1
|
Su Q, Lau RI, Liu Q, Li MKT, Yan Mak JW, Lu W, Lau ISF, Lau LHS, Yeung GTY, Cheung CP, Tang W, Liu C, Ching JYL, Cheong PK, Chan FKL, Ng SC. The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome. Cell Host Microbe 2024:S1931-3128(24)00122-7. [PMID: 38657605 DOI: 10.1016/j.chom.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.
Collapse
Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Raphaela I Lau
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Moses K T Li
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Joyce Wing Yan Mak
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ivan S F Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Louis H S Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Giann T Y Yeung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y L Ching
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pui Kuan Cheong
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
2
|
Lau RI, Su Q, Lau ISF, Ching JYL, Wong MCS, Lau LHS, Tun HM, Mok CKP, Chau SWH, Tse YK, Cheung CP, Li MKT, Yeung GTY, Cheong PK, Chan FKL, Ng SC. A synbiotic preparation (SIM01) for post-acute COVID-19 syndrome in Hong Kong (RECOVERY): a randomised, double-blind, placebo-controlled trial. Lancet Infect Dis 2024; 24:256-265. [PMID: 38071990 DOI: 10.1016/s1473-3099(23)00685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/11/2023] [Accepted: 10/26/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Post-acute COVID-19 syndrome (PACS) affects over 65 million individuals worldwide but treatment options are scarce. We aimed to assess a synbiotic preparation (SIM01) for the alleviation of PACS symptoms. METHODS In this randomised, double-blind, placebo-controlled trial at a tertiary referral centre in Hong Kong, patients with PACS according to the US Centers for Disease Control and Prevention criteria were randomly assigned (1:1) by random permuted blocks to receive SIM01 (10 billion colony-forming units in sachets twice daily) or placebo orally for 6 months. Inclusion criterion was the presence of at least one of 14 PACS symptoms for 4 weeks or more after confirmed SARS-CoV-2 infection, including fatigue, memory loss, difficulty in concentration, insomnia, mood disturbance, hair loss, shortness of breath, coughing, inability to exercise, chest pain, muscle pain, joint pain, gastrointestinal upset, or general unwellness. Individuals were excluded if they were immunocompromised, were pregnant or breastfeeding, were unable to receive oral fluids, or if they had received gastrointestinal surgery in the 30 days before randomisation. Participants, care providers, and investigators were masked to group assignment. The primary outcome was alleviation of PACS symptoms by 6 months, assessed by an interviewer-administered 14-item questionnaire in the intention-to-treat population. Forward stepwise multivariable logistical regression was performed to identify predictors of symptom alleviation. The trial is registered with ClinicalTrials.gov, NCT04950803. FINDINGS Between June 25, 2021, and Aug 12, 2022, 463 patients were randomly assigned to receive SIM01 (n=232) or placebo (n=231). At 6 months, significantly higher proportions of the SIM01 group had alleviation of fatigue (OR 2·273, 95% CI 1·520-3·397, p=0·0001), memory loss (1·967, 1·271-3·044, p=0·0024), difficulty in concentration (2·644, 1·687-4·143, p<0·0001), gastrointestinal upset (1·995, 1·304-3·051, p=0·0014), and general unwellness (2·360, 1·428-3·900, p=0·0008) compared with the placebo group. Adverse event rates were similar between groups during treatment (SIM01 22 [10%] of 232 vs placebo 25 [11%] of 231; p=0·63). Treatment with SIM01, infection with omicron variants, vaccination before COVID-19, and mild acute COVID-19, were predictors of symptom alleviation (p<0·0036). INTERPRETATION Treatment with SIM01 alleviates multiple symptoms of PACS. Our findings have implications on the management of PACS through gut microbiome modulation. Further studies are warranted to explore the beneficial effects of SIM01 in other chronic or post-infection conditions. FUNDING Health and Medical Research Fund of Hong Kong, Hui Hoy and Chow Sin Lan Charity Fund, and InnoHK of the HKSAR Government. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
Collapse
Affiliation(s)
- Raphaela I Lau
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China
| | - Qi Su
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China
| | - Ivan S F Lau
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China
| | - Martin C S Wong
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Louis H S Lau
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hein M Tun
- Microbiota I-Center, Hong Kong Special Administrative Region, China; The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chris K P Mok
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Steven W H Chau
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yee Kit Tse
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Medical Data Analytics Centre, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chun Pan Cheung
- Microbiota I-Center, Hong Kong Special Administrative Region, China
| | - Moses K T Li
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China
| | - Giann T Y Yeung
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Pui Kuan Cheong
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Francis K L Chan
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Siew C Ng
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Microbiota I-Center, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
3
|
Yau YK, Su Q, Xu Z, Tang W, Ching JYL, Cheung CP, Fung M, Ip M, Chan PKS, Chan FKL, Ng SC. Faecal microbiota transplantation for patients with irritable bowel syndrome: abridged secondary publication. Hong Kong Med J 2024; 30 Suppl 1:34-38. [PMID: 38413211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Affiliation(s)
- Y K Yau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Q Su
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Z Xu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - W Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - J Y L Ching
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - C P Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - M Fung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - M Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - P K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - F K L Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - S C Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
4
|
Yau YK, Su Q, Xu Z, Tang W, Ching JYL, Mak JWY, Cheung CP, Fung M, Ip M, Chan PKS, Wu JCY, Chan FKL, Ng SC. Randomised clinical trial: Faecal microbiota transplantation for irritable bowel syndrome with diarrhoea. Aliment Pharmacol Ther 2023; 58:795-804. [PMID: 37667968 DOI: 10.1111/apt.17703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/11/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Faecal microbiota transplantation (FMT) has been shown to improve symptoms in a proportion of patients with irritable bowel syndrome (IBS). AIM We performed a randomised trial to assess the efficacy of FMT in patients with IBS. METHODS We randomised 56 patients with diarrhoea-predominant IBS 1:1 to FMT or placebo via the duodenal route at baseline and week 4. The primary outcome was > 50 points decrease in IBS severity scoring system (IBS-SSS) score at week 12. Secondary outcomes were improvement in bloating and change in gut microbiota at week 12. After 12-week follow-up, those in the placebo group were assigned to receive open-label FMT. RESULTS At week 12, 57.1% in the FMT group and 46.4% in the placebo group achieved the primary endpoint (p = 0.42). More patients receiving FMT than placebo had improvement in bloating (72% vs 30%; p = 0.005). In an open-label extension, 65.2% and 82.4% of patients achieved, respectively, the primary endpoint and improvement in bloating. Faecal microbiome of patients in the FMT group showed a reduction in bacteria like Ruminococcus gnavus and enrichment of bacteria such as Lawsonibacter at week 12, while no change in the placebo group. Functional analyses showed that the hydrogen sulphide-producing pathway decreased in patients who had FMT (p < 0.05) accompanied by a reduction in contributing bacteria. There were no serious adverse events related to FMT. CONCLUSION FMT performed twice at an interval of four weeks did not significantly reduce IBS-SSS score. However, more patients had improvement in abdominal bloating, which was associated with a reduction in hydrogen sulphide-producing bacteria. (ClinicalTrials.gov NCT03125564).
