2021	Dec. 31, 2020
Investments in marketable securities:
Fair value assets transfers between level 1, level 2 or level 3	$ 0	$ 0
Short-term and Long-term marketable securities
Investments in marketable securities:
Available for sale securities maturity term	less than two years

Fair Value Measurements and I_5

Fair Value Measurements and Investments in Marketable Securities - Schedule of Fair Value of Financial Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Short-term marketable securities
Short-term marketable securities	$ 110,142	$ 156,969
Long-term marketable securities
Marketable securities - long-term	9,180
Recurring
Cash equivalents
Cash equivalents	67,893	54,051
Short-term marketable securities
Short-term marketable securities	110,142	156,969
Long-term marketable securities
Marketable securities - long-term	9,180
Total assets measured at fair value	187,215	211,020
Recurring | U.S and foreign corporate debt securities
Short-term marketable securities
Short-term marketable securities	12,054	16,939
Recurring | U.S. and foreign commercial paper
Cash equivalents
Cash equivalents		6,498
Short-term marketable securities
Short-term marketable securities	85,950	103,356
Recurring | Asset-backed securities
Short-term marketable securities
Short-term marketable securities	12,138	12,675
Recurring | U.S and foreign corporate debt securities
Long-term marketable securities
Marketable securities - long-term	9,180
Recurring | U.S. treasury securities
Short-term marketable securities
Short-term marketable securities		23,999
Recurring | Money market fund
Cash equivalents
Cash equivalents	67,893	47,553
Recurring | Level 1
Cash equivalents
Cash equivalents	67,893	47,553
Short-term marketable securities
Short-term marketable securities	0	0
Long-term marketable securities
Marketable securities - long-term	0
Total assets measured at fair value	67,893	47,553
Recurring | Level 1 | U.S and foreign corporate debt securities
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 1 | U.S. and foreign commercial paper
Cash equivalents
Cash equivalents		0
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 1 | Asset-backed securities
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 1 | U.S and foreign corporate debt securities
Long-term marketable securities
Marketable securities - long-term	0
Recurring | Level 1 | U.S. treasury securities
Short-term marketable securities
Short-term marketable securities		0
Recurring | Level 1 | Money market fund
Cash equivalents
Cash equivalents	67,893	47,553
Recurring | Level 2
Cash equivalents
Cash equivalents	0	6,498
Short-term marketable securities
Short-term marketable securities	110,142	156,969
Long-term marketable securities
Marketable securities - long-term	9,180
Total assets measured at fair value	119,322	163,467
Recurring | Level 2 | U.S and foreign corporate debt securities
Short-term marketable securities
Short-term marketable securities	12,054	16,939
Recurring | Level 2 | U.S. and foreign commercial paper
Cash equivalents
Cash equivalents		6,498
Short-term marketable securities
Short-term marketable securities	85,950	103,356
Recurring | Level 2 | Asset-backed securities
Short-term marketable securities
Short-term marketable securities	12,138	12,675
Recurring | Level 2 | U.S and foreign corporate debt securities
Long-term marketable securities
Marketable securities - long-term	9,180
Recurring | Level 2 | U.S. treasury securities
Short-term marketable securities
Short-term marketable securities		23,999
Recurring | Level 2 | Money market fund
Cash equivalents
Cash equivalents	0	0
Recurring | Level 3
Cash equivalents
Cash equivalents	0	0
Short-term marketable securities
Short-term marketable securities	0	0
Long-term marketable securities
Marketable securities - long-term	0
Total assets measured at fair value	0	0
Recurring | Level 3 | U.S and foreign corporate debt securities
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 3 | U.S. and foreign commercial paper
Cash equivalents
Cash equivalents		0
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 3 | Asset-backed securities
Short-term marketable securities
Short-term marketable securities	0	0
Recurring | Level 3 | U.S and foreign corporate debt securities
Long-term marketable securities
Marketable securities - long-term	0
Recurring | Level 3 | U.S. treasury securities
Short-term marketable securities
Short-term marketable securities		0
Recurring | Level 3 | Money market fund
Cash equivalents
Cash equivalents	$ 0	$ 0

