151
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Guetterman HM, Huey SL, Knight R, Fox AM, Mehta S, Finkelstein JL. Vitamin B-12 and the Gastrointestinal Microbiome: A Systematic Review. Adv Nutr 2021; 13:S2161-8313(22)00075-8. [PMID: 34612492 PMCID: PMC8970816 DOI: 10.1093/advances/nmab123] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Vitamin B-12 deficiency is a major public health problem affecting individuals across the lifespan, with known hematological, neurological, and obstetric consequences. Emerging evidence suggests that vitamin B-12 may have an important role in other aspects of human health, including the composition and function of the gastrointestinal (gut) microbiome. Vitamin B-12 is synthesized and utilized by bacteria in the human gut microbiome and is required for over a dozen enzymes in bacteria, compared to only two in humans. However, the impact of vitamin B-12 on the gut microbiome has not been established. This systematic review was conducted to examine the evidence that links vitamin B-12 and the gut microbiome. A structured search strategy was used to identify in vitro, animal, and human studies that assessed vitamin B-12 status, dietary intake, or supplementation, and the gut microbiome using culture-independent techniques. A total of 22 studies (3 in vitro, 8 animal, 11 human observational studies) were included. Nineteen studies reported vitamin B-12 intake, status, or supplementation was associated with gut microbiome outcomes, including beta-diversity, alpha-diversity, relative abundance of bacteria, functional capacity, or short chain fatty acid production. Evidence suggests vitamin B-12 may be associated with changes in bacterial abundance. While results from in vitro studies suggest vitamin B-12 may increase alpha-diversity and shift gut microbiome composition (beta-diversity), findings from animal studies and observational human studies were heterogeneous. Based on evidence from in vitro and animal studies, microbiome outcomes may differ by cobalamin form and co-intervention. To date, few prospective observational studies and no randomized trials have been conducted to examine the effects of vitamin B-12 on the human gut microbiome. The impact of vitamin B-12 on the gut microbiome needs to be elucidated to inform screening and public health interventions. Statement of significance: Vitamin B-12 is synthesized and utilized by bacteria in the human gut microbiome and is required by over a dozen enzymes in bacteria. However, to date, no systematic reviews have been conducted to evaluate the impact of vitamin B-12 on the gut microbiome, or its implications for human health.
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Affiliation(s)
| | - Samantha L Huey
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Allison M Fox
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Saurabh Mehta
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA,Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medical College, New York, NY, USA,Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, NY, USA
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152
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Dasgupta S, Maricic I, Tang J, Wandro S, Weldon K, Carpenter CS, Eckmann L, Rivera-Nieves J, Sandborn W, Knight R, Dorrestein P, Swafford AD, Kumar V. Class Ib MHC-Mediated Immune Interactions Play a Critical Role in Maintaining Mucosal Homeostasis in the Mammalian Large Intestine. Immunohorizons 2021; 5:953-971. [PMID: 34911745 PMCID: PMC10026853 DOI: 10.4049/immunohorizons.2100090] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022] Open
Abstract
Lymphocytes within the intestinal epithelial layer (IEL) in mammals have unique composition compared with their counterparts in the lamina propria. Little is known about the role of some of the key colonic IEL subsets, such as TCRαβ+CD8+ T cells, in inflammation. We have recently described liver-enriched innate-like TCRαβ+CD8αα regulatory T cells, partly controlled by the non-classical MHC molecule, Qa-1b, that upon adoptive transfer protect from T cell-induced colitis. In this study, we found that TCRαβ+CD8αα T cells are reduced among the colonic IEL during inflammation, and that their activation with an agonistic peptide leads to significant Qa-1b-dependent protection in an acute model of colitis. Cellular expression of Qa-1b during inflammation and corresponding dependency in peptide-mediated protection suggest that Batf3-dependent CD103+CD11b- type 1 conventional dendritic cells control the protective function of TCRαβ+CD8αα T cells in the colonic epithelium. In the colitis model, expression of the potential barrier-protective gene, Muc2, is enhanced upon administration of a Qa-1b agonistic peptide. Notably, in steady state, the mucin metabolizing Akkermansia muciniphila was found in significantly lower abundance amid a dramatic change in overall microbiome and metabolome, increased IL-6 in explant culture, and enhanced sensitivity to dextran sulfate sodium in Qa-1b deficiency. Finally, in patients with inflammatory bowel disease, we found upregulation of HLA-E, a Qa-1b analog with inflammation and biologic non-response, in silico, suggesting the importance of this regulatory mechanism across species.
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Affiliation(s)
- Suryasarathi Dasgupta
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Igor Maricic
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Jay Tang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Lars Eckmann
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Jesus Rivera-Nieves
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - William Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA; and
- Department of Bioengineering, University of California San Diego, La Jolla, CA
| | - Peter Dorrestein
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
| | - Vipin Kumar
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA;
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA
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153
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Wang Z, Usyk M, Vázquez-Baeza Y, Chen GC, Isasi CR, Williams-Nguyen JS, Hua S, McDonald D, Thyagarajan B, Daviglus ML, Cai J, North KE, Wang T, Knight R, Burk RD, Kaplan RC, Qi Q. Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity. Genome Biol 2021; 22:336. [PMID: 34893089 PMCID: PMC8665519 DOI: 10.1186/s13059-021-02559-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 11/23/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos. RESULTS The fecal shotgun metagenomics data indicate that greater US exposure is associated with reduced ɑ-diversity, reduced functions of fiber degradation, and alterations in individual taxa, potentially related to a westernized diet. However, a majority of gut bacterial genera show paradoxical associations, being reduced with US exposure and increased with fiber intake, but increased with obesity. The observed paradoxical associations are not explained by host characteristics or variation in bacterial species but might be related to potential microbial co-occurrence, as seen by positive correlations among Roseburia, Prevotella, Dorea, and Coprococcus. In the conditional analysis with mutual adjustment, including all genera associated with both obesity and US exposure in the same model, the positive associations of Roseburia and Prevotella with obesity did not persist, suggesting that their positive associations with obesity might be due to their co-occurrence and correlations with obesity-related taxa, such as Dorea and Coprococcus. CONCLUSIONS Among US Hispanics/Latinos, US exposure is associated with unfavorable gut microbiome profiles for obesity risk, potentially related to westernized diet during acculturation. Microbial co-occurrence could be an important factor to consider in future studies relating individual gut microbiome taxa to environmental factors and host health and disease.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Mykhaylo Usyk
- Departments of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA USA
- Jacobs School of Engineering, University of California, San Diego, La Jolla, CA USA
| | - Guo-Chong Chen
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | | | - Simin Hua
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | | | | | - Jianwen Cai
- University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Kari E. North
- University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA USA
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154
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Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Maya MC, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Ostrander RT, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. medRxiv 2021. [PMID: 34909793 DOI: 10.1101/2021.03.16.21253743v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
UNLABELLED Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.
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Affiliation(s)
- Victor J Cantú
- These authors contributed equally.,Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- These authors contributed equally.,Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA.,Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Celestine G Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Martin Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,San Diego State University, San Diego, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Christopher A Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tara Shwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Thomas Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
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155
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Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Maya MC, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Ostrander RT, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. medRxiv 2021:2021.12.06.21267101. [PMID: 34909793 PMCID: PMC8669860 DOI: 10.1101/2021.12.06.21267101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.
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Affiliation(s)
- Victor J Cantú
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Celestine G Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Rady Children's Hospital, San Diego, CA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Martin Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- San Diego State University, San Diego, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Christopher A Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tara Shwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Thomas Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
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156
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Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. Clean room microbiome complexity impacts planetary protection bioburden. Microbiome 2021; 9:238. [PMID: 34861887 PMCID: PMC8643001 DOI: 10.1186/s40168-021-01159-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/13/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Spacecraft Assembly Facility (SAF) at the NASA's Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. RESULTS Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. CONCLUSION This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. Video abstract.