Collapse
Affiliation(s)
- Yuk Kam Yau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Joyce Wing Yan Mak
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Matthew Fung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul Kay Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Justin Che Yuen Wu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis Ka Leung Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
5
|
Su Q, Liu Q, Lau RI, Zhang J, Xu Z, Yeoh YK, Leung TWH, Tang W, Zhang L, Liang JQY, Yau YK, Zheng J, Liu C, Zhang M, Cheung CP, Ching JYL, Tun HM, Yu J, Chan FKL, Ng SC. Faecal microbiome-based machine learning for multi-class disease diagnosis. Nat Commun 2022; 13:6818. [PMID: 36357393 PMCID: PMC9649010 DOI: 10.1038/s41467-022-34405-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/21/2022] [Indexed: 11/12/2022] Open
Abstract
Systemic characterisation of the human faecal microbiome provides the opportunity to develop non-invasive approaches in the diagnosis of a major human disease. However, shared microbial signatures across different diseases make accurate diagnosis challenging in single-disease models. Herein, we present a machine-learning multi-class model using faecal metagenomic dataset of 2,320 individuals with nine well-characterised phenotypes, including colorectal cancer, colorectal adenomas, Crohn's disease, ulcerative colitis, irritable bowel syndrome, obesity, cardiovascular disease, post-acute COVID-19 syndrome and healthy individuals. Our processed data covers 325 microbial species derived from 14.3 terabytes of sequence. The trained model achieves an area under the receiver operating characteristic curve (AUROC) of 0.90 to 0.99 (Interquartile range, IQR, 0.91-0.94) in predicting different diseases in the independent test set, with a sensitivity of 0.81 to 0.95 (IQR, 0.87-0.93) at a specificity of 0.76 to 0.98 (IQR 0.83-0.95). Metagenomic analysis from public datasets of 1,597 samples across different populations observes comparable predictions with AUROC of 0.69 to 0.91 (IQR 0.79-0.87). Correlation of the top 50 microbial species with disease phenotypes identifies 363 significant associations (FDR < 0.05). This microbiome-based multi-disease model has potential clinical application in disease diagnostics and treatment response monitoring and warrants further exploration.
Collapse
Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Raphaela Iris Lau
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jingwan Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Thomas W. H. Leung
- grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessie Q. Y. Liang
- grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuk Kam Yau
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jiaying Zheng
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mengjing Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y. L. Ching
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M. Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K. L. Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C. Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China ,grid.10784.3a0000 0004 1937 0482Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
6
|
Liang JQ, Zeng Y, Kwok G, Cheung CP, Suen BY, Ching JYL, To KF, Yu J, Chan FKL, Ng SC. Novel microbiome signatures for non-invasive diagnosis of adenoma recurrence after colonoscopic polypectomy. Aliment Pharmacol Ther 2022; 55:847-855. [PMID: 35224756 PMCID: PMC9303256 DOI: 10.1111/apt.16799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/14/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND We previously reported a panel of novel faecal microbiome gene markers for diagnosis of colorectal adenoma and cancer. AIM To evaluate whether these markers are useful in detecting adenoma recurrence after polypectomy. METHODS Subjects were enrolled in a polyp surveillance study from 2009 to 2019. Stool samples were collected before bowel preparation of index colonoscopy (baseline) and surveillance colonoscopy (follow-up). Fusobacterium nucleatum (Fn), Lachnoclostridium marker (m3), Clostridium hathewayi (Ch) and Bacteroides clarus were quantified in baseline and follow-up samples by quantitative polymerase chain reaction (qPCR) to correlate with adenoma recurrence. Recurrence was defined as new adenomas detected >6 months after polypectomy. Faecal immunochemical test (FIT) was performed for comparison. RESULTS A total of 161 baseline and 104 follow-up samples were analysed. Among patients with adenoma recurrence, Fn and m3 increased (both P < 0.05) while Ch were unchanged in follow-up versus baseline samples. Among patients without recurrence, Fn and m3 were unchanged while Ch decreased (P < 0.05) in follow-up versus baseline samples. Logistic regression that included changes of m3, Fn and Ch at follow-up compared with baseline achieved an area under receiver operating characteristic curve (AUROC) of 0.95 (95%CI: 0.84-0.99) with 90.0% sensitivity and 87.0% specificity for detecting recurrent adenoma. Combination of m3, Fn and Ch at follow-up sample achieved AUROC of 0.74 (95%CI: 0.65-0.82) with 81.3% sensitivity and 55.4% specificity for detecting recurrent adenoma. FIT showed limited sensitivity (8.3%) in detecting recurrent adenomas. CONCLUSION Our combinations of faecal microbiome gene markers can be potentially useful non-invasive tools for detecting adenoma recurrence.
