Gastroenterology 2020;-:1–12

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Alterations in Gut Microbiota of Patients With COVID-19 During 64
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6 Time of Hospitalization 66
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8 Q7 Tao Zuo,1,2,3,* Fen Zhang,1,2,3,* Grace C. Y. Lui,3,4,* Yun Kit Yeoh,1,5 Amy Y. L. Li,3 68
9 Hui Zhan,1,2,3 Yating Wan,1,2,3 Arthur Chung,1,2,3 Chun Peng Cheung,1,2,3 Nan Chen,1,2,3 69
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Christopher K. C. Lai,5 Zigui Chen,5 Eugene Y. K. Tso,6 Kitty S. C. Fung,7 Veronica Chan,6 71
12 Lowell Ling,8 Gavin Joynt,8 David S. C. Hui,3,4 Francis K. L. Chan,1,3 Paul K. S. Chan,1,5 and 72
13 Siew C. Ng1,2,3 73
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Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; 75
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16 State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese 76
17 University of Hong Kong, Shatin, Hong Kong, China; 3Department of Medicine and Therapeutics, Faculty of Medicine, The 77
18 Chinese University of Hong Kong, Shatin, Hong Kong, China; 4Stanley Ho Centre for Emerging Infectious Diseases, The 78
Chinese University of Hong Kong, Shatin, Hong Kong, China; 5Department of Microbiology, The Chinese University of Hong
19 Kong, Shatin, Hong Kong, China; 6Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China; 79
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Department of Pathology, United Christian Hospital, Hong Kong, China; and 8Department of Anaesthesia and Intensive Care, 80
21 Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China 81
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BASIC AND
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47 BACKGROUND & AIMS: Although severe acute respiratory oxygen saturation 93% when breathing ambient air), or 107
48 syndrome coronavirus 2 (SARS-CoV-2) infects gastrointestinal critical (respiratory failure requiring mechanical ventilation, 108
49 tissues, little is known about the roles of gut commensal mi- shock, or organ failure requiring intensive care). We compared 109
50 crobes in susceptibility to and severity of infection. We inves- microbiome data with those from 6 subjects with community- 110
51 tigated changes in fecal microbiomes of patients with SARS- acquired pneumonia and 15 healthy individuals (controls). 111
CoV-2 infection during hospitalization and associations with We assessed gut microbiome profiles in association with dis-
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severity and fecal shedding of virus. METHODS: We performed ease severity and changes in fecal shedding of SARS-CoV-2.
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shotgun metagenomic sequencing analyses of fecal samples RESULTS: Patients with COVID-19 had significant alterations in
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from 15 patients with Coronavirus Disease 2019 (COVID-19) in fecal microbiomes compared with controls, characterized by
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Hong Kong, from February 5 through March 17, 2020. Fecal enrichment of opportunistic pathogens and depletion of bene-
56 samples were collected 2 or 3 times per week from time of ficial commensals, at time of hospitalization and at all time- 116
57 hospitalization until discharge; disease was categorized as mild points during hospitalization. Depleted symbionts and gut 117
58 (no radiographic evidence of pneumonia), moderate (pneu- dysbiosis persisted even after clearance of SARS-CoV-2 118
59 monia was present), severe (respiratory rate
30/min, or (determined from throat swabs) and resolution of respiratory 119
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symptoms. The baseline abundance of Coprobacillus, Clos-

121 WHAT YOU NEED TO KNOW 181
tridium ramosum, and Clostridium hathewayi correlated with
122 182
COVID-19 severity; there was an inverse correlation between BACKGROUD AND CONTEXT
123 183
abundance of Faecalibacterium prausnitzii (an anti-
124 SARS-CoV-2 infects gastrointestinal tissues. The authors 184
inflammatory bacterium) and disease severity. Over the investigated changes in fecal microbiomes of patients
125 course of hospitalization, Bacteroides dorei, Bacteroides the- 185
126 with SARS-CoV-2 infection during hospitalization and 186
taiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, associations with severity and fecal shedding of virus.
127 which downregulate expression of angiotensin-converting 187
128 enzyme 2 in murine gut, correlated inversely with SARS-CoV- NEW FINDINGS 188
129 2 load in fecal samples from patients. CONCLUSIONS: In a pi- Fecal microbiomes from patients with COVID-19 had 189
130 lot study of 15 patients with COVID-19, we found persistent depletion of symbionts and enrichment of opportunistic 190
131 alterations in the fecal microbiome during the time of hospi- pathogens, which persisted after clearance of SARS- 191
132 talization, compared with controls. Fecal microbiota alterations CoV-2. Baseline microbiome composition associated 192
133 were associated with fecal levels of SARS-CoV-2 and COVID-19 with COVID-19 severity. Multiple species from the 193
Bacteroidetes phylum correlated inversely with fecal
134 severity. Strategies to alter the intestinal microbiota might
shedding of SARS-CoV-2. 194
135 reduce disease severity. 195
136 LIMITATIONS 196
137 This was a pilot exploratory study of 15 patients with 197
138 Keywords: Coronavirus; Bacteria; Gut Microbiome; Fecal COVID-19; further studies are needed of alterations in 198
139 Nucleic Acid. intestinal microbiomes of these patients over time. 199
140 IMPACT 200
141 201
These findings indicate the prolonged effect of SARS-
142
143
C oronavirus Disease 2019 (COVID-19) is a respiratory
illness caused by a novel coronavirus (severe acute
respiratory syndrome coronavirus 2 [SARS-CoV-2]) and
CoV-2 infection on the gut microbiomes of patients with
COVID-19. Strategies to alter the gut microbiome might
202
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144 be developed to manage gastrointestinal effects of the 204
more than 3.3 million people worldwide have been infected
145 virus in these patients. 205
as of May 1, 2020. Although most cases of COVID-19 are
146 206
mild, disease can be severe, resulting in hospitalization,
147 understand host microbial perturbations that underlie 207
respiratory failure, or death.1 Early reports from Wuhan
148 SARS-CoV-2 infection, which may affect response to infec- 208
showed that 2% to 10% of patients with COVID-19 had
149 209
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tion and efficacy of various future immune interventions,

gastrointestinal (GI) symptoms, including diarrhea, but a
150 such as vaccines.22 210
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recent meta-analysis reported that up to 20% had GI

