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Usyk M, Peters BA, Karthikeyan S, McDonald D, Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, Thyagarajan B, Knight R, Qi Q, Kaplan R, Burk RD. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. Cell Rep Methods 2023; 3:100391. [PMID: 36814836 PMCID: PMC9939430 DOI: 10.1016/j.crmeth.2022.100391] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christopher C. Sollecito
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yoshiki Vazquez-Baeza
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Justin P. Shaffer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marc D. Gellman
- Department of Psychology, University of Miami, Miami, FL, USA
| | - Gregory A. Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L. Daviglus
- Department of Medicine, University of Illinois-Chicago, Chicago, IL, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Departments of Computer Science and Engineering, and Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D. Burk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Microbiology & Immunology, and Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
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Hu T, Zhu Y, Zhu J, Yang M, Wang Y, Zheng Q. Wine-processed radix scutellariae alleviates ARDS by regulating tryptophan metabolism through gut microbiota. Front Pharmacol 2023; 13:1104280. [PMID: 36686672 PMCID: PMC9849372 DOI: 10.3389/fphar.2022.1104280] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is an acute and diffuse pulmonary inflammation, characterized by severe hypoxic respiratory failure caused by inflammatory tissue damage, which is a common cause of respiratory failure. Currently, there is no treatment available that can prevent or reverse the devastating effects caused by these conditions. The purpose of this study was to determine the effects of WRS on gut microbiota and the potential effect of gut microbiota on the treatment of lung disease by using a staphylococcal enterotoxin B (SEB)-induced ARDS model. The results showed that WRS could significantly reduce the pathological damage to lung and colon tissues and improve the lung and intestinal functions of ARDS mice. WRS was able to improve the level of cytokines in serum and lung tissue. Additionally, WRS could reverse the gut microbiota dysbiosis caused by SEB in ARDS mice. WRS increases the production of short-chain fatty acids (SCFAs) in the gut. This increase in SCFAs may lead to increased migration of SCFAs to the lungs and activation of free fatty acid receptors (FFAR) three and FFAR2 in lung epithelial cells, alleviating the symptoms of ARDS. Interestingly, WRS improves the faecal metabolite profiles in SEB-induced ARDS mice via tryptophan metabolism. On the basis of the component-target-metabolism strategy, baicalin, oroxylin A-7-O-glucuronide and skullcapflavon II were identified as the potential bioactive markers in WRS for the treatment of ARDS. Our study showed that WRS could ameliorate SEB-induced ARDS by regulating the structure of gut microbiota, increasing the production of SCFAs and modifying the faecal metabolite profiles through the lung-gut axis, and providing alternative treatment strategies for lung disease.
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Affiliation(s)
- Tingting Hu
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Ying Zhu
- Blood Transfusion Department, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jing Zhu
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Ming Yang
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yaqi Wang
- Jiangxi University of Chinese Medicine, Nanchang, China,*Correspondence: Yaqi Wang,
| | - Qin Zheng
- Jiangxi University of Chinese Medicine, Nanchang, China
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