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Affiliation(s)
- Ryan Hendrickson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Cameron Martino
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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157
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Batra R, Heinken A, Karu N, Arnold M, Kastenmüller G, Hankemeier T, Bennett DA, Knight R, Krumsiek J, Thiele I, Kaddurah‐Daouk RF. Mapping the human brain metabolome and influences of gut microbiome. Alzheimers Dement 2021. [DOI: 10.1002/alz.056270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Almut Heinken
- National University of Ireland Galway Galway Ireland
| | - Naama Karu
- Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- German Center for Diabetes Research (DZD) Neuherberg Germany
- Duke University Durham NC USA
| | | | | | | | - Rob Knight
- University of California at San Diego San Diego CA USA
| | | | - Ines Thiele
- National University of Ireland Galway Ireland
| | - Rima F. Kaddurah‐Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Duke Institute for Brain Sciences, Duke University Durham NC USA
- Department of Medicine, Duke University Durham NC USA
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158
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Barker K, Room J, Knight R, Dutton S, Toye F, Leal J, Kenealy N, Schussel M, Collins G, Beard D, Price A, Underwood M, Drummond A, Lamb S. Community-based rehabilitation after knee arthroplasty: A randomised controlled trial with economic evaluations (CORKA trial): ISRCTN: 13517704. Physiotherapy 2021. [DOI: 10.1016/j.physio.2021.10.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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159
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Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS. Development of a Rapid and Sensitive CasRx-Based Diagnostic Assay for SARS-CoV-2. ACS Sens 2021; 6:3957-3966. [PMID: 34714054 PMCID: PMC8577378 DOI: 10.1021/acssensors.1c01088] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/14/2021] [Indexed: 12/18/2022]
Abstract
The development of an extensive toolkit for potential point-of-care diagnostics that is expeditiously adaptable to new emerging pathogens is of critical public health importance. Recently, a number of novel CRISPR-based diagnostics have been developed to detect SARS-CoV-2. Herein, we outline the development of an alternative CRISPR nucleic acid diagnostic utilizing a Cas13d ribonuclease derived from Ruminococcus flavefaciens XPD3002 (CasRx) to detect SARS-CoV-2, an approach we term SENSR (sensitive enzymatic nucleic acid sequence reporter) that can detect attomolar concentrations of SARS-CoV-2. We demonstrate 100% sensitivity in patient-derived samples by lateral flow and fluorescence readout with a detection limit of 45 copy/μL. This technology expands the available nucleic acid diagnostic toolkit, which can be adapted to combat future pandemics.
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Affiliation(s)
- Daniel J. Brogan
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Duverney Chaverra-Rodriguez
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Calvin P. Lin
- Department of Chemistry and Biochemistry,
University of California San Diego, La Jolla, California
92092, United States
| | - Andrea L. Smidler
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Lenissa M. Alcantara
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering,
California Institute of Technology, Pasadena, California
91125, United States
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Robyn R. Raban
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of
California San Diego, La Jolla, California 92161, United
States
| | - Rob Knight
- Department of Pediatrics, University of
California San Diego, La Jolla, California 92161, United
States
- Center for Microbiome Innovation,
University of California San Diego, La Jolla, California
92093, United States
- Department of Computer Science and Engineering,
University of California San Diego, La Jolla, California
92093, United States
- Department of Bioengineering, University
of California San Diego, La Jolla, California 92093, United
States
| | - Elizabeth A. Komives
- Department of Chemistry and Biochemistry,
University of California San Diego, La Jolla, California
92092, United States
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and
Developmental Biology, University of California San Diego, La
Jolla, California 92093, United States
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160
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Wu Z, Hullings AG, Ghanbari R, Etemadi A, Wan Y, Zhu B, Poustchi H, Fahraji BB, Sakhvidi MJZ, Shi J, Knight R, Malekzadeh R, Sinha R, Vogtmann E. Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts. BMC Microbiol 2021; 21:324. [PMID: 34809575 PMCID: PMC8607576 DOI: 10.1186/s12866-021-02387-9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. Results We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. Conclusions As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02387-9.
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Affiliation(s)
- Zeni Wu
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Autumn G Hullings
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran
| | - Arash Etemadi
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yunhu Wan
- Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc., Frederick, MD, USA.,Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bin Zhu
- Frederick National Laboratory for Cancer Research/Leidos Biomedical Research Laboratory, Inc., Frederick, MD, USA.,Cancer Genomics Research Laboratory, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran
| | - Behnam Bagheri Fahraji
- Department of Epidemiology, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Javad Zare Sakhvidi
- Department of Occupational Health, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Science, Tehran, Iran.
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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161
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Ferrell M, Bazeley P, Wang Z, Levison BS, Li XS, Jia X, Krauss RM, Knight R, Lusis AJ, Garcia‐Garcia JC, Hazen SL, Tang WHW. Fecal Microbiome Composition Does Not Predict Diet-Induced TMAO Production in Healthy Adults. J Am Heart Assoc 2021; 10:e021934. [PMID: 34713713 PMCID: PMC8751816 DOI: 10.1161/jaha.121.021934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Trimethylamine-N-oxide (TMAO) is a small molecule derived from the metabolism of dietary nutrients by gut microbes and contributes to cardiovascular disease. Plasma TMAO increases following consumption of red meat. This metabolic change is thought to be partly because of the expansion of gut microbes able to use nutrients abundant in red meat. Methods and Results We used data from a randomized crossover study to estimate the degree to which TMAO can be estimated from fecal microbial composition. Healthy participants received a series of 3 diets that differed in protein source (red meat, white meat, and non-meat), and fecal, plasma, and urine samples were collected following 4 weeks of exposure to each diet. TMAO was quantitated in plasma and urine, while shotgun metagenomic sequencing was performed on fecal DNA. While the cai gene cluster was weakly correlated with plasma TMAO (rho=0.17, P=0.0007), elastic net models of TMAO were not improved by abundances of bacterial genes known to contribute to TMAO synthesis. A global analysis of all taxonomic groups, genes, and gene families found no meaningful predictors of TMAO. We postulated that abundances of known genes related to TMAO production do not predict bacterial metabolism, and we measured choline- and carnitine-trimethylamine lyase activity during fecal culture. Trimethylamine lyase genes were only weakly correlated with the activity of the enzymes they encode. Conclusions Fecal microbiome composition does not predict systemic TMAO because, in this case, gene copy number does not predict bacterial metabolic activity. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT01427855.
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Affiliation(s)
- Marc Ferrell
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
- Department of Systems Biology and BioinformaticsCase Western Reserve UniversityClevelandOH
| | - Peter Bazeley
- Department of Quantitative Health SciencesLerner Research InstituteCleveland ClinicClevelandOH
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
| | - Bruce S. Levison
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
| | - Xinmin S. Li
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
| | - Xun Jia
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
| | | | - Rob Knight
- Department of PediatricsDepartment of Computer Science and EngineeringDepartment of Bioengineering, and The Center for Microbiome InnovationUniversity of California, San DiegoLa JollaCA
| | - Aldons J. Lusis
- Departments of Human Genetics and MedicineDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCA
| | - J. C. Garcia‐Garcia
- Life Sciences Transformative Platform TechnologiesProcter & GambleCincinnatiOH
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
- Department of Cardiovascular MedicineHeart, Vascular and Thoracic Institute, Cleveland ClinicClevelandOH
| | - W. H. Wilson Tang
- Department of Cardiovascular and Metabolic SciencesLerner Research InstituteCleveland ClinicClevelandOH
- Department of Cardiovascular MedicineHeart, Vascular and Thoracic Institute, Cleveland ClinicClevelandOH
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162
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Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck KL, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R. Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. Genome Res 2021; 31:2131-2137. [PMID: 34479875 PMCID: PMC8559715 DOI: 10.1101/gr.275777.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/01/2021] [Indexed: 02/01/2023]
Abstract
The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.