151 In this pilot study, we hypothesize that the intestinal 211
symptoms.2–5 Studies have detected SARS-CoV-2 virus in
152 microbiota is altered in SARS-CoV-2 infection and is asso- 212
anal swabs and stool samples in almost 50% of patients
153 ciated with susceptibility to severe disease. We prospec- 213
with COVID-19, suggesting that the digestive tract might be
154 tively included 15 hospitalized patients with COVID-19 214
an extrapulmonary site for virus replication and activity.6,7
155 admitted between February 16, 2020, and March 2, 2020, in 215
Moreover, fecal calprotectin was found to be elevated in
156 Hong Kong, China, followed from hospital admission until 216
patients with COVID-19 with diarrhea,8 an indicator of in-
157 discharge. Through the application of deep shotgun meta- 217
flammatory responses in the gut. SARS-CoV-2 uses the
158 genomics, we investigated longitudinal changes of the gut 218
angiotensin-converting enzyme 2 (ACE2) receptor to enter
159 microbiome in COVID-19. 219
the host, and this receptor is highly expressed in both the
160 220
respiratory and GI tracts.9–11 ACE2 is important in con-
161 221
trolling intestinal inflammation and gut microbial ecology.12 Methods
162 222
With trillions of diverse bacteria dwelling in our gut, the gut
163 Study Subject and Design 223
microbiome has a myriad of effects on gene regulation of
164 224
immune response and metabolism. The commensal micro- This prospective study involved 15 patients with COVID-19
165 hospitalized with laboratory-confirmed SARS-CoV-2 infection, 6
225
biota ecosystem in the gut is dynamic and can be regulated
166 patients hospitalized with community-acquired pneumonia 226
by invading viruses to facilitate a stimulatory or suppressive
167 (pneumonia controls), and 15 healthy individuals 227
response.13 Studies have shown that respiratory viral in-
168 (healthy controls) (Table 1, Supplementary Table 1, Figure 1). 228
fections may be associated with altered gut microbiome,
169 229
which predispose patients to secondary bacterial in-
170 230
fections.14,15 Recent meta-transcriptome sequencing of *Authors share co-first authorship.
171 231
bronchoalveolar lavage fluid showed that the microbiota in
172 Abbreviations used in this paper: ACE2, angiotensin-converting enzyme 2; 232
SARS-CoV-2–infected patients was dominated by pathogens
173 COVID-19, coronavirus disease 2019; GI, gastrointestinal; RT-PCR, 233
or oral and upper respiratory commensal bacteria.16 In reverse-transcriptase polymerase chain reaction; SARS-CoV-2, severe
174 acute respiratory syndrome coronavirus 2. 234
addition, comorbidities commonly associated with severe
175 235
COVID-19 are known to be associated with alterations in
176 © 2020 by the AGA Institute. Published by Elsevier Inc. This is an open 236
bacteria taxa from the phyla Bacteroidetes and access article under the CC BY-NC-ND license (http://creativecommons.
177 237
Firmicutes,17–20 which were reported to regulate ACE2 org/licenses/by-nc-nd/4.0/).
178 0016-5085 238
expression in rodents.21 There is an urgent need to https://doi.org/10.1053/j.gastro.2020.05.048
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 - 2020 Alterations in Gut Microbiota in COVID-19 3

241 Table 1.Subject Characteristics 301

242 Variables COVID-19 cases Pneumonia controls Healthy controls 302
243 303
244 Number 15 6 15 304
245 Male 7 (47) 4 (67) 9 (60) 305
246 Median age, y (IQR) 55 (44, 67.5) 50 (44, 65) 48 (45, 48) 306
Comorbidities, n (%) 6 (40) 6 (100) 0 (0)
247 307
Recent exposure history, n (%)
248 Travel to cities of Hubei province 1 (7) 0 (0) 0 (0) 308
249 Contact with person with COVID-19 5 (33) 0 (0) 0 (0) 309
250 Have family cluster outbreak 4 (27) 0 (0) 0 (0) 310
251 Symptoms at admission, n (%) 311
252 Fever 9 (60) 4 (67) 312
253 Gastrointestinal symptoms 313
Diarrhea 1 (7) 2(33)
254 Respiratory symptoms
314
255 Cough 11 (73) 4 (67) 315
256 Sputum 5 (33) 3 (50) 316
257 Rhinorrhea 3 (20) 1 (17) 317
258 Shortness of breath 4 (27) 3 (50) 318
259 Blood result 319
Lymphocyte counts (x 109/L, normal range 1.1–2.9) 0.9 (0.7, 1.1) 1.1 (0.9, 1.2)
260 320
Antibiotic therapy at presentation, n (%) 7 (47) 6 (100)
261 Amoxycillin Clavulanate 4 (27) 3 (50)
321
262 Cephalosporin 5 (33) 6 (100) 322
263 Tetracycline 4 (27) 0 (0) 323
264 Antiviral therapy, n (%) 13 (87) 0 (0) 324
265 Lopinavir-Ritonavir 13 (87) 0 (0) 325
266 Ribavirin 7 (47) 0 (0) 326
Interferon beta-1b 1 (7) 0 (0)
267 327
Death, n (%) 0 (0) 0 (0)
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269 329

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270 NOTE. Values are expressed in number (percentage) and median (interquartile range). 330