Other Accrued Expenses - Schedu

Other Accrued Expenses - Schedule of Other Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Accrued expenses:
Accrued compensation	$ 4,871	$ 7,016
Accrued restructuring charges	232	4,164
Accrued professional fees and other	354	807
Total accrued expenses	$ 5,457	$ 11,987

Restructurings - Summary of Res

Restructurings - Summary of Restructuring Costs (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred	$ 0	$ 0	$ (1,348,000)	$ 0
Cumulative restructuring costs incurred through September 30, 2021	6,430,000		6,430,000
Employee Severance and Related Benefits
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred			(2,959,000)
Cumulative restructuring costs incurred through September 30, 2021	3,240,000		3,240,000
Asset Impairment and Other Costs
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred			1,611,000
Cumulative restructuring costs incurred through September 30, 2021	$ 3,190,000		$ 3,190,000

Restructurings - Summary of R_2

Restructurings - Summary of Restructuring Costs (Parenthetical) (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred	$ 0	$ 0	$ (1,348,000)	$ 0
Employee Severance and Related Benefits
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred			$ (2,959,000)

Restructurings - Schedule of Re

Restructurings - Schedule of Restructuring Charges (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Restructuring Cost And Reserve [Line Items]
Restructuring charges	$ 0	$ 0	$ (1,348,000)	$ 0
Research and Development
Restructuring Cost And Reserve [Line Items]
Restructuring charges			(1,625,000)
General and Administrative
Restructuring Cost And Reserve [Line Items]
Restructuring charges			$ 277,000

Restructurings - Additional Inf

Restructurings - Additional Information (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred	$ 0	$ 0	$ (1,348,000)	$ 0
Asset Impairment and Other Costs
Restructuring Cost And Reserve [Line Items]
Restructuring costs incurred			1,611,000
Costs incurred for remaining payment obligations of leased equipment			$ 1,400,000

Restructurings - Schedule of Ac

Restructurings - Schedule of Accrued Restructuring Charges (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2021USD ($)
Restructuring Cost And Reserve [Line Items]
Accrued balance as of December 31, 2020	$ 4,164
Costs incurred	1,611
Reductions for cash payments	(5,543)
Accrued balance as of September 30, 2021	232
Employee Severance and Related Benefits
Restructuring Cost And Reserve [Line Items]
Accrued balance as of December 31, 2020	4,164
Reductions for cash payments	(3,932)
Accrued balance as of September 30, 2021	232
Asset Impairment and Other Costs
Restructuring Cost And Reserve [Line Items]
Costs incurred	1,611
Reductions for cash payments	$ (1,611)

Restructurings - Schedule of _2

Restructurings - Schedule of Accrued Restructuring Charges (Parenthetical) (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Restructuring And Related Activities [Abstract]
Proceeds received from the sale of assets	$ 857	$ 0

Stockholders' Equity - Addition

Stockholders' Equity - Additional Information (Details) - USD ($) $ in Millions	1 Months Ended		3 Months Ended		9 Months Ended
	Jul. 31, 2021	Jun. 30, 2021	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Dec. 31, 2020	Aug. 31, 2020
Subsidiary Sale Of Stock [Line Items]
Preferred stock, shares authorized			5,000,000		5,000,000		5,000,000
Common stock, shares authorized			100,000,000		100,000,000		100,000,000
Preferred stock, shares issued			0		0		0
Preferred stock, shares outstanding			0		0		0
Initial public offering value of shares authorized								$ 300
Number of warrants exercised	315,102	2,109,140	315,102	0	2,424,242	0
Number of pre-funded warrants sold to purchase of common stock			2,423,634		2,423,634
2020 At the Market Offerings
Subsidiary Sale Of Stock [Line Items]
Number of shares sold					10,399,548
Net proceeds from the issuance of common stock through equity plans					$ 50.2
2020 At the Market Offerings | Maximum
Subsidiary Sale Of Stock [Line Items]
Initial public offering value of shares authorized								$ 100