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Affiliation(s)
- George Armstrong
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, California 92093, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10562, USA
| | | | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85281, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
| | - Imran McGrath
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Kristen L Beck
- IBM Almaden Research Center, San Jose, California 95120, USA
| | - Daniel Hakim
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, California 92093, USA
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki 00271, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki 00271, Finland
- Department of Internal Medicine, University of Turku, Turku 20014, Finland
- Division of Medicine, Turku University Hospital, Turku 20014, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku 20014, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mohit Jain
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California, San Diego, California 92093, USA
- Department of Pharmacology, University of California, San Diego, California 92093, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- Department of Public Health and Primary Care, Cambridge University, Cambridge CB2 1TN, United Kingdom
| | - Austin D Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Ho-Cheol Kim
- IBM Almaden Research Center, San Jose, California 95120, USA
| | - Laxmi Parida
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10562, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, California 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
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163
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Dokoshi T, Seidman JS, Cavagnero KJ, Li F, Liggins MC, Taylor BC, Olvera J, Knight R, Chang JT, Salzman NH, Gallo RL. Skin inflammation activates intestinal stromal fibroblasts and promotes colitis. J Clin Invest 2021; 131:147614. [PMID: 34720087 DOI: 10.1172/jci147614] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 01/12/2021] [Accepted: 09/16/2021] [Indexed: 01/01/2023] Open
Abstract
Inflammatory disorders of the skin are frequently associated with inflammatory bowel diseases (IBDs). To explore mechanisms by which these organs communicate, we performed single-cell RNA-Seq analysis on fibroblasts from humans and mice with IBD. This analysis revealed that intestinal inflammation promoted differentiation of a subset of intestinal stromal fibroblasts into preadipocytes with innate antimicrobial host defense activity. Furthermore, this process of reactive adipogenesis was exacerbated if mouse skin was inflamed as a result of skin wounding or infection. Since hyaluronan (HA) catabolism is activated during skin injury and fibroblast-to-adipocyte differentiation is dependent on HA, we tested the hypothesis that HA fragments could alter colon fibroblast function by targeted expression of human hyaluronidase-1 in basal keratinocytes from mouse skin. Hyaluronidase expression in the skin activated intestinal stromal fibroblasts, altered the fecal microbiome, and promoted excessive reactive adipogenesis and increased inflammation in the colon after challenge with dextran sodium sulfate. The response to digested HA was dependent on expression of TLR4 by preadipocytes. Collectively, these results suggest that the association between skin inflammation and IBD may be due to recognition by mesenchymal fibroblasts in the colon of HA released during inflammation of the skin.
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Affiliation(s)
| | | | | | | | | | | | | | - Rob Knight
- Department of Pediatrics, UCSD, La Jolla, California, USA
| | | | - Nita H Salzman
- Departments of Pediatrics, Microbiology, and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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164
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Armstrong G, Martino C, Rahman G, Gonzalez A, Vázquez-Baeza Y, Mishne G, Knight R. Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data. mSystems 2021; 6:e0069121. [PMID: 34609167 PMCID: PMC8547469 DOI: 10.1128/msystems.00691-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/19/2021] [Indexed: 11/29/2022] Open
Abstract
Microbiome data are sparse and high dimensional, so effective visualization of these data requires dimensionality reduction. To date, the most commonly used method for dimensionality reduction in the microbiome is calculation of between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold Approximation and Projection (UMAP) is an alternative method that can reduce the dimensionality of beta diversity distance matrices. Here, we demonstrate the benefits and limitations of using UMAP for dimensionality reduction on microbiome data. Using real data, we demonstrate that UMAP can improve the representation of clusters, especially when the clusters are composed of multiple subgroups. Additionally, we show that UMAP provides improved correlation of biological variation along a gradient with a reduced number of coordinates of the resulting embedding. Finally, we provide parameter recommendations that emphasize the preservation of global geometry. We therefore conclude that UMAP should be routinely used as a complementary visualization method for microbiome beta diversity studies. IMPORTANCE UMAP provides an additional method to visualize microbiome data. The method is extensible to any beta diversity metric used with PCoA, and our results demonstrate that UMAP can indeed improve visualization quality and correspondence with biological and technical variables of interest. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/knightlab-analyses/umap-microbiome-benchmarking; additionally, we have provided a QIIME 2 plugin for UMAP at https://github.com/biocore/q2-umap.
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Affiliation(s)
- George Armstrong
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, California, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, California, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, California, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Gal Mishne
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
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Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr 2021; 115:432-443. [PMID: 34617562 PMCID: PMC8827078 DOI: 10.1093/ajcn/nqab332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Individual diet components and specific dietary regimens have been shown to impact the gut microbiome. OBJECTIVES Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort. METHODS Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants. RESULTS Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P ≤ 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P ≤ 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P ≤ 1.2 × 10-7), which was better explained by diet than health status. CONCLUSIONS We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.
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Affiliation(s)
| | | | - Nicole S Litwin
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | - Diana Gutierrez Lopez
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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166
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Sepich-Poore G, Fraraccio S, Wandro S, Miller-Montgomery S, Knight R, Adams E. FP05.04 Robust Discrimination of Lung Cancer via Microbial DNA Detection and Machine Learning Classification. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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167
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Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J 2021; 15:3005-3018. [PMID: 33953361 PMCID: PMC8443620 DOI: 10.1038/s41396-021-00935-9] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/07/2021] [Accepted: 02/10/2021] [Indexed: 02/03/2023]
Abstract
Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood-Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b-3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Peng-Fei Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, PR China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, PR China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Areas, Chengdu, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China.
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168
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Kosciolek T, Victor TA, Kuplicki R, Rossi M, Estaki M, Ackermann G, Knight R, Paulus MP. Individuals with substance use disorders have a distinct oral microbiome pattern. Brain Behav Immun Health 2021; 15:100271. [PMID: 34589776 PMCID: PMC8474247 DOI: 10.1016/j.bbih.2021.100271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/22/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022] Open
Abstract
Background Substance use disorder emerges from a complex interaction between genetic predisposition, life experiences, exposure, and subsequent adaptation of biological systems to the repeated use of drugs. Recently, investigators have proposed that the human microbiota may play a role in brain health and disease. In particular, the human oral microbiome is a distinct and diverse ecological niche with its composition influenced by external factors such as lifestyle, diet, and oral hygiene. This investigation examined whether individuals with substance use disorder (SU) show a different oral microbiome pattern and whether this pattern is sufficient to delineate the SU group from healthy comparison (HC) subjects. Methods Participants were a sub-sample (N = 177) of the Tulsa 1000 (T-1000) project. We analyzed 123 SU and 54 HC subjects using 16S rRNA marker gene sequencing to characterize the oral microbiome. Results The groups differed significantly based on the UniFrac distance, a phylogenetic-based measure of beta diversity, but did not differ in alpha diversity. Using a machine learning approach, microbiome features combined with socio-demographic variables successfully categorized group membership with 87%–92% accuracy, even after controlling for external factors such as smoking or alcohol consumption. SU individuals with relatively lower diversity also reported higher levels of negative reinforcement experiences associated with their primary substance of abuse. Conclusions Oral microbiome features are useful to sufficiently differentiate SU from HC subjects. There is some evidence that subjects whose drug use is driven by negative reinforcement show an impoverished oral microbiome. Taken together, the oral microbiome may help to understand the dysfunctional biological processes that promote substance use or may be pragmatically useful as a risk or severity biological marker. Oral microbiome features differentiate substance use disorder and healthy subjects. Machine learning with microbiome and socio-demographic variables categorizes groups. Substance use individuals have lower microbiome diversity. Substance use individuals have higher levels of negative reinforcement. Oral microbiome may be useful as a risk or severity biological marker.
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Affiliation(s)
- Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | | | - Maret Rossi
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, CA, USA.,Department of Bioengineering, University of California San Diego, CA, USA
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169
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Thompson RS, Gaffney M, Hopkins S, Kelley T, Gonzalez A, Bowers SJ, Vitaterna MH, Turek FW, Foxx CL, Lowry CA, Vargas F, Dorrestein PC, Wright KP, Knight R, Fleshner M. Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms. Brain Behav Immun 2021; 97:150-166. [PMID: 34242738 DOI: 10.1016/j.bbi.2021.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 02/24/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.
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Affiliation(s)
- Robert S Thompson
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA.
| | - Michelle Gaffney
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Shelby Hopkins
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Tel Kelley
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Samuel J Bowers
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Martha Hotz Vitaterna
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Fred W Turek
- Department of Neurobiology, Northwestern University, Center for Sleep and Circadian Biology, Evanston, IL, USA
| | - Christine L Foxx
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO, USA; Center for Neuroscience, University of Colorado at Boulder, Boulder, CO, USA.