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274 SARS-CoV-2 infection was confirmed by 2 consecutive reverse- the Hong Kong Hospital Authority clinical management system. 334
275 transcriptase polymerase chain reaction (RT-PCR) tests tar- Fecal samples from patients with COVID-19 were collected 335
276 geting different regions of the RdRp gene performed by the serially 2 to 3 times per week until discharge. This study was 336
277 local hospital and Public Health Laboratory Service. Pneumonia conducted in accordance with the Declaration of Helsinki. 337
controls were patients admitted with community-acquired
278 338
pneumonia tested negative for SARS-CoV-2 PCR on 2 respira-
279 Detection of Fecal SARS-CoV-2 Viral Load 339
tory samples. Patients with COVID-19 and pneumonia controls
280 340
were admitted to the Prince of Wales Hospital or the United SARS-CoV-2 viral loads in stool were measured using real-
281 Christian Hospital, Hong Kong. Healthy controls were in- time RT-PCR assay. Viral RNA from stool samples was extrac-
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282 dividuals with no past medical history or history of antibiotic ted using QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Ger- 342
283 intake in the past 3 months recruited via advertisement from many); 0.1g of stool was suspended in 1 mL of viral transport 343
284 the general population and tested negative for SARS-CoV-2. All medium (in 1:10 dilution) and centrifuged for 20 minutes at 344
285 subjects were recruited between February 5 and March 17, 4000g. A 140-mL aliquot of the filtrate was used as starting 345
286 2020. Severity of COVID-19 infection was categorized as (1) material following the manufacturer’s protocol. SARS-CoV-2 346
287 mild, if there was no radiographic evidence of pneumonia; (2) RNA was quantified using real-time RT-PCR. The primer- 347
288 moderate, if pneumonia was present along with fever and probe set N1 (2019-nCoV_N1-F: 5ʹ-GAC CCC AAA ATC AGC 348
289 respiratory tract symptoms; (3) severe, if respiratory rate
30/ GAA AT-3ʹ, 2019-nCoV_N1-R: 5ʹ-TCT GGT TAC TGC CAG TTG 349
290 min, oxygen saturation 93% when breathing ambient air, or AAT CTG-3ʹ, and 2019-nCoV_N1-P: 5ʹ-FAM-ACC CCG CAT TAC 350
291 PaO2 / FiO2 300 mm Hg (1 mm Hg ¼ 0.133 kPa); or (4) GTT TGG ACC-BHQ1-3ʹ) designed by US Centers for Disease 351
292 critical, if there was respiratory failure requiring mechanical Control and Prevention were purchased from Integrated DNA 352
293 ventilation, shock, or organ failure requiring intensive care.23 Technologies (Coralville, IA). The 1-step real-time RT-PCR re- 353
294 This study was approved by the Joint Chinese University of action contained 10 mL of the extracted preparation, 4 mL 354
295 Hong Kong–New Territories East Cluster Clinical Research TaqMan Fast Virus 1-Step Master Mix (Applied Biosystems, 355
296 Ethics Committees (2020.076). All patients provided informed Foster City, CA) in a final reaction volume of 20 mL. The primer 356
297 consent to participate in this study. Data including de- and probe concentration were 0.5 mM and 0.125 mM, respec- 357
298 mographics, laboratory results, imaging results, and medical tively. The cycling conditions, 25 C for 2 minutes, 50 C for 15 358
299 therapy were extracted from the electronic medical records in minutes, 95 C for 2 minutes, followed by 45 cycles of 95 C for 359
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386 Figure 1. Schematic diagram of stool sample collection, SARS-CoV-2 PCR test results and hospitalization duration in patients 446
387 with COVID-19 (n ¼ 15). “CoV” denotes patient with COVID-19. Stool specimens were serially collected for shotgun meta- 447
388 genomics sequencing and quantitative RT-PCR test for SARS-CoV-2 virus; “D0” denotes baseline date when the first stool 448
389 was collected after hospitalization; the following timepoints starting with “D” represent days since baseline stool collection. 449
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390 “þve throat swab”: the first positive result for SARS-CoV-2 virus in nasopharyngeal/throat/pooled swabs; “-ve throat swab”: 450
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the first negative result for SARS-CoV-2 virus in 2 consecutive negative nasopharyngeal/throat/pooled swab tests, on which
391 451
patient was then discharged.
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394 15 seconds, and 55 C for 30 seconds, were performed with the subject to DNA libraries construction, completed through the 454
395 StepOnePlus Real-Time PCR System (Applied Biosystems). The processes of end repairing, adding A to tails, purification and 455
396 cycle threshold values of real-time RT-PCR were converted into PCR amplification, using Nextera DNA Flex Library Preparation 456
397 viral RNA copies based on a standard curve prepared from 10- kit (Illumina, San Diego, CA). Libraries were subsequently 457
398 fold serial dilutions of known copies of plasmid containing the sequenced on our in-house sequencer Illumina NextSeq 550 458
399 full N gene (2019-nCoV_N_Positive Control; Integrated DNA (150 base pairs paired-end) at the Center for Microbiota 459
400 Technologies). Samples were considered as negative if the cycle Research, The Chinese University of Hong Kong. Raw sequence 460
401 threshold values exceeded 39.9 cycles. The detection limit of reads were filtered and quality-trimmed using Trimmomatic 461
real-time RT-PCR was 347 copies/mL. v0.3624 as follows: (1) trimming low-quality base (quality score
402 462
<20); (2) removing reads shorter than 50 base pairs; (3)
403 463
removing sequencing adapters. Contaminating human reads
404 Microbial Profiling of Fecal Samples With 464
were filtering using Kneaddata (Reference database: GRCh38
405 Metagenomic Sequencing 465
p12) with default parameters. Profiling of bacterial commu-
406 An approximately 0.1 g fecal sample was prewashed with 1 nities was performed using MetaPhlAn2 (V2.9) by mapping 466
407 mL double-distilled H2O and pelleted by centrifugation at reads to clade-specific markers.25 467
408 13,000g for 1 minute. The fecal DNA was subsequently 468
409 extracted from the pellet using Maxwell RSC PureFood GMO 469
410 and Authentication Kit (Promega, Madison, WI) following the Statistical Analysis 470
411 manufacturer’s instructions. Briefly, the fecal pellet was added Relative data from MetaPhlAn2 were imported into R 471
412 to 1 mL of CTAB buffer and vortexed for 30 seconds, then the v3.5.1. Nonmetric multidimensional scaling analyses were 472
413 sample was heated at 95 C for 5 minutes. After that, the sam- performed on all baseline fecal microbiomes between groups, 473
414 ples were vortexed thoroughly with beads at maximum speed and serial fecal microbiomes in each COVID-19 case during the 474
415 for 15 minutes. Then, 40 mL of proteinase K and 20 mL of RNase disease course, based on Bray-Curtis dissimilarities using vegan 475
416 A was added to the sample and the mixture was incubated at package (v2.5–3). Differential bacterial taxa between patients 476
417 70 C for 10 minutes. The supernatant was then obtained by with COVID-19 (with or without antibiotics treatment at in- 477
418 centrifuging at 13,000g for 5 minutes and was added into the clusion), patients with community-acquired pneumonia, and 478
419 Maxwell RSC machine for DNA extraction. Extracted DNA was healthy controls were identified using Multivariate Association 479
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Table 2.Gut Microbiome Features in Patients With COVID-19

-
2020
Gut microbiome
feature Taxon Group Coefficient P value Q value

COVID-19 (antibiotics naïve: abxL)