Collapse
Affiliation(s)
- Jessie Qiaoyi Liang
- Department of Microbiology, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Yao Zeng
- Department of Microbiology, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Grace Kwok
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Bing Yee Suen
- Department of SurgeryThe Chinese University of Hong KongHong KongChina
| | - Jessica Y. L. Ching
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Ka Fai To
- Department of Anatomy Chemical PathologyThe Chinese University of Hong KongHong KongChina
| | - Jun Yu
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina
| | - Francis K. L. Chan
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| | - Siew Chien Ng
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Centre for Gut Microbiota Research, Faculty of MedicineThe Chinese University of Hong KongHong KongChina,Institute of Digestive Disease, State Key Laboratory for Digestive Disease, Li Ka Shing Institute of Health Science, CUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina,Microbiota I‐Centre (MagIC) LimitedThe Chinese University of Hong KongHong KongChina
| |
Collapse
|
7
|
Zhang F, Wan Y, Zuo T, Yeoh YK, Liu Q, Zhang L, Zhan H, Lu W, Xu W, Lui GC, Li AY, Cheung CP, Wong CK, Chan PK, Chan FK, Ng SC. Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19. Gastroenterology 2022; 162:548-561.e4. [PMID: 34687739 PMCID: PMC8529231 DOI: 10.1053/j.gastro.2021.10.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/16/2021] [Accepted: 10/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with altered gut microbiota composition. Phylogenetic groups of gut bacteria involved in the metabolism of short chain fatty acids (SCFAs) were depleted in SARS-CoV-2-infected patients. We aimed to characterize a functional profile of the gut microbiome in patients with COVID-19 before and after disease resolution. METHODS We performed shotgun metagenomic sequencing on fecal samples from 66 antibiotics-naïve patients with COVID-19 and 70 non-COVID-19 controls. Serial fecal samples were collected (at up to 6 times points) during hospitalization and beyond 1 month after discharge. We assessed gut microbial pathways in association with disease severity and blood inflammatory markers. We also determined changes of microbial functions in fecal samples before and after disease resolution and validated these functions using targeted analysis of fecal metabolites. RESULTS Compared with non-COVID-19 controls, patients with COVID-19 with severe/critical illness showed significant alterations in gut microbiome functionality (P < .001), characterized by impaired capacity of gut microbiome for SCFA and L-isoleucine biosynthesis and enhanced capacity for urea production. Impaired SCFA and L-isoleucine biosynthesis in gut microbiome persisted beyond 30 days after recovery in patients with COVID-19. Targeted analysis of fecal metabolites showed significantly lower fecal concentrations of SCFAs and L-isoleucine in patients with COVID-19 before and after disease resolution. Lack of SCFA and L-isoleucine biosynthesis significantly correlated with disease severity and increased plasma concentrations of CXCL-10, NT- proB-type natriuretic peptide, and C-reactive protein (all P < .05). CONCLUSIONS Gut microbiome of patients with COVID-19 displayed impaired capacity for SCFA and L-isoleucine biosynthesis that persisted even after disease resolution. These 2 microbial functions correlated with host immune response underscoring the importance of gut microbial functions in SARS-CoV-2 infection pathogenesis and outcome.
Collapse
Affiliation(s)
- Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qin Liu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Lin Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hui Zhan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wenqi Lu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wenye Xu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Grace C.Y. Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Amy Y.L. Li
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chun Kwok Wong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Paul K.S. Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Francis K.L. Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Microbiota I-Center (MagIC), Shatin, Hong Kong, China
| | - Siew C. Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Microbiota I-Center (MagIC), Shatin, Hong Kong, China,Correspondence Address correspondence to: Siew C. Ng, PhD, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, 9/F, Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong
| |
Collapse
|
8
|
Zuo T, Liu Q, Zhang F, Yeoh YK, Wan Y, Zhan H, Lui GCY, Chen Z, Li AYL, Cheung CP, Chen N, Lv W, Ng RWY, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC. Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity. Microbiome 2021; 9:91. [PMID: 33853691 PMCID: PMC8044506 DOI: 10.1186/s40168-021-01008-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need. METHODS We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters. RESULTS Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. CONCLUSIONS Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.
Collapse
Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qin Liu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Hui Zhan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Grace C Y Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zigui Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Amy Y L Li
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wenqi Lv
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Rita W Y Ng
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Eugene Y K Tso
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China
| | - Kitty S C Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Veronica Chan
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Gavin Joynt
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - David S C Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- State Key Laboratory for Digestive disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Microbiota I-Center (MagIC), The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
9
|
Yeoh YK, Zuo T, Lui GCY, Zhang F, Liu Q, Li AYL, Chung ACK, Cheung CP, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chow KM, Ng SSS, Li TCM, Ng RWY, Yip TCF, Wong GLH, Chan FKL, Wong CK, Chan PKS, Ng SC. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut 2021; 70:698-706. [PMID: 33431578 PMCID: PMC7804842 DOI: 10.1136/gutjnl-2020-323020] [Citation(s) in RCA: 667] [Impact Index Per Article: 222.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus. METHODS In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma. RESULTS Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase. CONCLUSION Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.