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170
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Ellis RJ, Iudicello JE, Heaton RK, Isnard S, Lin J, Routy JP, Gianella S, Hoenigl M, Knight R. Markers of Gut Barrier Function and Microbial Translocation Associate with Lower Gut Microbial Diversity in People with HIV. Viruses 2021; 13:1891. [PMID: 34696320 PMCID: PMC8537977 DOI: 10.3390/v13101891] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 12/14/2022] Open
Abstract
People with human immunodeficiency virus (HIV) (PWH) have reduced gut barrier integrity ("leaky gut") that permits diffusion of microbial antigens (microbial translocation) such as lipopolysaccharide (LPS) into the circulation, stimulating inflammation. A potential source of this disturbance, in addition to gut lymphoid tissue CD4+ T-cell depletion, is the interaction between the gut barrier and gut microbes themselves. We evaluated the relationship of gut barrier integrity, as indexed by plasma occludin levels (higher levels corresponding to greater loss of occludin from the gut barrier), to gut microbial diversity. PWH and people without HIV (PWoH) participants were recruited from community sources and provided stool, and 16S rRNA amplicon sequencing was used to characterize the gut microbiome. Microbial diversity was indexed by Faith's phylogenetic diversity (PD). Participants were 50 PWH and 52 PWoH individuals, mean ± SD age 45.6 ± 14.5 years, 28 (27.5%) women, 50 (49.0%) non-white race/ethnicity. PWH had higher gut microbial diversity (Faith's PD 14.2 ± 4.06 versus 11.7 ± 3.27; p = 0.0007), but occludin levels were not different (1.84 ± 0.311 versus 1.85 ± 0.274; p = 0.843). Lower gut microbial diversity was associated with higher plasma occludin levels in PWH (r = -0.251; p = 0.0111), but not in PWoH. A multivariable model demonstrated an interaction (p = 0.0459) such that the correlation between Faith's PD and plasma occludin held only for PWH (r = -0.434; p = 0.0017), but not for PWoH individuals (r = -0.0227; p = 0.873). The pattern was similar for Shannon alpha diversity. Antiretroviral treatment and viral suppression status were not associated with gut microbial diversity (ps > 0.10). Plasma occludin levels were not significantly related to age, sex or ethnicity, nor to current or nadir CD4 or plasma viral load. Higher occludin levels were associated with higher plasma sCD14 and LPS, both markers of microbial translocation. Together, the findings suggest that damage to the gut epithelial barrier is an important mediator of microbial translocation and inflammation in PWH, and that reduced gut microbiome diversity may have an important role.
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Affiliation(s)
- Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, University of California, San Diego, CA 92093, USA
| | - Jennifer E. Iudicello
- Department of Psychiatry, University of California, San Diego, CA 92093, USA; (J.E.I.); (R.K.H.)
| | - Robert K. Heaton
- Department of Psychiatry, University of California, San Diego, CA 92093, USA; (J.E.I.); (R.K.H.)
| | - Stéphane Isnard
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - John Lin
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - Jean-Pierre Routy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; (S.I.); (J.L.); (J.-P.R.)
| | - Sara Gianella
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.G.); (M.H.)
| | - Martin Hoenigl
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.G.); (M.H.)
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
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171
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Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms 2021; 9:2003. [PMID: 34683324 PMCID: PMC8541168 DOI: 10.3390/microorganisms9102003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.
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Affiliation(s)
- Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rena Yadlapati
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
| | - Shailja Shah
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
- Veterans Affairs, San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
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Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell 2021; 184:4939-4952.e15. [PMID: 34508652 PMCID: PMC8313480 DOI: 10.1016/j.cell.2021.07.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
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Affiliation(s)
- Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allison R Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John A Vanchiere
- Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA
| | | | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maximilian Marshall
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Amy K Feehan
- Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Rona S Scott
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Arnaud C Drouin
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kaylynn J Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Sarah Topol
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura Nicholson
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | | | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada
| | - Dahlene N Fusco
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.
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173
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Jing G, Zhang Y, Liu L, Wang Z, Sun Z, Knight R, Su X, Xu J. A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity. mSystems 2021; 6:e0039421. [PMID: 34254819 PMCID: PMC8407412 DOI: 10.1128/msystems.00394-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here, we propose as a solution a search-based microbiome transition network. By traversing a composition-similarity-based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiomes at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes. IMPORTANCE It remains unclear whether and how compositional changes at the "community to community" level among microbiomes are linked to the origin and evolution of global microbiome diversity. Here we propose a microbiome transition model and a network-based analysis framework to describe and simulate the variation and dispersal of the global microbial beta-diversity across multiple habitats. The traversal of a transition network with 177,022 samples shows the inherent homology of microbiome at the global scale. Then a global roadmap of microbiome dispersal derived from the network tracks the potential paths of formulating and propagating microbiome diversity. Such search-based microbiome network provides a readily expanded reference for tracing the origin and evolution of existing or new microbiomes at the global scale.
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Affiliation(s)
- Gongchao Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Lu Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- University of California, San Diego, California, USA
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
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174
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Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere 2021; 6:e0045521. [PMID: 34259562 PMCID: PMC8386422 DOI: 10.1128/msphere.00455-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bones of decomposing vertebrates are colonized by a succession of diverse microbial communities. If this succession is similar across individuals, microbes may provide clues about the postmortem interval (PMI) during forensic investigations in which human skeletal remains are discovered. Here, we characterize the human bone microbial decomposer community to determine whether microbial succession is a marker for PMI. Six human donor subjects were placed outdoors to decompose on the soil surface at the Southeast Texas Applied Forensic Science facility. To also assess the effect of seasons, three decedents were placed each in the spring and summer. Once ribs were exposed through natural decomposition, a rib was collected from each body for eight time points at 3 weeks apart. We discovered a core bone decomposer microbiome dominated by taxa in the phylum Proteobacteria and evidence that these bone-invading microbes are likely sourced from the surrounding decomposition environment, including skin of the cadaver and soils. Additionally, we found significant overall differences in bone microbial community composition between seasons. Finally, we used the microbial community data to develop random forest models that predict PMI with an accuracy of approximately ±34 days over a 1- to 9-month time frame of decomposition. Typically, anthropologists provide PMI estimates based on qualitative information, giving PMI errors ranging from several months to years. Previous work has focused on only the characterization of the bone microbiome decomposer community, and this is the first known data-driven, quantitative PMI estimate of terrestrially decomposed human skeletal remains using microbial abundance information. IMPORTANCE Microbes are known to facilitate vertebrate decomposition, and they can do so in a repeatable, predictable manner. The succession of microbes in the skin and associated soil can be used to predict time since death during the first few weeks of decomposition. However, when remains are discovered after months or years, often the only evidence are skeletal remains. To determine if microbial succession in bone would be useful for estimating time since death after several months, human subjects were placed to decompose in the spring and summer seasons. Ribs were collected after 1 to 9 months of decomposition, and the bone microbial communities were characterized. Analysis revealed a core bone decomposer microbial community with some differences in microbial assembly occurring between seasons. These data provided time since death estimates of approximately ±34 days over 9 months. This may provide forensic investigators with a tool for estimating time since death of skeletal remains, for which there are few current methods.
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Affiliation(s)
- Heather Deel
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra L. Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer Kiely
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | | | - David O. Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, USA
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, Hawaii, USA
| | - Aaron Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Jessica L. Metcalf
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
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175
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Koponen KK, Salosensaari A, Ruuskanen MO, Havulinna AS, Männistö S, Jousilahti P, Palmu J, Salido R, Sanders K, Brennan C, Humphrey GC, Sanders JG, Meric G, Cheng S, Inouye M, Jain M, Niiranen TJ, Valsta LM, Knight R, Salomaa VV. Associations of healthy food choices with gut microbiota profiles. Am J Clin Nutr 2021; 114:605-616. [PMID: 34020448 PMCID: PMC8326043 DOI: 10.1093/ajcn/nqab077] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant. OBJECTIVES To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential. METHODS This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models. RESULTS Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system. CONCLUSIONS Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.
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Affiliation(s)
- Kari K Koponen
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aaro Salosensaari
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Turku, Finland
- Department of Future Technologies, University of Turku, Turku, Finland
| | - Matti O Ruuskanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Satu Männistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Joonatan Palmu
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Turku, Finland
- Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Rodolfo Salido
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Cornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, NY, USA
| | - Guillaume Meric
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Teemu J Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Turku, Finland
- Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Liisa M Valsta
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Veikko V Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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176
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Abstract
The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: (a) Can diet modify the composition, diversity, or function of the gut microbiome, and (b) will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York 14853, USA; .,Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Samantha L Huey
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Daniel McDonald
- Center for Microbiome Innovation and Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation and Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Departments of Bioengineering and Computer Science & Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Julia L Finkelstein
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York 14853, USA; .,Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
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177
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Salido RA, Cantú VJ, Clark AE, Leibel SL, Foroughishafiei A, Saha A, Hakim A, Nouri A, Lastrella AL, Castro-Martínez A, Plascencia A, Kapadia B, Xia B, Ruiz C, Marotz CA, Maunder D, Lawrence ES, Smoot EW, Eisner E, Crescini ES, Kohn L, Vargas LF, Chacón M, Betty M, Machnicki M, Wu MY, Baer NA, Belda-Ferre P, Hoff PD, Seaver P, Ostrander RT, Tsai R, Sathe S, Aigner S, Morgan SC, Ngo TT, Barber T, Cheung W, Carlin AF, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. bioRxiv 2021:2021.07.16.452756. [PMID: 34312621 PMCID: PMC8312891 DOI: 10.1101/2021.07.16.452756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods.