Specifically p_Actinobacteriajc_Actinobacteriajo_Actinomycetalesjf_Actinomycetaceaejg_Actinomycesjs_Actinomyces_ COVID-19 (Abx) 0.243 8.2E-08 6.4E-05
enriched in viscosus
COVID-19(abx) p_Firmicutesjc_Clostridiajo_Clostridialesjf_Clostridiaceaejg_Clostridiumjs_Clostridium_hathewayi COVID-19 (Abx) 1.130 4.8E-06 2.5E-03
p_Bacteroidetesjc_Bacteroidiajo_Bacteroidalesjf_Bacteroidaceaejg_Bacteroidesjs_Bacteroides_nordii COVID-19 (Abx) 0.164 2.3E-05 8.5E-03
Underrepresented p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceaejg_Eubacteriumjs_Eubacterium_ventriosum COVID-19 (Abx) -0.280 1.2E-04 2.5E-02
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in both
COVID-19 and
pneumonia
COVID-19 (antibiotics exposed: abxD)
Underrepresented p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Doreajs_Dorea_formicigenerans COVID-19 (Abxþ) -0.812 2.6E-05 0.00853
in COVID- p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Blautia COVID-19 (Abxþ) -0.441 6.1E-05 0.01491
19(abxþ) p_Firmicutesjc_Clostridiajo_Clostridialesjf_Ruminococcaceaejg_Faecalibacterium COVID-19 (Abxþ) -0.537 3.2E-05 0.00924
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Ruminococcaceaejg_Faecalibacteriumjs_Faecalibacterium_prausnitzii COVID-19 (Abxþ) -0.537 3.2E-05 0.00924
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceae COVID-19 (Abxþ) -0.289 4.6E-05 0.01236
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceaejg_Eubacterium COVID-19 (Abxþ) -0.289 4.6E-05 0.01236
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceaejg_Eubacteriumjs_Eubacterium_rectale COVID-19 (Abxþ) -0.903 1.7E-04 0.03316
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Ruminococcaceae COVID-19 (Abxþ) -0.300 2.0E-04 0.03709
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Roseburia COVID-19 (Abxþ) -0.598 2.3E-04 0.04018
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Coprococcus COVID-19 (Abxþ) -0.447 1.6E-04 0.03239
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Blautiajs_Ruminococcus_obeum COVID-19 (Abxþ) -0.623 4.3E-06 0.00243
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Lachnospiraceae_nonamejs_Lachnospiraceae_ COVID-19 (Abxþ) -0.341 2.5E-05 0.00853
bacterium_5_1_63FAA
Underrepresented p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceaejg_Eubacteriumjs_Eubacterium_ventriosum COVID-19 (Abxþ) -0.307 8.6E-06 0.00376
in both
COVID-19 and
pneumonia
Pneumonia patients

Alterations in Gut Microbiota in COVID-19

Underrepresented p_Firmicutesjc_Bacillijo_Lactobacillalesjf_Enterococcaceaejg_Enterococcusjs_Enterococcus_faecium Pneumonia 0.228 5.0E-05 0.01261
in pneumonia p_Firmicutesjc_Erysipelotrichiajo_Erysipelotrichalesjf_Erysipelotrichaceaejg_Erysipelotrichaceae_nonamejs_ Pneumonia 0.195 3.1E-06 0.00190
Clostridium_ramosum
p_Firmicutesjc_Erysipelotrichiajo_Erysipelotrichalesjf_Erysipelotrichaceaejg_Coprobacillus Pneumonia 0.402 5.2E-06 0.00257
p_Firmicutesjc_Clostridiajo_Clostridialesjf_Lachnospiraceaejg_Lachnospiraceae_nonamejs_Lachnospiraceae_ Pneumonia -0.348 7.6E-05 0.01752
bacterium_5_1_63FAA
Underrepresented p_Firmicutesjc_Clostridiajo_Clostridialesjf_Eubacteriaceaejg_Eubacteriumjs_Eubacterium_ventriosum Pneumonia -0.256 3.5E-04 0.03539
in both
COVID-19 and
pneumonia

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620 Figure 2. Gut microbiome alterations in patients with COVID-19 and longitudinal changes over the disease course. (A) The 680
621 effect size of subject metadata in gut microbiome composition, as determined by PERMANOVA test. **P < .01; *P < .05. (B) 681
622 Microbiome community alterations in COVID-19, viewed by NMDS (nonmetric multidimensional scaling) plot based upon Bray- 682
623 Curtis dissimilarities. The microbiomes were compared among healthy controls (n ¼ 15), COVID-19 (abx, n ¼ 7), COVID-19 683
(abxþ, n ¼ 8), and pneumonia controls (n ¼ 6). (C) Dissimilarity of the gut microbiome of patients with COVID-19 to that of
624 healthy controls during the disease course. The microbiome dissimilarity was calculated as Bray-Curtis dissimilarity. The gray 684
625 area denotes the range of Bray-Curtis dissimilarities among gut microbiomes of healthy controls, and the solid black line 685
626 indicates the median dissimilarity among healthy individuals. “CoV” denotes patient with COVID-19. “D0” denotes baseline 686
627 date when the first stool was collected after hospitalization; the following timepoints starting with “D” represent days since 687
628 baseline stool collection. 688
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630 690
BASIC AND