Stockholders' Equity - Summary

Stockholders' Equity - Summary of Warrants to Purchase Shares of Company's Common Stock (Details) - Warrants Issued on December 16, 2019 - $ / shares	9 Months Ended
	Sep. 30, 2021	Dec. 31, 2020
Subsidiary Sale Of Stock [Line Items]
Issue date	Dec. 16, 2019
Exercise Price per Share	$ 0.001
Number of warrants outstanding		2,424,242

Stock Plans and Stock-Based C_3

Stock Plans and Stock-Based Compensation - Additional Information (Details) - USD ($)	Jul. 31, 2021	Jul. 31, 2021	Sep. 30, 2019	Sep. 30, 2021	Mar. 31, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	May 31, 2021	Dec. 31, 2020	Jun. 30, 2020	May 31, 2019	May 31, 2018
Share-based Compensation Arrangement by Share-based Payment Award
Shares reserved for issuance (in shares)									6,600,000		4,600,000	3,000,000	1,900,000
Weighted-average grant-date fair value of options granted							$ 3.08	$ 11.01
Total intrinsic value of options exercised								$ 2,000,000
Options exercised							0
Stock-based compensation expense				$ 1,592,000		$ 6,048,000	$ 3,292,000	$ 18,106,000
Unrecognized stock-based compensation expense				$ 12,000,000			$ 12,000,000
Unrecognized stock-based compensation expense expected to be recognized, term							1 year 8 months 12 days
2018 ESPP
Share-based Compensation Arrangement by Share-based Payment Award
Number of common stock purchased by employees							42,803	42,266
RSUs
Share-based Compensation Arrangement by Share-based Payment Award
Total fair value of awards vested and settled							$ 3,500,000	$ 6,200,000
Total intrinsic value of awards vested and settled							$ 800,000	$ 3,900,000
Granted							721,341
Forfeited							285,634
Outstanding awards				1,138,188			1,138,188			886,868
RSUs | Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award
Granted			100,000
Forfeited	25,000				25,000
Outstanding awards				50,000			50,000
Total fair value of awards							$ 400,000
Stock-based compensation expense							$ 0
RSUs | Employees Including Executive Officers
Share-based Compensation Arrangement by Share-based Payment Award
Granted		324,214
Total fair value of awards		$ 1,200,000
Stock-based compensation expense		$ 0
Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award
Shares reserved for issuance (in shares)									1,300,000				400,000

Stock Plans and Stock-Based C_4

Stock Plans and Stock-Based Compensation - Summary of Stock Option Activity and Related Information (Details) - Options - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2021	Dec. 31, 2020
Number of Shares
Options, Outstanding at beginning of period	6,696,592
Option, Granted	1,484,370
Option, Forfeited	(1,864,895)
Option, Expired	(9,200)
Option, Outstanding at end of period	6,306,867	6,696,592
Options vested and exercisable	3,767,464
Weighted Average Exercise Price Per Share
Options, Outstanding at beginning of period	$ 15.70
Option, Granted	4.28
Option, Forfeited	18.70
Option, Expired	30
Option, Outstanding at end of period	12.10	$ 15.70
Options vested and exercisable	$ 13.77
Options Outstanding, Weighted Average Remaining Contractual Term (Years)	6 years 8 months 12 days	6 years 10 months 24 days
Options Exercisable, Weighted Average Remaining Contractual Term (Years)	5 years 2 months 12 days
Total Intrinsic Value
Option, Outstanding	$ 588	$ 1,856
Options vested and exercisable	$ 587