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Affiliation(s)
- Rodolfo A Salido
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor J Cantú
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Anahid Foroughishafiei
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anushka Saha
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Bhavika Kapadia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Bing Xia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Christopher Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Clarisse A Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Daniel Maunder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Lizbeth Franco Vargas
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Rady Children's Hospital, San Diego, CA
| | - Michal Machnicki
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Min Yi Wu
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- San Diego State University, San Diego, CA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine; University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
- Co-corresponding authors
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Co-corresponding authors
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Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. ACTA ACUST UNITED AC 2021; 70:e100. [PMID: 32343490 PMCID: PMC9285460 DOI: 10.1002/cpbi.100] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
QIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐based platform, to re‐use available data for meta‐analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug‐ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta‐analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses
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Affiliation(s)
- Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Lingjing Jiang
- Division of Biostatistics, University of California San Diego, La Jolla, California
| | - Nicholas A Bokulich
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona.,Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California.,Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California.,Jacobs School of Engineering, University of California San Diego, La Jolla, California
| | - Matthew R Dillon
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona.,Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California.,Department of Bioengineering, University of California San Diego, La Jolla, California
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179
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Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J. Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome. Microbiome 2021; 9:151. [PMID: 34193290 PMCID: PMC8247228 DOI: 10.1186/s40168-021-01102-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/24/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods. RESULTS We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10-70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice. CONCLUSIONS Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans. Video abstract.
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Affiliation(s)
- Shi Huang
- School of Food Science and Engineering, Hainan University, Haikou, China
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Shuaiming Jiang
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Dongxue Huo
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Celeste Allaband
- Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Mehrbod Estaki
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Victor Cantu
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Pedro Belda-Ferre
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yoshiki Vázquez-Baeza
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Qiyun Zhu
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chenchen Ma
- School of Food Science and Engineering, Hainan University, Haikou, China
| | - Congfa Li
- School of Food Science and Engineering, Hainan University, Haikou, China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China
| | - Amir Zarrinpar
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- UCSD Division of Gastroenterology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- VA San Diego Healthcare, 3350 La Jolla Village Dr, San Diego, CA, 92161, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Rob Knight
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Biomedical Sciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Jiachao Zhang
- School of Food Science and Engineering, Hainan University, Haikou, China.
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China.
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180
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Allaband C, Lingaraju A, Martino C, Russell B, Tripathi A, Poulsen O, Dantas Machado AC, Zhou D, Xue J, Elijah E, Malhotra A, Dorrestein PC, Knight R, Haddad GG, Zarrinpar A. Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome. mSystems 2021; 6:e0011621. [PMID: 34184915 PMCID: PMC8269208 DOI: 10.1128/msystems.00116-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
Obstructive sleep apnea (OSA), characterized by intermittent hypoxia and hypercapnia (IHC), affects the composition of the gut microbiome and metabolome. The gut microbiome has diurnal oscillations that play a crucial role in regulating circadian and overall metabolic homeostasis. Thus, we hypothesized that IHC adversely alters the gut luminal dynamics of key microbial families and metabolites. The objective of this study was to determine the diurnal dynamics of the fecal microbiome and metabolome of Apoe-/- mice after a week of IHC exposure. Individually housed, 10-week-old Apoe-/- mice on an atherogenic diet were split into two groups. One group was exposed to daily IHC conditions for 10 h (Zeitgeber time 2 [ZT2] to ZT12), while the other was maintained in room air. Six days after the initiation of the IHC conditions, fecal samples were collected every 4 h for 24 h (6 time points). We performed 16S rRNA gene amplicon sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in the microbiome and metabolome. IHC induced global changes in the cyclical dynamics of the gut microbiome and metabolome. Ruminococcaceae, Lachnospiraceae, S24-7, and Verrucomicrobiaceae had the greatest shifts in their diurnal oscillations. In the metabolome, bile acids, glycerolipids (phosphocholines and phosphoethanolamines), and acylcarnitines were greatly affected. Multi-omic analysis of these results demonstrated that Ruminococcaceae and tauro-β-muricholic acid (TβMCA) cooccur and are associated with IHC conditions and that Coriobacteriaceae and chenodeoxycholic acid (CDCA) cooccur and are associated with control conditions. IHC significantly change the diurnal dynamics of the fecal microbiome and metabolome, increasing members and metabolites that are proinflammatory and proatherogenic while decreasing protective ones. IMPORTANCE People with obstructive sleep apnea are at a higher risk of high blood pressure, type 2 diabetes, cardiac arrhythmias, stroke, and sudden cardiac death. We wanted to understand whether the gut microbiome changes induced by obstructive sleep apnea could potentially explain some of these medical problems. By collecting stool from a mouse model of this disease at multiple time points during the day, we studied how obstructive sleep apnea changed the day-night patterns of microbes and metabolites of the gut. Since the oscillations of the gut microbiome play a crucial role in regulating metabolism, changes in these oscillations can explain why these patients can develop so many metabolic problems. We found changes in microbial families and metabolites that regulate many metabolic pathways contributing to the increased risk for heart disease seen in patients with obstructive sleep apnea.
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Affiliation(s)
- Celeste Allaband
- Division of Gastroenterology, University of California, San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, California, USA
| | - Cameron Martino
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Baylee Russell
- Division of Gastroenterology, University of California, San Diego, La Jolla, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - Orit Poulsen
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | | | - Dan Zhou
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Jin Xue
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Emmanuel Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - Atul Malhotra
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Gabriel G. Haddad
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Neuroscience, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
- VA Health Sciences San Diego, La Jolla, California, USA
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181
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome 2021; 9:132. [PMID: 34103074 PMCID: PMC8186369 DOI: 10.1186/s40168-021-01083-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. METHODS We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. RESULTS Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. CONCLUSIONS These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mac Kenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | | | - Laxmi Parida
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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182
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Cotillard A, Chaumont S, Saccareau M, Litwin NS, Lopez DG, Tap J, Lejzerowicz F, Demaretz L, McDonald D, Song SJ, Knight R, Cartier-Meheust A, Veiga P. Unsupervised Diet Partitions Better Explain Variations of the Gut Microbiome Compared to Individual Dietary Markers in U.S. Adults of the American Gut Project Cohort. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab038_009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
Eating habits have been shown to impact the gut microbiome. Here we aimed to define several types of dietary patterns in a U.S. adult cohort and test their associations with the gut microbiome.
Methods
Using supervised and unsupervised approaches, we built dietary patterns based on a food frequency questionnaire of the American Gut Project database. Focusing on 1800 adult participants living in the United States, we defined patterns as partitions (groups of participants) or factors (combinations of food variables) driven by specific dietary criteria: fibers, proteins, Healthy Eating Index (HEI 2010), food items, food groups and micronutrients. We then associated these patterns with 16S gut microbiome data for 744 participants, excluding those reporting antibiotic intake in the last year or specific diseases. Analyses were adjusted for age, sex and BMI.
Results
Compared to individual features like fibers and proteins, or to factors representing reduced numbers of features, five unsupervised partitions based on food groups were best associated with gut microbiome beta-diversity. Two partitions presented a lower consumption of animal products, with one being almost completely exclusive and the other, close to a flexitarian diet, presenting the best diet quality as measured by HEI. A third one consisted mostly of participants under low carbohydrate diets with nearly no consumption of starchy foods or sweet products. Finally, the last two partitions presented Western-like diets with increased consumption of mixed dishes, sweet products and refined cereals, one of them being more diverse with increased nuts and whole cereals. Gut microbiome alpha-diversity was slightly increased in the flexitarian partition compared to the most westernized one. Strikingly, the low carbohydrate partition was associated with low levels of the Bifidobacterium genus.
Conclusions
We showed in a U.S. adult cohort that a global diet may be more associated with gut microbiome variations than individual features like fibers or proteins. Five diet partitions were identified and their specific associations with gut microbiome were studied. These results confirm the importance to consider diet as a whole when studying gut microbiota diversity.
Funding Sources
Danone Research.