Collapse
Affiliation(s)
- Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong,Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Grace Chung-Yan Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Qin Liu
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Amy YL Li
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Arthur CK Chung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Eugene YK Tso
- Department of Medicine and Geriatrics, United Christian Hospital, Kwun Tong, Hong Kong
| | - Kitty SC Fung
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong
| | - Veronica Chan
- Department of Medicine and Geriatrics, United Christian Hospital, Kwun Tong, Hong Kong
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Gavin Joynt
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - David Shu-Cheong Hui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kai Ming Chow
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Susanna So Shan Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Timothy Chun-Man Li
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Rita WY Ng
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Terry CF Yip
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Grace Lai-Hung Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Francis KL Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun Kwok Wong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Paul KS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong,Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| |
Collapse
|
10
|
Zhang F, Zuo T, Yeoh YK, Cheng FWT, Liu Q, Tang W, Cheung KCY, Yang K, Cheung CP, Mo CC, Hui M, Chan FKL, Li CK, Chan PKS, Ng SC. Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nat Commun 2021; 12:65. [PMID: 33397897 PMCID: PMC7782528 DOI: 10.1038/s41467-020-20240-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/23/2020] [Indexed: 02/07/2023] Open
Abstract
Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacterial engraftment from FMT donor to recipient has been reported, however the fate of fungi and viruses after FMT remains unclear. Here we report longitudinal dynamics of the gut bacteriome, mycobiome and virome in a teenager with GvHD after receiving four doses of FMT at weekly interval. After serial FMTs, the gut bacteriome, mycobiome and virome of the patient differ from compositions before FMT with variable temporal dynamics. Diversity of the gut bacterial community increases after each FMT. Gut fungal community initially shows expansion of several species followed by a decrease in diversity after multiple FMTs. In contrast, gut virome community varies substantially over time with a stable rise in diversity. The bacterium, Corynebacterium jeikeium, and Torque teno viruses, decrease after FMTs in parallel with an increase in the relative abundance of Caudovirales bacteriophages. Collectively, FMT may simultaneously impact on the various components of the gut microbiome with distinct effects.
Collapse
Affiliation(s)
- Fen Zhang
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Zuo
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Frankie W T Cheng
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Qin Liu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kitty C Y Cheung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Keli Yang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chow Chung Mo
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Mamie Hui
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Kong Li
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Siew C Ng
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
11
|
Sun Y, Zuo T, Cheung CP, Gu W, Wan Y, Zhang F, Chen N, Zhan H, Yeoh YK, Niu J, Du Y, Zhang F, Wen Y, Yu J, Sung JJY, Chan PKS, Chan FKL, Wang K, Ng SC, Miao Y. Population-Level Configurations of Gut Mycobiome Across 6 Ethnicities in Urban and Rural China. Gastroenterology 2021; 160:272-286.e11. [PMID: 32956679 DOI: 10.1053/j.gastro.2020.09.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity, and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association with host factors, environmental factors, and diets. METHODS Using shotgun metagenomic sequencing, we profiled and compared the fecal mycobiome of 942 healthy individuals across different geographic regions in China (Hong Kong and Yunnan), spanning 6 ethnicities: Han, Zang, Bai, Hani, Dai, and Miao (including both urban and rural residents of each ethnicity). In parallel to fecal sampling, we collected participant metadata (environmental exposure, bowel habits, anthropometrics, and medication), diet, and clinical blood measurement results (a total of 118 variables) and investigated their impact on the gut mycobiome variation in humans. RESULTS The human gut mycobiome was highly variable across populations. Urbanization-related factors had the strongest impact on gut mycobiome variation, followed by geography, dietary habit, and ethnicity. The Hong Kong population (highly urbanized) had a significantly lower fungal richness compared with Yunnan population. Saccharomyces cerevisiae was highly enriched in urban compared with rural populations and showed significant inverse correlations with liver pathology-associated blood parameters, including aspartate transaminase, alanine transaminase, gamma-glutamyltransferase, and direct bilirubin. Candida dubliniensis, which was decreased in urban relative to rural populations, showed correlations with host metabolism-related parameters in blood, including a positive correlation with fasting high-density lipoprotein cholesterol levels and a negative correlation with fasting glucose levels. The fungal-blood parameter correlations were highly geography- and ethnicity-specific. Food choices had differential influences on gut mycobiome and bacterial microbiome, where taxa from the same genus tended to be coregulated by food and thereby cobloom. Ethnicity-specific fungal signatures were associated with distinct habitual foods in each ethnic group. CONCLUSIONS Our data highlight, for the first time to our knowledge, that geography, urbanization, ethnicity, and habitual diet play an important role in shaping the gut mycobiome composition. Gut fungal configurations in combination with population characteristics (such as residing region, ethnicity, diet, lifestyle) influence host metabolism and health.