Stock Plans and Stock-Based C_5

Stock Plans and Stock-Based Compensation - Summary of Restricted Stock Units and Related Information (Details) - RSUs	9 Months Ended
	Sep. 30, 2021$ / sharesshares
Number of Shares
Beginning of period | shares	886,868
Granted | shares	721,341
Vested | shares	(184,387)
Forfeited | shares	(285,634)
Ending of period | shares	1,138,188
Weighted Average Fair Value Per RSU at Grant Price
Beginning of period | $ / shares	$ 20.36
Granted | $ / shares	3.78
Vested | $ / shares	18.27
Forfeited | $ / shares	14.51
Ending of period | $ / shares	$ 17.03

Stock Plans and Stock-Based C_6

Stock Plans and Stock-Based Compensation - Summary of Restricted Stock Units and Related Information (Parenthetical) (Details) - RSUs	9 Months Ended
	Sep. 30, 2021shares
Share-based Compensation Arrangement by Share-based Payment Award
Vested and subject to deferred settlement	140,000
Weighted average remaining contractual term subject to deferred settlement	1 month 6 days

Stock Plans and Stock-Based C_7

Stock Plans and Stock-Based Compensation - Summary of Assumptions Used to Estimate Fair Values of Stock Options Grants (Details) - $ / shares	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Share-based Compensation Arrangement by Share-based Payment Award
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Minimum
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price	$ 3.47	$ 20.14	$ 3.47	$ 14.45
Expected volatility	79.70%	68.90%	79.70%	66.40%
Risk-free rate	0.73%	0.26%	0.50%	0.26%
Expected term (years)	5 years 6 months	5 years 6 months	5 years 6 months	5 years 6 months
Maximum
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price	$ 3.90	$ 23.30	$ 5.79	$ 23.30
Expected volatility	88.90%	81.60%	91.20%	82.20%
Risk-free rate	1.24%	0.52%	1.37%	1.44%
Expected term (years)	7 years 6 months	7 years	7 years 6 months	7 years 6 months

Stock Plans and Stock-Based C_8

Stock Plans and Stock-Based Compensation -Schedule of Recognized Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Compensation expense:
Stock-based compensation expense	$ 1,592	$ 6,048	$ 3,292	$ 18,106
Research and Development
Compensation expense:
Stock-based compensation expense	1,108	2,759	(240)	8,310
General and Administrative
Compensation expense:
Stock-based compensation expense	$ 484	$ 3,289	$ 3,532	$ 9,796

Stock Plans and Stock-Based C_9

Stock Plans and Stock-Based Compensation -Schedule of Stock-Based Compensation Expense (Parenthetical) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Compensation expense:
Stock-based compensation expense	$ 1,592	$ 6,048	$ 3,292	$ 18,106
Terminated Employees
Compensation expense:
Stock-based compensation expense			(4,100)
Wind-down of Microbiome Program
Compensation expense:
Stock-based compensation expense			$ (2,700)