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Affiliation(s)
| | | | | | - Nicole S Litwin
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine - University of California San Diego
| | - Se Jin Song
- Center for Microbiome Innovation - University of California San Diego
| | - Rob Knight
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine & Department of Bioengineering & Department of Computer Science and Engineering & Scripps Institution of Oceanography - University of California San Diego
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183
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Sinha R, Zhao N, Goedert JJ, Byrd DA, Wan Y, Hua X, Hullings AG, Knight R, Breda SV, Mathijs K, de Kok TM, Ward MH. Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study. Environ Res 2021; 197:111084. [PMID: 33785324 PMCID: PMC8388086 DOI: 10.1016/j.envres.2021.111084] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND One mechanism that can explain the link between processed meat consumption and colorectal cancer (CRC) is the production of carcinogenic N-nitroso compounds (NOCs) in the gastrointestinal tract. Oral and gut microbes metabolize ingested proteins (a source of secondary and tertiary amines and amides) and can reduce nitrate to nitrite, generating potentially carcinogenic NOCs. OBJECTIVE We evaluated whether nitrate/nitrite in processed meat or water influences the fecal or salivary microbiota. DESIGN In this dietary intervention study, 63 volunteers consumed diets high in conventional processed meats for two weeks, switched to diets high in poultry for two weeks, and then consumed phytochemical-enriched conventional processed or low-nitrite processed meat diets for two weeks. During the intervention, they drank water with low nitrate concentrations and consumed a healthy diet with low antioxidants. Then the volunteers drank nitrate-enriched water for 1 week, in combination with one of the four different diets. We measured creatinine-adjusted urinary nitrate levels and characterized the oral and fecal microbiota using 16S rRNA amplicon sequencing. RESULTS Using linear mixed models, we found that, compared to baseline, urinary nitrate levels were reduced during the phytochemical-enriched low-nitrite meat diet (p-value = 0.009) and modestly during the poultry diet (p-value = 0.048). In contrast, urinary nitrate increased after 1-week of drinking nitrate-enriched water (p-value<10-5). Nitrate-enriched water, but not processed meats with or without phytochemicals, altered the saliva microbial population (p-value ≤0.001), and significantly increased abundance of 8 bacterial taxa, especially genus Neisseria and other nitrate-reducing taxa. Meats, phytochemicals and nitrate-enriched water had no significant effects on saliva alpha diversity or any diversity parameter measured for the fecal microbiota. CONCLUSION These findings support the hypothesis that drinking high nitrate water increases oral nitrate-reducing bacteria, which likely results in increased NOC. However, meat nitrate/nitrite at the levels tested had no effect on either the gut or oral bacteria. CLINICALTRIALS. GOV IDENTIFIER NCT04138654.
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Affiliation(s)
- Rashmi Sinha
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ni Zhao
- Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University Baltimore, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Doratha A Byrd
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yunhu Wan
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Autumn G Hullings
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rob Knight
- Departments of Pediatrics, Bioengineering, and Computer Science & Engineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Simone van Breda
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O Box 616, 6200, MD, Maastricht, the Netherlands
| | - Karen Mathijs
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O Box 616, 6200, MD, Maastricht, the Netherlands
| | - Theo M de Kok
- Department of Toxicogenomics, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, P.O Box 616, 6200, MD, Maastricht, the Netherlands
| | - Mary H Ward
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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184
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Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY. Challenges in benchmarking metagenomic profilers. Nat Methods 2021; 18:618-626. [PMID: 33986544 PMCID: PMC8184642 DOI: 10.1038/s41592-021-01141-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/02/2021] [Indexed: 02/02/2023]
Abstract
Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that were analyzed and interpreted and clearly stating the strategy used for metagenomic profiling.
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Affiliation(s)
- Zheng Sun
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shi Huang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA
| | | | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Laxmi Parida
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Department of Computer Science & Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,# Correspondence: and
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA,# Correspondence: and
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185
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Byrd DA, Vogtmann E, Wu Z, Han Y, Wan Y, Clegg-Lamptey JN, Yarney J, Wiafe-Addai B, Wiafe S, Awuah B, Ansong D, Nyarko K, Hullings AG, Hua X, Ahearn T, Goedert JJ, Shi J, Knight R, Figueroa JD, Brinton LA, Garcia-Closas M, Sinha R. Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study. Int J Cancer 2021; 148:2712-2723. [PMID: 33460452 PMCID: PMC8386185 DOI: 10.1002/ijc.33473] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The gut microbiota may play a role in breast cancer etiology by regulating hormonal, metabolic and immunologic pathways. We investigated associations of fecal bacteria with breast cancer and nonmalignant breast disease in a case-control study conducted in Ghana, a country with rising breast cancer incidence and mortality. To do this, we sequenced the V4 region of the 16S rRNA gene to characterize bacteria in fecal samples collected at the time of breast biopsy (N = 379 breast cancer cases, N = 102 nonmalignant breast disease cases, N = 414 population-based controls). We estimated associations of alpha diversity (observed amplicon sequence variants [ASVs], Shannon index, and Faith's phylogenetic diversity), beta diversity (Bray-Curtis and unweighted/weighted UniFrac distance), and the presence and relative abundance of select taxa with breast cancer and nonmalignant breast disease using multivariable unconditional polytomous logistic regression. All alpha diversity metrics were strongly, inversely associated with odds of breast cancer and for those in the highest relative to lowest tertile of observed ASVs, the odds ratio (95% confidence interval) was 0.21 (0.13-0.36; Ptrend < .001). Alpha diversity associations were similar for nonmalignant breast disease and breast cancer grade/molecular subtype. All beta diversity distance matrices and multiple taxa with possible estrogen-conjugating and immune-related functions were strongly associated with breast cancer (all Ps < .001). There were no statistically significant differences between breast cancer and nonmalignant breast disease cases in any microbiota metric. In conclusion, fecal bacterial characteristics were strongly and similarly associated with breast cancer and nonmalignant breast disease. Our findings provide novel insight into potential microbially-mediated mechanisms of breast disease.
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Affiliation(s)
- Doratha A. Byrd
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Yongli Han
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | | | | | - Seth Wiafe
- Loma Linda University, School of Public Health, Loma Linda, CA, USA
| | | | | | | | - Autumn G. Hullings
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Jonine D. Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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186
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Ganguly S, Muench GA, Shang L, Rosenthal SB, Rahman G, Wang R, Wang Y, Kwon HC, Diomino AM, Kisseleva T, Soorosh P, Hosseini M, Knight R, Schnabl B, Brenner DA, Dhar D. Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet. Cell Mol Gastroenterol Hepatol 2021; 12:891-920. [PMID: 34062281 PMCID: PMC8342972 DOI: 10.1016/j.jcmgh.2021.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 01/20/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS How benign liver steatosis progresses to nonalcoholic steatohepatitis (NASH), fibrosis, and hepatocellular carcinoma (HCC) remains elusive. NASH progression entails diverse pathogenic mechanisms and relies on complex cross-talk between multiple tissues such as the gut, adipose tissues, liver, and the brain. Using a hyperphagic mouse fed with a Western diet (WD), we aimed to elucidate the cross-talk and kinetics of hepatic and extrahepatic alterations during NASH-HCC progression, as well as regression. METHODS Hyperphagic mice lacking a functional Alms1 gene (Foz/Foz) and wild-type littermates were fed WD or standard chow for 12 weeks for NASH/fibrosis and for 24 weeks for HCC development. NASH regression was modeled by switching back to normal chow after NASH development. RESULTS Foz+WD mice were steatotic within 1 to 2 weeks, developed NASH by 4 weeks, and grade 3 fibrosis by 12 weeks, accompanied by chronic kidney injury. Foz+WD mice that continued on WD progressed to cirrhosis and HCC within 24 weeks and had reduced survival as a result of cardiac dysfunction. However, NASH mice that were switched to normal chow showed NASH regression, improved survival, and did not develop HCC. Transcriptomic and histologic analyses of Foz/Foz NASH liver showed strong concordance with human NASH. NASH was preceded by an early disruption of gut barrier, microbial dysbiosis, lipopolysaccharide leakage, and intestinal inflammation. This led to acute-phase liver inflammation in Foz+WD mice, characterized by neutrophil infiltration and increased levels of several chemokines/cytokines. The liver cytokine/chemokine profile evolved as NASH progressed, with subsequent predominance by monocyte recruitment. CONCLUSIONS The Foz+WD model closely mimics the pathobiology and gene signature of human NASH with fibrosis and subsequent HCC. Foz+WD mice provide a robust and relevant preclinical model of NASH, NASH-associated HCC, chronic kidney injury, and heart failure.