Collapse
Affiliation(s)
- Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Tao Zuo
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenxi Gu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yating Wan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Hui Zhan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Junkun Niu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yan Du
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Fengrui Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yunling Wen
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Jun Yu
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kunhua Wang
- National Health Commission Key Laboratory of Drug Addiction Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan, China.
| | - Siew C Ng
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China.
| |
Collapse
|
12
|
Zuo T, Sun Y, Wan Y, Yeoh YK, Zhang F, Cheung CP, Chen N, Luo J, Wang W, Sung JJY, Chan PKS, Wang K, Chan FKL, Miao Y, Ng SC. Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization. Cell Host Microbe 2020; 28:741-751.e4. [PMID: 32910902 DOI: 10.1016/j.chom.2020.08.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents for each ethnicity. Twenty host factors were found to significantly correlate with the human-gut virome variation, with geography carrying the strongest impact and ethnicity-distinct diets associating with certain viral species. Urbanization enhances interindividual dissimilarities between gut viromes, with the duration of urban residence associating with multiple bacteriophages, including Lactobacillus phage and Lactococcus phage. Overall, the gut virome presents more heterogeneity relative to the bacterial microbiome across the examined Chinese populations. This study highlights population-based variations and the importance of host and environmental factors in shaping the DNA virome in the human gut.
Collapse
Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yang Sun
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Juan Luo
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Wen Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kunhua Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yinglei Miao
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China.
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
13
|
Zuo T, Zhang F, Lui GC, Yeoh YK, Li AY, Zhan H, Wan Y, Chung AC, Cheung CP, Chen N, Lai CK, Chen Z, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chan FK, Chan PK, Ng SC. Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. Gastroenterology 2020; 159:944-955.e8. [PMID: 32442562 PMCID: PMC7237927 DOI: 10.1053/j.gastro.2020.05.048] [Citation(s) in RCA: 896] [Impact Index Per Article: 224.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus. METHODS We performed shotgun metagenomic sequencing analyses of fecal samples from 15 patients with Coronavirus Disease 2019 (COVID-19) in Hong Kong, from February 5 through March 17, 2020. Fecal samples were collected 2 or 3 times per week from time of hospitalization until discharge; disease was categorized as mild (no radiographic evidence of pneumonia), moderate (pneumonia was present), severe (respiratory rate ≥30/min, or oxygen saturation ≤93% when breathing ambient air), or critical (respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care). We compared microbiome data with those from 6 subjects with community-acquired pneumonia and 15 healthy individuals (controls). We assessed gut microbiome profiles in association with disease severity and changes in fecal shedding of SARS-CoV-2. RESULTS Patients with COVID-19 had significant alterations in fecal microbiomes compared with controls, characterized by enrichment of opportunistic pathogens and depletion of beneficial commensals, at time of hospitalization and at all timepoints during hospitalization. Depleted symbionts and gut dysbiosis persisted even after clearance of SARS-CoV-2 (determined from throat swabs) and resolution of respiratory symptoms. The baseline abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity; there was an inverse correlation between abundance of Faecalibacterium prausnitzii (an anti-inflammatory bacterium) and disease severity. Over the course of hospitalization, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate expression of angiotensin-converting enzyme 2 (ACE2) in murine gut, correlated inversely with SARS-CoV-2 load in fecal samples from patients. CONCLUSIONS In a pilot study of 15 patients with COVID-19, we found persistent alterations in the fecal microbiome during the time of hospitalization, compared with controls. Fecal microbiota alterations were associated with fecal levels of SARS-CoV-2 and COVID-19 severity. Strategies to alter the intestinal microbiota might reduce disease severity.
Collapse
Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Grace C.Y. Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Amy Y.L. Li
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hui Zhan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Arthur C.K. Chung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Nan Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Christopher K.C. Lai
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Eugene Y.K. Tso
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China
| | - Kitty S.C. Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Veronica Chan
- Department of Medicine and Geriatrics, United Christian Hospital, Hong Kong, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Gavin Joynt
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - David S.C. Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Francis K.L. Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Paul K.S. Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Paul K.S. Chan, PhD, Department of Microbiology, The Chinese University of Hong Kong, 9/F, Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong. fax: (852) 2647 3227
| | - Siew C. Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China,Correspondence Address correspondence to: Siew C. Ng, PhD, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, 9/F, Lui Che Woo Clinical Sciences Building, Prince of Wales Hospital, Shatin, Hong Kong. fax: (852) 3505 3852
| |
Collapse
|
14
|
Zuo T, Lu XJ, Zhang Y, Cheung CP, Lam S, Zhang F, Tang W, Ching JYL, Zhao R, Chan PKS, Sung JJY, Yu J, Chan FKL, Cao Q, Sheng JQ, Ng SC. Gut mucosal virome alterations in ulcerative colitis. Gut 2019; 68:1169-1179. [PMID: 30842211 PMCID: PMC6582748 DOI: 10.1136/gutjnl-2018-318131] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/04/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The pathogenesis of UC relates to gut microbiota dysbiosis. We postulate that alterations in the viral community populating the intestinal mucosa play an important role in UC pathogenesis. This study aims to characterise the mucosal virome and their functions in health and UC. DESIGN Deep metagenomics sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on the rectal mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76). Virome and bacteriome alterations in UC mucosa were assessed and correlated with patient metadata. We applied partition around medoids clustering algorithm and classified mucosa viral communities into two clusters, referred to as mucosal virome metacommunities 1 and 2. RESULTS In UC, there was an expansion of mucosa viruses, particularly Caudovirales bacteriophages, and a decrease in mucosa Caudovirales diversity, richness and evenness compared with healthy controls. Altered mucosal virome correlated with intestinal inflammation. Interindividual dissimilarity between mucosal viromes was higher in UC than controls. Escherichia phage and Enterobacteria phage were more abundant in the mucosa of UC than controls. Compared with metacommunity 1, metacommunity 2 was predominated by UC subjects and displayed a significant loss of various viral species. Patients with UC showed substantial abrogation of diverse viral functions, whereas multiple viral functions, particularly functions of bacteriophages associated with host bacteria fitness and pathogenicity, were markedly enriched in UC mucosa. Intensive transkingdom correlations between mucosa viruses and bacteria were significantly depleted in UC. CONCLUSION We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis.