Collaboration Agreements - Addi

Collaboration Agreements - Additional Information (Details) - USD ($)	Jul. 17, 2020	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020	Dec. 31, 2020	Dec. 31, 2019
Collaboration Agreements:
Collaboration revenue		$ 6,254,000	$ 34,611,000	$ 6,254,000	$ 78,068,000
Accounts receivable from collaborations		769,000		769,000		$ 1,230,000
Contract liability/deferred revenue		2,733,000	8,987,000	2,733,000	8,987,000	8,987,000	$ 37,048,000
Contract with customer, liability, noncurrent		2,733,000		2,733,000		8,987,000
Research and development expense		18,474,000	26,941,000	53,777,000	73,314,000
Allergan Agreement
Collaboration Agreements:
Collaboration revenue		0	$ 3,600,000	0	$ 47,100,000
Accounts receivable from collaborations		0		0		1,000,000
Contract liability/deferred revenue		0		0		0
BeiGene Agreement
Collaboration Agreements:
Collaboration revenue	$ 31,000,000	6,300,000
Upfront cash payment received				40,000,000
Agreed to pay maximum amount development and regulatory costs				45,000,000
Contract with customer, liability, noncurrent		2,700,000		2,700,000		9,000,000
Research and development expense		0		0
Incremental costs				3,500,000
BeiGene Agreement | Other Assets
Collaboration Agreements:
Incremental costs				200,000		$ 800,000
BeiGene Agreement | Maximum
Collaboration Agreements:
Potential milestone payments				500,000,000
BeiGene Agreement | Development and Regulatory | Maximum
Collaboration Agreements:
Potential milestone payments				113,800,000
BeiGene Agreement | Sales Milestone Payments | Maximum
Collaboration Agreements:
Potential milestone payments				385,000,000
Bei Gene Limited
Collaboration Agreements:
Contract liability/deferred revenue	$ 40,000,000
Arbutus Biopharma Agreement
Collaboration Agreements:
Research and development expense		500,000		1,300,000
Antios Agreement
Collaboration Agreements:
Costs incurred		$ 0		$ 0

Collaboration Agreements - Sche

Collaboration Agreements - Schedule of Changes in Contract Liabilities (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Collaboration Agreement [Abstract]
Balance at Beginning of Period	$ 8,987	$ 37,048
Additions	0	40,000
Deductions	(6,254)	(68,061)
Balance at End of Period	$ 2,733	$ 8,987

Milestones and Research Agree_2

Milestones and Research Agreements - Additional Information (Details) - USD ($)	1 Months Ended	3 Months Ended	9 Months Ended
	Nov. 30, 2020	Sep. 30, 2021	Sep. 30, 2021	Dec. 31, 2020	Sep. 30, 2020
Milestone and Research Agreements:
Potential milestone payment		$ 800,000	$ 800,000
Performance milestone payment			0
Accrued expenses		5,457,000	5,457,000	$ 11,987,000
Microbiome Targeted Colonic Delivery Program
Milestone and Research Agreements:
Accrued expenses		0	0		$ 0
Door Pharma Agreement
Milestone and Research Agreements:
License agreement term	2 years
Up-front payment	$ 1,800,000
Milestone payments		200,000
Research and development funding charges		$ 500,000	$ 1,300,000
Door Pharma Agreement | Maximum
Milestone and Research Agreements:
Success-based milestones	35,000,000
Exercise and annual fees	2,000,000
Door Pharma Agreement | Minimum
Milestone and Research Agreements:
Exercise and annual fees	$ 100,000

Leases - Additional Information

Leases - Additional Information (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Leases [Abstract]
Operating lease, liability	$ 7,235
Operating lease, ROU assets	$ 6,773	$ 9,131
Weighted-average remaining lease term - operating leases	2 years 2 months 12 days	2 years 8 months 12 days
Weighted-average discount rate - operating leases	9.70%	9.20%

Leases - Schedule of Quantitati

Leases - Schedule of Quantitative Information of Operating Leases (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Lease cost
Operating lease cost	$ 902	$ 1,164	$ 2,940	$ 3,463
Short-term lease cost	32	101	227	301
Variable lease cost	312	409	1,063	1,101
Sublease income	(38)		(104)
Total lease cost	$ 1,208	$ 1,674	4,126	4,865
Operating cash flows from operating leases			2,856	3,382
ROU assets exchanged for new operating lease liabilities			$ 126	$ 1,063

Leases - Schedule of Maturities

Leases - Schedule of Maturities Operating Lease Liabilities (Details) $ in Thousands	Sep. 30, 2021USD ($)
Lease Cost [Abstract]
Three months ending December 31, 2021	$ 927
Year Ending December 31, 2022	3,643
Year Ending December 31, 2023	3,491
Year Ended December 31, 2024	13
Total	8,074
Less: present value discount	(839)
Operating lease liabilities	$ 7,235