with Linear Models (MaAsLin).26 Spearman correlation ana- To understand alterations of the gut microbiome that
631 691
lyses were conducted to associate baseline microbiome profiles underlie SARS-CoV-2 infection, we compared baseline fecal
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of 7 antibiotics-naïve patients at baseline with COVID-19 microbiome of patients with COVID-19 with healthy con-
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severity, and to associate longitudinal fecal SARS-CoV-2 loads trols and pneumonia controls adjusting for age, gender,
634 694
with timepoint-matched bacterial profiles across all 15 patients antibiotic use, and comorbidities. Antibiotic-naïve patients
635 with COVID-19, while adjusting for confounding factors. 695
636 with COVID-19 were enriched in opportunistic pathogens 696
637 known to cause bacteremia,27,28 including Clostridium 697
638 hathewayi, Actinomyces viscosus, and Bacteroides nordii 698
Data Availability
639 compared with controls (Table 2). COVID-19(abxþ) patients 699
Metagenomics Sequencing dataset was deposited to the
640 demonstrated a further depletion of multiple bacterial 700
National Center for Biotechnology Information Sequence Read
641 species, which are symbionts beneficial to host immunity 701
Archive under BioProject accession number PRJNA624223.
642 including Faecalibacterium prausnitzii, Lachnospiraceae 702
643 bacterium 5_1_63FAA, Eubacterium rectale, Ruminococcus 703
644 obeum, and Dorea formicigenerans compared with COVID- 704
Results 19(abx) patients (Table 2). Regardless of antibiotic use,
645 705
646 Fecal Microbiome Alterations in COVID-19 underrepresented bacterial species in patients with COVID- 706
647 Among the 15 patients with COVID-19, 7 were antibiotics- 19 were consistently absent or present at very low abun- 707
648 naïve (COVID-19[abx]) and 8 received empirical antibiotics dance during the disease course, even when SARS-CoV-2 708
649 (COVID-19[abxþ]) at baseline (defined as date of the first stool virus was cleared from the nasopharyngeal swab and 709
650 collection after hospitalization). The median ages of patients stool, and respiratory symptoms had resolved 710
651 with COVID-19, pneumonia controls, and healthy controls (Supplementary Figures 1–6). 711
652 were 55, 50, and 48 years, respectively; 40% and 100% of Among all host factors, COVID-19 infection showed the 712
653 patients with COVID-19 and pneumonia controls, respectively, largest effect size in affecting the gut microbiome (PER- 713
654 had underlying comorbidities (Table 1, Supplementary MANOVA test, R2 ¼ 0.066, P ¼ .002, Figure 2A), followed by 714
655 Table 1). All patients with COVID-19 presented with respira- hyperlipidemia, pneumonia, and antibiotics, whereas age 715
656 tory symptoms but only 1 had diarrhea at presentation. None and gender showed no significant effects on gut microbiome 716
657 of the patients developed GI symptoms during hospitalization. alterations (Figure 2A). At the whole microbiome commu- 717
658 Median duration of hospitalization was 21 ± 2.4 days (mean ± nity level, healthy subjects’ fecal microbiome clustered 718
659 SE) in COVID-19 and pneumonia cases. together, whereas that of COVID-19(abx) patients 719
660 720

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Table 3.Correlation of Gut Bacteria With COVID-19 Severity
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Correlation
coefficient
Correlation Bacteria taxa Rho P value

Positive p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichalesjf__Erysipelotrichaceaejg__Coprobacillus 0.92 .003

correlation with p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichalesjf__Erysipelotrichaceaejg__Erysipelotrichaceae_nonamejs__Clostridium_ramosum 0.92 .003
COVID-19 severity p__Firmicutesjc__Clostridiajo__Clostridialesjf__Clostridiaceaejg__Clostridiumjs__Clostridium_hathewayi 0.90 .005
p__Firmicutesjc__Erysipelotrichia 0.90 .006
p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichales 0.90 .006
p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichalesjf__Erysipelotrichaceae 0.90 .006
p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichalesjf__Erysipelotrichaceaejg__Erysipelotrichaceae_noname 0.90 .006
p__Actinobacteriajc__Actinobacteriajo__Actinomycetalesjf__Actinomycetaceaejg__Actinomycesjs__Actinomyces_odontolyticus 0.87 .011
p__Firmicutesjc__Erysipelotrichiajo__Erysipelotrichalesjf__Erysipelotrichaceaejg__Erysipelotrichaceae_nonamejs__Erysipelotrichaceae_ 0.87 .011
bacterium_6_1_45
p__Proteobacteriajc__Gammaproteobacteriajo__Enterobacterialesjf__Enterobacteriaceaejg__Enterobacter 0.87 .011
p__Proteobacteriajc__Gammaproteobacteriajo__Enterobacterialesjf__Enterobacteriaceaejg__Enterobacterjs__Enterobacter_cloacae 0.87 .011
p__Bacteroidetesjc__Bacteroidiajo__Bacteroidalesjf__Porphyromonadaceaejg__Parabacteroidesjs__Parabacteroides_unclassified 0.81 .029
p__Bacteroidetesjc__Bacteroidiajo__Bacteroidalesjf__Rikenellaceaejg__Alistipesjs__Alistipes_indistinctus 0.81 .029
Negative p__Actinobacteriajc__Actinobacteriajo__Bifidobacterialesjf__Bifidobacteriaceaejg__Bifidobacteriumjs__Bifidobacterium_pseudocatenulatum 0.81 .026
correlation with p__Firmicutesjc__Clostridiajo__Clostridialesjf__Lachnospiraceaejg__Dorea 0.81 .026
COVID-19 severity p__Firmicutesjc__Clostridiajo__Clostridialesjf__Lachnospiraceaejg__Doreajs__Dorea_longicatena 0.81 .026
p__Bacteroidetesjc__Bacteroidiajo__Bacteroidalesjf__Bacteroidaceaejg__Bacteroidesjs__Bacteroides_ovatus 0.84 .019

Alterations in Gut Microbiota in COVID-19

p__Firmicutesjc__Clostridiajo__Clostridialesjf__Lachnospiraceaejg__Anaerostipesjs__Anaerostipes_hadrus 0.87 .011
p__Firmicutesjc__Clostridiajo__Clostridialesjf__Lachnospiraceaejg__Lachnospiraceae_nonamejs__Lachnospiraceae_bacterium_5_1_63FAA 0.87 .011
p__Firmicutesjc__Clostridiajo__Clostridialesjf__Lachnospiraceaejg__Roseburia 0.87 .011
p__Firmicutesjc__Clostridiajo__Clostridialesjf__Ruminococcaceaejg__Faecalibacterium 0.87 .011
p__Firmicutesjc__Clostridiajo__Clostridialesjf__Ruminococcaceaejg__Faecalibacteriumjs__Faecalibacterium_prausnitzii 0.87 .011
p__Bacteroidetesjc__Bacteroidiajo__Bacteroidalesjf__Rikenellaceaejg__Alistipesjs__Alistipes_onderdonkii 0.90 .005