Collapse
Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Xiao-Juan Lu
- Department of Gastroenterology, The General Hospital of the People’s Liberation Army, Beijing, China
| | - Yu Zhang
- Faculty of Medicine, Zhejiang University, Hangzhou, China
| | - Chun Pan Cheung
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Siu Lam
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fen Zhang
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Risheng Zhao
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Joseph J Y Sung
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Jun Yu
- State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qian Cao
- Faculty of Medicine, Zhejiang University, Hangzhou, China,Department of Gastroenterology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jian-Qiu Sheng
- Department of Gastroenterology, The General Hospital of the People’s Liberation Army, Beijing, China
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,State Key Laboratory for digestive disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese Univetsity of Hong Kong, Shatin, Hong Kong, China
| |
Collapse
|
15
|
Zuo T, Wong SH, Cheung CP, Lam K, Lui R, Cheung K, Zhang F, Tang W, Ching JYL, Wu JCY, Chan PKS, Sung JJY, Yu J, Chan FKL, Ng SC. Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection. Nat Commun 2018; 9:3663. [PMID: 30202057 PMCID: PMC6131390 DOI: 10.1038/s41467-018-06103-6] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Bacterial colonization in recipients after FMT has been studied, but little is known about the role of the gut fungal community, or mycobiota. Here, we show evidence of gut fungal dysbiosis in CDI, and that donor-derived fungal colonization in recipients is associated with FMT response. CDI is accompanied by over-representation of Candida albicans and decreased fungal diversity, richness, and evenness. Cure after FMT is associated with increased colonization of donor-derived fungal taxa in recipients. Recipients of successful FMT (“responders”) display, after FMT, a high relative abundance of Saccharomyces and Aspergillus, whereas “nonresponders” and individuals treated with antibiotics display a dominant presence of Candida. High abundance of C. albicans in donor stool also correlates with reduced FMT efficacy. Furthermore, C. albicans reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy, supporting a potential causal relationship between gut fungal dysbiosis and FMT outcome. Fecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Here, the authors show that the composition of the gut fungal microbiota of donors and recipients, and especially the abundance of Candida, correlates with FMT outcome in CDI patients.
Collapse
Affiliation(s)
- Tao Zuo
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kelvin Lam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Rashid Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kitty Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Justin C Y Wu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew C Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China. .,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China. .,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
16
|
Abstract
A 69-year-old man presented with multiple spontaneous bruises in the past 2 weeks. Several large-sized hematomas were found on examination. The initial investigation revealed a prolonged activated partial thromboplastin time (aPTT) with normal platelet count and international normalized ratio. Further investigation revealed a low factor VIII activity secondary to presence of factor VIII inhibitor, making the diagnosis of acquired hemophilia A. Further work-up revealed that pernicious anemia was present and acted as an associated disease. After steroids therapy, his aPTT was normalized and the factor VIII inhibitor titer became undetectable. 2 months later, a relapse occurred and new hematomas appeared at his retropharyngeal space and left arm. His bleeding was controlled by administration of recombinant factor VIIa, and a combined therapy of intravenous steroids and rituximab was given to eradicate the inhibitor. The approach to workup of bleeding disorders as well as treatment of acquired hemophilia A are herein discussed.
Collapse
Affiliation(s)
- H Chen
- Department of Medicine, Kingsbrook Jewish Medical Center, Brooklyn, NY, USA
| | | | | | | |
Collapse
|
17
|
Bauerly KA, Storms DH, Harris CB, Hajizadeh S, Sun MY, Cheung CP, Satre MA, Fascetti AJ, Tchaparian E, Rucker RB. Pyrroloquinoline quinone nutritional status alters lysine metabolism and modulates mitochondrial DNA content in the mouse and rat. Biochim Biophys Acta Gen Subj 2006; 1760:1741-8. [PMID: 17029795 DOI: 10.1016/j.bbagen.2006.07.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2005] [Revised: 07/20/2006] [Accepted: 07/20/2006] [Indexed: 11/21/2022]
Abstract
Pyrroloquinoline quinone (PQQ) added to purified diets devoid of PQQ improves indices of perinatal development in rats and mice. Herein, PQQ nutritional status and lysine metabolism are described, prompted by a report that PQQ functions as a vitamin-like enzymatic cofactor important in lysine metabolism (Nature 422 [2003] 832). Alternatively, we propose that PQQ influences lysine metabolism, but by mechanisms that more likely involve changes in mitochondrial content. PQQ deprivation in both rats and mice resulted in a decrease in mitochondrial content. In rats, alpha-aminoadipic acid (alphaAA), which is derived from alpha-aminoadipic semialdehyde (alphaAAS) and made from lysine in mitochondria, and the plasma levels of amino acids known to be oxidized in mitochondria (e.g., Thr, Ser, and Gly) were correlated with changes in the liver mitochondrial content of PQQ-deprived rats, but not PQQ-supplemented rats. In contrast, the levels of NAD dependent alpha-aminoadipate-delta-semialdehyde dehydrogenase (AASDH), a cytosolic enzyme important to alphaAA production from alphaAAS, was not influenced by PQQ dietary status. Moreover, the levels of U26 mRNA were not significantly changed even when diets differed markedly in PQQ and dietary lysine content. U26 mRNA levels were measured, because of U26's proposed, albeit questionable role as a PQQ-dependent enzyme involved in alphaAA formation.