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Affiliation(s)
- Souradipta Ganguly
- Department of Medicine, University of California San Diego, La Jolla, California
| | | | - Linshan Shang
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Sara Brin Rosenthal
- Department of Medicine, University of California San Diego, La Jolla, California,Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California
| | - Gibraan Rahman
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California
| | - Ruoyu Wang
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Yanhan Wang
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Hyeok Choon Kwon
- Department of Gastroenterology and Hepatology, National Medical Center, Jung-Gu, Seoul, South Korea
| | - Anthony M. Diomino
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Tatiana Kisseleva
- Department of Surgery, University of California San Diego, La Jolla, California
| | | | - Mojgan Hosseini
- Department of Pathology, University of California San Diego, La Jolla, California
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California,Center for Microbiome Innovation, University of California San Diego, La Jolla, California,Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California
| | - David A. Brenner
- Department of Medicine, University of California San Diego, La Jolla, California,Correspondence Address correspondence to: David A. Brenner, MD, or Debanjan Dhar, PhD, Department of Medicine, University of California San Diego, 9500 Gilman Drive, MC0063, La Jolla, California 92093. fax: (858) 246-1788.
| | - Debanjan Dhar
- Department of Medicine, University of California San Diego, La Jolla, California,Correspondence Address correspondence to: David A. Brenner, MD, or Debanjan Dhar, PhD, Department of Medicine, University of California San Diego, 9500 Gilman Drive, MC0063, La Jolla, California 92093. fax: (858) 246-1788.
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187
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Jala VR, Bodduluri SR, Ghosh S, Chheda Z, Singh R, Smith ME, Chilton PM, Fleming CJ, Mathis SP, Sharma RK, Knight R, Yan J, Haribabu B. Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the Apc Min /+ mouse model. Int J Cancer 2021; 148:2594-2607. [PMID: 33497467 DOI: 10.1002/ijc.33477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022]
Abstract
The biological activities of chemokine (C-C motif) ligand 2 (CCL2) are mediated via C-C chemokine receptor-2 (CCR2). Increased CCL2 level is associated with metastasis of many cancers. In our study, we investigated the role of the CCL2/CCR2 axis in the development of spontaneous intestinal tumorigenesis using the ApcMin/+ mouse model. Ablation of CCR2 in ApcMin/+ mice significantly increased the overall survival and reduced intestinal tumor burden. Immune cell analysis showed that CCR2-/- ApcMin/+ mice exhibited significant reduction in the myeloid cell population and increased interferon γ (IFN-γ) producing T cells both in spleen and mesenteric lymph nodes compared to ApcMin/+ mice. The CCR2-/- ApcMin/+ tumors showed significantly reduced levels of interleukin (IL)-17 and IL-23 and increased IFN-γ and Granzyme B compared to ApcMin/+ tumors. Transfer of CCR2+/+ ApcMin/+ CD4+ T cells into Rag2-/- mice led to development of colitis phenotype with increased CD4+ T cells hyper proliferation and IL-17 production. In contrast, adoptive transfer of CCR2-/- ApcMin/+ CD4+ T cells into Rag2-/- mice failed to enhance colonic inflammation or IL-17 production. These results a suggest novel additional role for CCR2, where it regulates migration of IL-17 producing cells mediating tumor-promoting inflammation in addition to its role in migration of tumor associated macrophages.
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Affiliation(s)
- Venkatakrishna Rao Jala
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Sobha Rani Bodduluri
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Sweta Ghosh
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Zinal Chheda
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Rajbir Singh
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Michelle E Smith
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Paula M Chilton
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Christopher J Fleming
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Steven Paul Mathis
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Rajesh Kumar Sharma
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Jun Yan
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Bodduluri Haribabu
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
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188
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Salosensaari A, Laitinen V, Havulinna AS, Meric G, Cheng S, Perola M, Valsta L, Alfthan G, Inouye M, Watrous JD, Long T, Salido RA, Sanders K, Brennan C, Humphrey GC, Sanders JG, Jain M, Jousilahti P, Salomaa V, Knight R, Lahti L, Niiranen T. Taxonomic signatures of cause-specific mortality risk in human gut microbiome. Nat Commun 2021; 12:2671. [PMID: 33976176 PMCID: PMC8113604 DOI: 10.1038/s41467-021-22962-y] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.
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Affiliation(s)
- Aaro Salosensaari
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
- Department of Computing, University of Turku, Turku, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Ville Laitinen
- Department of Computing, University of Turku, Turku, Finland
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | - Guillaume Meric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Liisa Valsta
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Georg Alfthan
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Tao Long
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Rodolfo A Salido
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Gregory C Humphrey
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California San Diego, San Diego, CA, USA
| | | | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland.
| | - Teemu Niiranen
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland.
- Finnish Institute for Health and Welfare, Helsinki, Finland.
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189
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Li N, Hui H, Bray B, Gonzalez GM, Zeller M, Anderson KG, Knight R, Smith D, Wang Y, Carlin AF, Rana TM. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep 2021; 35:109091. [PMID: 33961823 PMCID: PMC8090989 DOI: 10.1016/j.celrep.2021.109091] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/18/2021] [Accepted: 04/16/2021] [Indexed: 01/05/2023] Open
Abstract
It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlining molecular mechanism. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. Here, we investigate m6A modification of the SARS-CoV-2 gene in regulating the host cell innate immune response. Our data show that the SARS-CoV-2 virus has m6A modifications that are enriched in the 3' end of the viral genome. We find that depletion of the host cell m6A methyltransferase METTL3 decreases m6A levels in SARS-CoV-2 and host genes, and m6A reduction in viral RNA increases RIG-I binding and subsequently enhances the downstream innate immune signaling pathway and inflammatory gene expression. METTL3 expression is reduced and inflammatory genes are induced in patients with severe coronavirus disease 2019 (COVID-19). These findings will aid in the understanding of COVID-19 pathogenesis and the design of future studies regulating innate immunity for COVID-19 treatment.
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Affiliation(s)
- Na Li
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Hui Hui
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bill Bray
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA
| | - Gwendolyn Michelle Gonzalez
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristian G Anderson
- Department of Immunology and Microbiology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Microbiome Innovations, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tariq M Rana
- Division of Genetics, Program in Immunology, Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0762, La Jolla, CA 92093, USA.
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190
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Abstract
The functional repertoire of intratumoral microorganisms and their local effects on the host remain poorly characterized. By revealing potentially immunogenic bacterial peptides on melanoma cells, a Nature paper provides evidence that intratumoral bacteria can directly modulate antitumor immune responses, and it details a new class of therapeutically relevant, non-human tumor antigens.
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Affiliation(s)
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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191
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Linton S, Sprecher K, Depner C, Burke T, Dorrestein P, Fleshner M, Knight R, Lowry C, Turek F, Vitaterna M, Wright K. 130 Individual Differences in Skin Temperature Responses to Cold Pressor Stress During Sleep Restriction and Circadian Misalignment. Sleep 2021. [DOI: 10.1093/sleep/zsab072.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Individual differences in cognition during sleep restriction and circadian misalignment have been shown to be trait-like. Here we explored the consistency of individual differences in cardiovascular responses to the cold pressor test (CPT) measured by changes in the distal-proximal skin temperature gradient (DPG) using the contralateral hand to that immersed in the ice water bath, which reflects a reflex cutaneous vasoconstriction.
Methods
Eighteen healthy participants (8 females) mean (±SD) age 25.28 (±4.3), underwent two identical in-laboratory combined sleep restriction and circadian misalignment protocols preceded by an 8h baseline in-laboratory sleep opportunity. The participants were given a 3h sleep opportunity on night 2 and a 3h sleep opportunity on days 3 and 4 followed by recovery sleep. The CPT occurred the morning after the baseline sleep opportunity and the morning before recovery sleep. Participants maintained a seated posture beginning 30 min prior to the CPT and skin temperature was assessed starting 15 min before until 45 min after the CPT. DPG (proximal=subclavicular; distal=hand palmar) data were averaged into 3 min bins. Changes in DPG from pre-CPT and 5 min post-CPT were assessed as the primary outcome using mixed-model ANOVAs. Intra-class correlation coefficients (ICC) were calculated to measure consistency of individual differences for DPG responses.