7
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852 912
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855 915
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857 Figure 3. Correlation between gut bacteria and fecal SARS-CoV-2 shedding in patients with COVID-19 over the disease 917
858 course. (A) Longitudinal changes in fecal viral loads of patients with COVID-19. (B) Bacteria significantly associated with fecal 918
859 viral load during disease course, as determined by Spearman correlation test. 919
860 920
861 921
862 clustered separately (PERMANOVA test, P ¼ .001) and were disease severity. These data are in line with a report 922
863 more heterogeneous (Figure 2B). Antibiotic treatment in showing that different Firmicutes bacteria have diverse 923
864 patients with COVID-19 was associated with a more het- roles in upregulating or downregulating ACE2 expression in 924
865 erogeneous microbiome configuration and accompanied by the murine gut.21 Our finding of the association of gut Fir- 925
866 further shift of the gut microbiome away from a healthy micutes bacteria with COVID-19 severity highlights the po- 926
867 microbiome (Figure 2B). tential importance of bacterial membership in modulating 927
868 We next explored whether recovery from SAR-CoV-2 human response to SARS-CoV-2 infection. 928
869 929
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infection was associated with restoration of gut micro- Three bacterial members from the Firmicutes phylum,
870 930
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biome to a community level similar to that of healthy in- the genus Coprobacillus, the species Clostridium ramosum
871 dividuals. Overall, the gut microbiome of all patients with and C. hathewayi, were the top bacteria positively associated 931
872 COVID-19 remained stable but were markedly disparate with COVID-19 disease severity (Spearman correlation co- 932
873 from that of healthy controls, both during the disease course efficient Rho >0.9, P < .01, Table 3). Both C. ramosum and 933
874 and after clearance of SARS-CoV-2 (Figure 2C). Although the C. hathewayi have been associated with human infection and 934
875 microbiome of 5 patients with COVID-19 (CoV1, 4, 7, 11, 15) bacteremia.27,29 Importantly, Coprobacillus bacterium has 935
876 showed closer proximity to healthy microbiomes over time, been shown to strongly upregulate colonic expression of 936
877 patients CoV3, 5, 8, 10, and 12 became more disparate from ACE2 in the murine gut.21 In contrast, 2 beneficial species, 937
878 healthy microbiomes over time (Supplementary Figure 7). Alistipes onderdonkii and Faecalibacterium prausnitzii, were 938
879 At the last follow-up, the gut microbiome of these 10 pa- top bacterial species to show a negative correlation with 939
880 tients remained substantially different from that of healthy COVID-19 severity (Table 3). Alistipes species are indole 940
881 controls, despite clearance of SARS-CoV-2 infection as positive, involved in the serotonin precursor tryptophan 941
882 defined by negative SARS-CoV-2 tests on nasopharyngeal metabolism and in maintaining gut immune homeosta- 942
883 swab or deep throat saliva (Figure 2C, Supplementary sis,30,31 whereas F. prausnitzii has anti-inflammatory prop- 943
884 Figure7). Of note, patient CoV4 was discharged on day 5 erties.32 Although we cannot assign a causative or 944
885 but his gut microbiome on day 22 was persistently different preventive role of these bacteria in disease pathogenesis or 945
886 from that of healthy individuals. severity, our data underscore a potential role for bacteria in 946
887 determining response to SARS-CoV-2 infection and intensity 947
888 of the infection in the host. 948
Baseline Gut Microbiome and Disease Severity of
889 949
890 COVID-19 950
To understand whether baseline gut microbiome affects Fecal SARS-CoV-2 Virus Load and Gut Bacterial
891 951
892 the severity of COVID-19, we assessed association between Abundance 952
893 baseline fecal microbiome and COVID-19 severity (mild, Eleven of the 15 patients had SARS-CoV-2 nucleic acid 953
894 moderate, severe, or critical) in 7 antibiotic-naïve COVID-19 detected in feces at hospitalization (median 3.86  103 954
895 cases. A total of 23 bacterial taxa were found to be signifi- copies per mL inoculum, as determined by RT-PCR) and 5 of 955
896 cantly associated with COVID-19 disease severity, most of them cleared the SARS-CoV-2 virus over time (Figure 3A). 956
897 which (15 of 23) were from the Firmicutes phylum We investigated whether gut bacteria were associated with 957
898 (Table 3). Among them, 8 and 7 Firmicutes members, fecal SARS-CoV-2 load over the course of hospitalization. A 958
899 respectively, showed positive and negative correlation with total of 14 bacterial species were identified to be 959
900 960

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983 1043
Figure 4. Schematic summary of the gut microbiome alterations in COVID-19. In healthy individuals, Eubacterium, Faecali-
984 bacterium prausnitzii, Roseburia, and Lachnospiraceae taxa are prevalent in their gut microbiome. However, the gut micro- 1044
985 biome of patients with COVID-19 is characterized by enrichment of opportunistic pathogens and depletion of commensals in 1045
986 the gut. Such gut dysbiosis persists during the COVID-19 disease course, even after clearance/recovery of SARS-CoV-2 1046
987 infection. Baseline fecal abundance of the bacteria Coprobacillus, Clostridium ramosum, and Clostridium hathewayi 1047
988 showed significant correlation with COVID-19 severity, whereas an anti-inflammatory bacterium Faecalibacterium prausnitzii 1048
989 showed an inverse correlation. Four Bacteroidetes members, including Bacteroides dorei, Bacteroides thetaiotaomicron, 1049

TRANSLATIONAL AT
Bacteroides massiliensis, and Bacteroides ovatus, known to downregulate ACE2 expression in the murine gut, showed sig-
990 1050