Collapse
Affiliation(s)
- K A Bauerly
- Department of Nutrition, College of Agriculture and Environmental Sciences, 3135 Meyer Hall, One Shields Avenue, UC Davis, Davis CA 95616, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Cheung CP, Yu S, Wong KB, Chan LW, Lai FMM, Wang X, Suetsugi M, Chen S, Chan FL. Expression and functional study of estrogen receptor-related receptors in human prostatic cells and tissues. J Clin Endocrinol Metab 2005; 90:1830-44. [PMID: 15598686 DOI: 10.1210/jc.2004-1421] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Estrogen receptor-related receptors (ERRs; alpha, beta, gamma) are orphan nuclear receptors and constitutively active without binding to estrogen. Like estrogen receptors (ERs), ERRs bind to estrogen receptor elements and estrogen receptor element-related repeats. Growing evidence suggests that ERRs can cross-talk with ERs in different cell types via competition for DNA sites and coactivators. We hypothesize that ERRs might play regulatory roles in normal and neoplastic prostatic cells by sharing similar ER-mediated pathways or acting independently. In this study, we investigated mRNA and protein expression patterns of three ERR members in normal human prostate epithelial cells, established cell lines, cancer xenografts, and prostatic tissues. Additionally, effects of transient transfection of ERRs on prostatic cell proliferation and ER expression were also examined. RT-PCR showed that ERRalpha and ERRgamma transcripts were detected in most cell lines and xenografts, whereas ERRbeta was detected in normal epithelial cells and few immortalized cell lines but not in most cancer lines. Similar results were demonstrated in clinical prostatic specimens. Western blottings and immunohistochemistry confirmed similar expression patterns that ERR proteins were detected as nuclear proteins in epithelial cells, whereas their expressions became reduced or undetected in neoplastic prostatic cells. Transient transfection confirmed that ERRs were expressed in prostatic cells as nuclear proteins and transcriptionally active in the absence of estradiol. Transfection results showed that overexpression of ERRs inhibited cell proliferation and repressed ERalpha transcription in PC-3 cells. Our study shows that ERRs, which are coexpressed with ERs in prostatic cells, could regulate cell growth and modulate ER-mediated pathways via interference on ERalpha transcription in prostatic cells.
Collapse
Affiliation(s)
- C P Cheung
- Department of Anatomy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Cheung CP, Chiu HS, Chung CH. Small bowel perforation after radiotherapy for cervical carcinoma. Hong Kong Med J 2003; 9:461-3. [PMID: 14660815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Radiotherapy is the treatment of choice for carcinoma of the uterine cervix. We report on a 62-year-old Chinese woman with cervical carcinoma, in whom a small bowel perforation developed 5 months after radiotherapy. Ten centimetres of small bowel, including the perforation site, were resected. No bowel adhesion was detected during the operation. The postoperative course was uneventful, and the patient was discharged home 7 days after surgery. Histological examination confirmed post-irradiation injury. The presenting complaints of patients with bowel perforation following radiotherapy vary, and signs of peritonitis may be absent. Emergency physicians must be alert for these complications in patients who have been treated with radiotherapy.
Collapse
Affiliation(s)
- C P Cheung
- Accident and Emergency Department, North District Hospital, 9 Po Kin Road, Sheung Shui, Hong Kong.
| | | | | |
Collapse
|
20
|
Unson CG, Wu CR, Cheung CP, Merrifield RB. Positively charged residues at positions 12, 17, and 18 of glucagon ensure maximum biological potency. J Biol Chem 1998; 273:10308-12. [PMID: 9553084 DOI: 10.1074/jbc.273.17.10308] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucagon is a peptide hormone that plays a central role in the maintenance of normal circulating glucose levels. Structure-activity studies have previously demonstrated the importance of histidine at position 1 and the absolute requirement for aspartic acid at position 9 for transduction of the hormonal signal. Site-directed mutagenesis of the receptor protein identified Asp64 on the extracellular N-terminal tail to be crucial for the recognition function of the receptor. In addition, antibodies generated against aspartic acid-rich epitopes from the extracellular region competed effectively with glucagon for receptor sites, which suggested that negative charges may line the putative glucagon binding pocket in the receptor. These observations led to the idea that positively charged residues on the hormone may act as counterions to these sites. Based on these initial findings, we synthesized glucagon analogs in which basic residues at positions 12, 17, and 18 were replaced with neutral or acidic residues to examine the effect of altering the positive charge on those sites on binding and adenylyl cyclase activity. The results indicate that unlike N-terminal histidine, Lys12, Arg17, and Arg18 of glucagon have very large effects on receptor binding and transduction of the hormonal signal, although they are not absolutely critical. They contribute strongly to the stabilization of the binding interaction with the glucagon receptor that leads to maximum biological potency.
Collapse
Affiliation(s)
- C G Unson
- Rockefeller University, New York, New York 10021, USA
| | | | | | | |
Collapse
|
21
|
Abstract
Patients with primary myelofibrosis (PMF) and myelofibrosis secondary to carcinoma (SMF) were compared with regard to circulating granulocyte macrophage progenitor cells (CFU-GM) using in vitro tissue culture techniques. Although increased numbers of CFU-GM had previously been well documented in PMF, few patients with the secondary variety had been studied. Our data indicate that there is an increase in circulating CFU-GM in patients with SMF but it is significantly lower than in those with PMF. It is suggested that in both conditions disruption of the marrow microvascular system results in a release of CFU-GM to the circulation. In PMF stem cell colonization of the spleen with its consequent myeloid metaplasia may be responsible for the additional increase in CFU-GM. The determination of CFU-GM numbers may provide additional data to help to distinguish PMF and SMF in atypical cases where the distinction is unclear.