BASIC AND
nificant inverse correlation with fecal SARS-CoV-2 viral load in patients with COVID-19.
991 1051
992 1052
993 significantly associated with fecal viral load of SARS-CoV-2 observed even in patients with COVID-19 naïve to antibiotic 1053
994 across all fecal samples (Figure 3B). Among them, 6 spe- therapy, were characterized by enrichment of opportunistic 1054
995 cies were from the Bacteroidetes phylum. Four Bacteroides pathogens and depletion of beneficial commensals 1055
996 species, including Bacteroides dorei, Bacteroides thetaiotao- (Figure 4). Loss of salutary species in COVID-19 persisted in 1056
997 micron, Bacteroides massiliensis, and Bacteroides ovatus, most patients despite clearance of SARS-CoV-2 virus, sug- 1057
998 showed significant inverse correlation with fecal SARS-CoV- gesting that exposure to SARS-CoV-2 infection and/or hos- 1058
999 2 load (all Spearman correlation coefficient Rho <0.2, P < pitalization may be associated with a more long-lasting 1059
1000 .05, Figure 3B). Interestingly, all these 4 species were detrimental effect to the gut microbiome. 1060
1001 associated with downregulation of ACE2 expression in the Studies have shown that respiratory viral infections can 1061
1002 murine colon.21 Taken together, these data suggest that alter the gut microbiome, such as pulmonary infections by 1062
1003 Bacteroides species may have a potential protective role in influenza and respiratory syncytial virus.15,34–36 Viral in- 1063
1004 combating SARS-CoV-2 infection by hampering host entry fections predispose patients to secondary bacterial in- 1064
1005 through ACE2. In contrast, Erysipelotrichaceae bacterium fections, which often have a more severe clinical course.14,37 1065
1006 2_2_44A, a Firmicutes species, showed the strongest positive We found that a number of pathogens and opportunistic 1066
1007 correlation with fecal SARS-CoV-2 load (Spearman correla- pathogens were enriched in the gut microbiome of patients 1067
1008 tion coefficient Rho ¼ 0.89, P ¼ .006, Figure 3B). Erysipe- with COVID-19, including C. hathewayi, B. nordii, A. viscosus, 1068
1009 lotrichaceae has been implicated in inflammation-related and a higher baseline abundance of C. hathewayi correlated 1069
1010 disorders of the GI tract.33 Considering the strong associa- with more severe COVID-19. Most of these bacteria are 1070
1011 tion of baseline abundance of Erysipelotrichaceae with bacteremia-associated bacteria, indicating susceptibility for 1071
1012 COVID-19 severity (Spearman correlation Rho ¼ 0.89, P ¼ severe disease course due to potential secondary bacterial 1072
1013 .006, Table 3), gut Erysipelotrichaceae may play a role in infection. We also identified an opportunistic pathogen of 1073
1014 augmenting SARS-CoV-2 infection in the host gut. the oral cavity and upper respiratory tract, A. viscosus, in the 1074
1015 gut of patients with COVID-19.38 Its presence suggests the 1075
1016 passage or transmission of extra-intestinal microbes into the 1076
1017
Discussion gut. 1077
1018 We showed for the first time that the gut microbiome Recently, a study provided direct evidence that SARS- 1078
1019 was disturbed in patients with COVID-19. The alterations, CoV-2 can bind to human ACE2 as host entry point.9 ACE2 1079
1020 1080

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 10 Zuo et al Gastroenterology Vol. -, No. -

1081 is highly expressed in the intestine especially in colonocytes gut barrier.45 In addition, antibiotics-driven gut microbiome 1141
1082 of healthy subjects and in patients with inflammatory bowel perturbation can alter immunity to vaccines in humans.46 1142
1083 disease,10 and can regulate amino acid transport, microbial Improving efficacy of future immune interventions such as 1143
1084 ecology, and inflammation in the gut.12 Interestingly, Bac- vaccines, through modulating the gut microbiome, in 1144
1085 teroidetes species have been shown to downregulate ACE2 combating COVID-19 should be considered. One approach 1145
1086 expression in the murine colon, whereas Firmicutes species for promoting a healthy microbiome may include measures 1146
1087 showed variable effects in modulating ACE2 expression.21 to enhance intestinal butyrate production through the pro- 1147
1088 We found that baseline abundance of Bacteroidetes spe- motion of microbial interactions by dietary changes, and 1148
1089 cies, A. onderdonkii and B. ovatus, negatively correlated with reduction of proinflammatory states. 1149
1090 COVID-19 severity, and 4 species from the genus Bacter- In conclusion, our study provides evidence of prolonged 1150
1091 oides of the phylum Bacteroidetes (B. dorei, gut microbiome dysbiosis in COVID-19 and its association 1151
1092 B. thetaiotaomicron, B. massiliensis, and B. ovatus) showed with fecal SARS-CoV-2 virus shedding and disease severity. 1152
1093 inverse correlation with fecal viral load of SARS-CoV-2 These data highlight a new concept that novel and targeted 1153
1094 (Figure 4). Among them, B. dorei has been reported to approach of modulation of the gut microbiota may represent 1154
1095 suppress colonic ACE2 expression21 and to calibrate host a therapeutic avenue for COVID-19 and its comorbidities. 1155
1096 immune response.39,40 The highest SARS-CoV-2 mortality 1156
1097 and morbidity have been reported in older patients and in 1157
1098 those with underlying chronic diseases that are associated Supplementary Material 1158
1099 with inflammation, such as hypertension, obesity, diabetes Note: To access the supplementary material accompanying 1159
1100 mellitus, and coronary artery disease.41–43 Interestingly, this article, visit the online version of Gastroenterology at 1160
1101 these subjects were also reported to have a lower abun- www.gastrojournal.org, and at https://doi.org/10.1053/ 1161
1102 dance of Bacteroides species than healthy individuals.17–20 j.gastro.2020.05.048. 1162
1103 These findings altogether suggest that an individual’s gut 1163
1104 microbiome configuration may affect the subject’s suscep- 1164
1105 tibility and response to SARS-CoV-2 infection. References 1165
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1246 trimmer for Illumina sequence data. Bioinformatics 2014; 19 in patients with diabetes. Metabolism 2020; 1306
1247 30:2114–2120. 107:154217. 1307
1248 25. Segata N, Waldron L, Ballarini A, et al. Metagenomic 44. Mendes V, Galvao I, Vieira AT. Mechanisms by which the 1308
1249 microbial community profiling using unique clade- gut microbiota influences cytokine production and 1309
1250 specific marker genes. Nat Methods 2012;9:811. modulates host inflammatory responses. J Interferon 1310
1251 26. Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the Cytokine Res 2019;39:393–409. 1311
1252 intestinal microbiome in inflammatory bowel disease and 45. Tulstrup MV-L, Christensen EG, Carvalho V, et al. Anti- 1312
1253 treatment. Genome Biol 2012;13:R79. biotic treatment affects intestinal permeability and gut 1313
1254 27. Elsayed S, Zhang K. Human infection caused by Clos- microbial composition in Wistar rats dependent on anti- 1314
1255 tridium hathewayi. Emerg Infect Dis 2004;10:1950. biotic class. PLoS One 2015;10:e0144854. 1315
1256 28. Dakshinamoorthy M, Venkatesh A, Arumugam K. 46. Hagan T, Cortese M, Rouphael N, et al. Antibiotics- 1316
1257 A literature review on dental caries vaccine-a prevention driven gut microbiome perturbation alters immunity to 1317
1258 strategy. Indian J Public Health 2019;10:3041–3043. vaccines in humans. Cell 2019;178:1313–1328.e13. 1318
1259 1319
1260 1320

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 12 Zuo et al Gastroenterology Vol. -, No. -

(Conceptualization: Equal; Resources: Lead; Writing – review & editing:

1321 Author names in bold designate shared co-first authorship. Equal). Yun Kit Yeoh, PhD (Writing – review & editing: Lead). Amy Y.L. Li, 1381
1322 Bachelor (Data curation: Lead). Hui Zhan, PhD (Investigation: Supporting). 1382
Received May 4, 2020. Accepted May 14, 2020. Yating Wan, PhD (Methodology: Supporting). Arthur Chung, PhD
1323 (Methodology: Supporting). Chun Peng Cheung, Bachelor (Project 1383
1324 Correspondence administration: Lead). Nan Chen, Master (Investigation: Supporting). 1384
Christopher K.C. Lai, PhD (Writing – review & editing: Supporting). Zigui
1325 Address correspondence to: Siew C. Ng, PhD, Department of Medicine
and Therapeutics, The Chinese University of Hong Kong. e-mail: Chen, PhD (Writing – review & editing: Equal). Eugene Y.K. Tso, MD
1385
1326 siewchienng@cuhk.edu.hk; fax: (852) 3505 3852; or Paul K.S. Chan, PhD, (Resources: Equal). Kitty S.C. Fung, MD (Resources: Equal). Veronica Chan, 1386
1327Q1 Department of Microbiology, The Chinese University of Hong Kong. e-mail: MD (Resources: Equal). Lowell Ling, MD (Resources: Equal). Gavin Joynt, 1387
paulkschan@cuhk.edu.hk; fax: (852) 2647 3227. PhD (Supervision: Supporting). David S.C. Hui, MD (Supervision: Supporting).
1328 Francis K.L. Chan, MD (Supervision: Lead). Paul K.S. Chan, PhD (Project 1388
1329 Acknowledgments administration: Lead). Siew C. Ng, PhD (Conceptualization: Lead; Funding 1389
We thank all health care workers working in isolation wards of Prince of acquisition: Lead; Resources: Lead; Supervision: Lead; Writing – review &
1330 Wales Hospital, Hong Kong, China. We thank Apple C.M. Yeung, Wendy editing: Lead). 1390
1331 C.S. Ho, Miu L. Chin, Rity Wong, and Vickie Li for their technical 1391
contributions in this study. We thank Whitney Tang for her assistance with Conflict of interest
1332 the graphical abstract. The authors disclose no conflicts. 1392
1333 1393
1334 CRediT Authorship Contributions Funding
This study was funded by the Center for Gut Microbiota Research Center,
1394
Tao Zuo, PhD (Formal analysis: Lead; Investigation: Equal; Methodology: Lead;
1335 Writing – original draft: Lead; Writing – review & editing: Lead). Fen Zhang, PhD Faculty of Medicine, The Chinese University of Hong Kong. Health and 1395
1336 (Formal analysis: Equal; Methodology: Equal). Grace C.Y. Lui, Dr Medical Research Fund, Hong Kong. Q6 Q2
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1469 Supplementary Figure 1-6. Longitudinal changes of fecal bacteria in patients with COVID-19 over the disease course. Only 1529
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1471 Faecalibacterium prausnitzii, Eubacterium rectale, Ruminococcus obeum, Lachnospiraceae bacterium_5_1_63FAA). Bacterial 1531
1472 species abundance is expressed as fractional abundance (%). “D0” denotes baseline date when the first stool was collected 1532
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1590 Supplementary Figure 1-6. (continued). 1650
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Supplementary Table 1.Detailed Clinical Characteristics of Patients With COVID-19 and Patients With Pneumonia

12.e8
Symptoms at admission
Recent exposure Admitted COVID-19

Zuo et al
Case Sex Age Comorbidities history Fever and respiratory GI to ICU Chest radiograph findings severity

CoV1 F 65 Hypertension, Chronic hepatitis B No Fever, cough, sputum Nil Yes Bilateral LZ haziness Critical
carrier
CoV2 F 55 None Contact with person with Fever, runny nose Nil No Bilateral LZ haziness Moderate
COVID-19
CoV3 M 42 None Travel to Hubei province Fever, cough Nil Yes RLZ haziness, Critical
RLL collapse
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CoV4 M 70 Hyperlipidemia, duodenal ulcer No Cough, shortness of breath Nil No Bilateral lung haziness Severe
CoV5 M 58 None No Fever, cough Diarrhea No Slight RLZ haziness Moderate
CoV6 M 71 None No Fever, cough, shortness of Nil No Bilateral lung infiltration Severe
breath
CoV7 M 48 Diabetes mellitus, hypertension, No Fever, cough Nil No LLZ haziness Moderate
hyperlipidemia
CoV8 F 38 None No Fever, cough, sputum, Nil No Bilateral LZ infiltrates Moderate
runny nose
CoV9 M 33 None Contact with person with Fever, cough Nil No Bilateral LZ haziness Moderate
COVID-19
CoV10 F 70 Obesity, hypertension No Cough Nil No Bilateral LZ haziness Moderate
CoV11 M 62 Diabetes, hyperlipidemia, left No Fever, cough, sputum, Nil No Bilateral lung infiltrates Severe
subclavian artery occlusion shortness of breath
CoV12 F 71 Hypertension, renal impairment, Contact with person with Cough Nil No Bilateral lung infiltrates Moderate
hyperlipidemia COVID-19
CoV13 F 47 None Contact with person with Cough Nil No Bilateral lung infiltrates Moderate
COVID-19
CoV14 F 22 None Contact with person with Fever, runny nose Nil No Bilateral lung infiltrates Moderate
COVID-19
CoV15 F 46 None Contact with person with Cough, shortness of breath Nil No Clear Mild
COVID-19
P1 F 69 Hypertension, diabetes mellitus, No Fever Nil No LMZ pneumonia N/A
Tricuspid regurgitation
P2 M 43 Nonalcoholic Fatty liver disease No Cough Nil No Right sided infiltrates N/A
P3 F 92 Diabetes, Hypertension, No Cough, sputum, shortness Nil No Bilateral lung infiltrate N/A
pulmonary fibrosis, of breath
Paroxysmal atrial fibrillation,

Gastroenterology Vol.
Acute coronary syndrome
P4 M 47 Diabetes mellitus No Fever, sputum Nil No Left effusion, LMZ infiltrates N/A
P5 M 36 Ischemic priapism No Fever, cough, sputum, Diarrhea No N/A N/A
shortness of breath
P6 M 52 Epilepsy, Hepatitis No Fever, cough, runny nose, Diarrhea No N/A N/A
shortness of breath

-,
*Value in x 109/L, normal range 1.1–2.9.
Q5

No.
GI, gastrointestinal; ICU, intensive care unit; LLZ, left lower zone; LMZ, left middle zone.

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