Collapse
|
22
|
|
23
|
Plaut GW, Cheung CP, Suhadolnik RJ, Aogaichi T. Cosubstrate and allosteric modifier activities of structural analogues of NAD and ADP for NAD-specific isocitrate dehydrogenase from bovine heart. Biochemistry 1979; 18:3430-8. [PMID: 223632 DOI: 10.1021/bi00582a034] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
24
|
Wu JM, Cheung CP, Bruzel AR, Suhadolnik RJ. The reversal of inhibition of protein synthesis by double-stranded RNA in lysed rabbit reticulocytes with fructose 6-phosphate. Biochem Biophys Res Commun 1979; 86:648-53. [PMID: 426811 DOI: 10.1016/0006-291x(79)91762-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
25
|
Abstract
The cellular content of UDP-glucose in isolated wheat (Triticum aestivum L.) embryo increases 8-fold during the first 40 minutes of imbibition. An additional 3-fold increase in the amount of UDP-glucose was observed in the next 5 hours of germination. This communication also describes a unique, quantitative method to achieve a high sensitivity in a direct determination of UDP-glucose with Na [(32)P]pyrophosphate and UDP-glucose pyrophosphorylase. The sensitivity of the assay for UDP-glucose is 10 picomoles.
Collapse
Affiliation(s)
- C P Cheung
- Department of Biochemistry, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | | |
Collapse
|
26
|
Wu JM, Cheung CP, Suhadolnik RJ. Stimulation of the protein synthetic process by adenosine 3':5'-monophosphate and hexose phosphates in gel-filtered rabbit reticulocyte lysates. J Biol Chem 1978; 253:8578-82. [PMID: 213436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The addition of 0.167 to 4.0 mM cAMP to gel-filtered rabbit reticulocyte lysates stimulates the initial rate and the extent of polypeptide synthesis. The stimulation is at the initiation step of polypeptide synthesis as measured by the (i) increased dipeptide, methionyl-valine, accumulation in the presence of the specific initiation inhibitor, pactamycin, and (ii) increased formation of the 40 S and 80 S initiation complex when gel-filtered lysates are incubated with [35S]Met-tRNAFMet. Furthermore, a synergistic stimulation of protein synthesis is observed when cAMP and hexose phosphates (which alone elicit a 1.8-fold stimulation of protein synthesis) are added simultaneously to gel-filtered rabbit reticulocyte lysates. These results indicate that cAMP and hexose phosphates are both essential to maintain the high rate of initiation.
Collapse
|
27
|
Wu JM, Cheung CP, Suhadolnik RJ. Stimulation and inhibition of the protein synthetic process by NAD+ in lysed rabbit reticulocytes. J Biol Chem 1978; 253:7295-300. [PMID: 212421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
NAD+ at 0.16 mM stimulates the initiation step of the protein synthetic process in lysed rabbit reticulocytes. This conclusion is based on the stimulation of (i) the transfer of formylmethionine from f[35S]Met-tRNAfMet into polypeptide, (ii) the accumulation of the initial dipeptide, methionylvaline, in the presence of pactamycin, and (iii) the formation of the 40 S initiation complex. The effect of NAD+ changes from a stimulatory role on protein synthesis to an inhibitory role at concentrations greater than 0.16 mM. At 4.0 mM NAD+, protein synthesis is inhibited. This has been demonstrated experimentally by using the same three assays described above. In addition, 4.0 mM NAD+ inhibits MettRNAfMet.initiation factor.GTP ternary complex formation. The elongation and termination steps of polypeptide synthesis are not affected by 0.16 to 4.0 mM NAD+. The data presented clearly show that the stimulatory activity of 0.16 mM NAD+ and the inhibitory activity of 4.0 mM NAD+ affects the initiation step of the protein synthetic process in lysed rabbit reticulocytes.
Collapse
|
28
|
Wu JM, Cheung CP, Suhadolnik RJ. Inhibition of protein synthesis by glucose 6-phosphate and fructose 1,6-diphosphate in lysed rabbit reticulocytes and the reversal of inhibition by NAD+. Biochem Biophys Res Commun 1978; 82:921-8. [PMID: 212031 DOI: 10.1016/0006-291x(78)90871-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
29
|
|
30
|
|
31
|
Cheung CP, Suhadolnik RJ. Analysis of glucose 1-phosphate at the picomole level with [14C]UTP and uridine 5'-diphosphoglucose pyrophosphorylase. Anal Biochem 1977; 83:57-60. [PMID: 920952 DOI: 10.1016/0003-2697(77)90509-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
32
|
Wu JM, Cheung CP, Suhadolnik RJ. Differential inhibition with partially purified and endogenous rabbit reticulocyte globin mRNA by 7-methylguanosine 5'-monophosphate. Biochem Biophys Res Commun 1977; 78:1079-86. [PMID: 199189 DOI: 10.1016/0006-291x(77)90531-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
33
|
|
34
|
|
35
|
Cheung CP, Stewart ML, Gupta NK. Protein synthesis in rabbit reticulocytes: evidence for the synthesis of initial dipeptides in the presence of pactamycin. Biochem Biophys Res Commun 1973; 54:1092-101. [PMID: 4753186 DOI: 10.1016/0006-291x(73)90805-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|