Results
Mixed-model ANOVA revealed significant effects of time and combined sleep restriction and circadian misalignment on DPG during the CPT (both p<0.05), such that the DPG was wider (i.e., more negative) post-CPT and during sleep restriction and circadian misalignment. Participants showed moderately consistent DPG responses across visits 1 and 2 at baseline (ICC=0.59) and substantially consistent DPG responses during sleep restriction and circadian misalignment (ICC=0.67). Further, participants showed moderately consistent DPG responses when comparing changes between baseline and sleep restriction and circadian misalignment across visits (ICC=0.58).
Conclusion
Findings support that combined sleep restriction and circadian misalignment is associated with sympathetic activation and that individual differences in the DPG response to cold pressor stress are consistent.
Support (if any)
Office of Naval Research MURI grant N00014-15-1-2809, NIH/NCATS Colorado CTSA Grant UL1TR002535
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Affiliation(s)
- Sabrina Linton
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Kate Sprecher
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Christopher Depner
- Department of Health and Kinesiology, University of Utah, Salt Lake City, UT, USA
| | - Tina Burke
- Behavioural Biology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Pediatrics, Center for Microbiome Innovation and Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Monika Fleshner
- Stress Physiology Laboratory, Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Rob Knight
- Departments of Pediatrics, Bioengineering, Computer Science and Engineering and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Christopher Lowry
- Behavioral Neuroendocrinology Laboratory, Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA
| | - Fred Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Martha Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Kenneth Wright
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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192
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Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res 2021; 31:934. [PMID: 33941606 DOI: 10.1101/gr.275614.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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193
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Withrow D, Gonzalez A, Sprecher K, Depner C, Burke T, Fleshner M, Lowry C, Turek F, Vitaterna M, Dorrestein P, Knight R, Wright K. 114 Stability of Gut Microbiome Alpha Diversity During Combined Sleep Restriction and Circadian Misalignment. Sleep 2021. [DOI: 10.1093/sleep/zsab072.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Disturbed gut microbiome diversity has been associated with poor health outcomes and various disease states. We investigated the impact of combined sleep restriction (3h time in bed [TIB] sleep opportunities per day) and circadian misalignment (daytime sleep and nighttime wakefulness) on gut microbiome alpha diversity in healthy young individuals in a controlled laboratory setting.
Methods
Twenty healthy adults (8 female), mean age (±SD) 25.65(±4.2) completed a 39-day protocol consisting of two laboratory visits lasting 4 days each. Two weeks of ambulatory monitoring prior to laboratory visits confirmed ~8h habitual sleep duration per night. Participants consumed energy-balanced diets, identical within participants, 2 days before and during the laboratory visits. The laboratory visits consisted of sleep opportunities as follows: night 1 (8h TIB), night 2 (3h TIB), day 3 (3h TIB) and day 4 (3h TIB). Fecal microbiome samples were obtained at baseline between day 1 and 2, and during sleep and circadian disruption (between day 3 and 4). Alpha diversity measures were calculated using Pielou’s evenness, Faith’s phylogenetic diversity and number of observed OTUs.
Results
Linear mixed models with subject as a random factor and visit as a fixed factor were performed to assess whether any alpha diversity measures changed during sleep and circadian disruption compared to baseline. Alpha diversity did not change significantly between baseline and sleep and circadian disruption (all p > 0.57). Additionally, intraclass correlation coefficients (ICCs) were calculated at baseline and during sleep and circadian disruption to determine if alpha diversity measures showed trait-like stability at both time points. ICCs were substantial to almost perfect (ICC 0.64–0.84) at baseline and substantial (ICC 0.70–0.80) during sleep and circadian disruption.
Conclusion
Four days of combined sleep restriction and circadian misalignment does not appear to alter alpha diversity of gut microbiota species in healthy adults. Further, substantial to almost perfect intraclass correlation coefficients suggest alpha diversity of the human microbiome is stable during combined sleep and circadian perturbation and that examination at the level of microbiota community composition and functional outcomes are needed.
Support (if any)
Office of Naval Research MURI (N00014- 15-1-2809), NIH/NCATS (UL1TR002535), NIH T32 HL149646, CU Undergraduate Research Opportunities.
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Affiliation(s)
- Dana Withrow
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kate Sprecher
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Christopher Depner
- Department of Health and Kinesiology, University of Utah, Salt Lake City, UT, USA
| | - Tina Burke
- Behavioural Biology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Monika Fleshner
- Stress Physiology Laboratory, Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Christopher Lowry
- Behavioral Neuroendocrinology Laboratory, Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA
| | - Fred Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Martha Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Pediatrics, Center for Microbiome Innovation and Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Departments of Pediatrics, Bioengineering, Computer Science and Engineering and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Wright
- Sleep and Chronobiology Lab, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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194
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Booth G, Knight R, Harlan R, Peterson K, Jacoby C, Berklich E, Slater S, Allen B, Neumann C, Dela Cruz J, Meyers G, Cook R, Maziarz R, Newell L. Characterization of chronic GVHD after day 4 versus day 5 G-CSF mobilized HLA-matched sibling donor allogeneic hematopoietic cell transplantation. Cytotherapy 2021. [DOI: 10.1016/s1465324921003881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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195
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Minich JJ, Nowak B, Elizur A, Knight R, Fielder S, Allen EE. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi. Front Mar Sci 2021; 8:676731. [PMID: 36248701 PMCID: PMC9563383 DOI: 10.3389/fmars.2021.676731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment "BE" and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut "allochthonous" microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.
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Affiliation(s)
- Jeremiah J. Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Barbara Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Abigail Elizur
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Stewart Fielder
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, NSW, Australia
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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196
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Knight R, Goslee K, Fuchs M, Maziarz R, Newell L. Safety and feasibility of delayed infusion of stem cell products: a pilot study. Cytotherapy 2021. [DOI: 10.1016/s1465324921005648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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197
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Sabey KA, Song SJ, Jolles A, Knight R, Ezenwa VO. Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. ISME J 2021; 15:1359-1371. [PMID: 33328653 PMCID: PMC8115229 DOI: 10.1038/s41396-020-00855-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/07/2023]
Abstract
Changes in the gut microbiota during pathogen infection are often predicted to influence disease outcomes. However, studies exploring whether pathogens induce microbiota shifts have yielded inconsistent results. This suggests that variation in infection, rather than the presence of infection alone, might shape pathogen-microbiota relationships. For example, most hosts are coinfected with multiple pathogens simultaneously, and hosts vary in how long they are infected, which may amplify or diminish microbial shifts expected in response to a focal pathogen. We used a longitudinal anthelmintic treatment study of free-ranging African buffalo (Syncerus caffer) to examine whether (i) coinfection with bovine tuberculosis (Mycobacterium bovis, TB) and gastrointestinal nematodes, and (ii) the duration of TB infection, modified effects of single pathogens on the gut microbiota. By accounting for the interaction between TB and nematodes, we found that coinfection affected changes in microbial abundance associated with single infections. Furthermore, the duration of TB infection predicted more microbiota variation than the presence of TB. Importantly, coinfection and infection duration had nearly as much influence on microbial patterns as demographic and environmental factors commonly examined in microbiota research. These findings demonstrate that acknowledging infection heterogeneities may be crucial to understanding relationships between pathogens and the gut microbiota.
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Affiliation(s)
- Kate A Sabey
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Se Jin Song
- 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
| | - Anna Jolles
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 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
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Vanessa O Ezenwa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
- Odum School of Ecology, University of Georgia, Athens, GA, USA.
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198
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Neumann C, Knight R, Booth G, Dela Cruz J, Maziarz R, Newell L. Second autologous hematopoietic cell transplantation using long-term cryopreserved cells is associated with increased platelet transfusion support and hospital readmissions, but not delayed engraftment. Cytotherapy 2021. [DOI: 10.1016/s146532492100387x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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199
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Tsan-Yuk Lam T, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ARXIV 2021. [PMCID: PMC8109901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA,Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, 30333 GA, USA,Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center “Digital biodesign and personalized healthcare”, I.M. Sechenov First Moscow State Medical University, Moscow, Russia,Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China,Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia,Translational Research Institute, Brisbane, Australia
| | - Adam L. Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA,Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A. Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv 2021:arXiv:2104.14005v3. [PMID: 33948451 PMCID: PMC8095210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 06/04/2021] [Indexed: 12/25/2022]
Abstract
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health. However, distinguishing the most epidemiologically relevant information encoded in these vast amounts of data requires substantial effort across the research and public health communities. Studies of SARS-CoV-2 genomes have been critical in tracking the spread of variants and understanding its epidemic dynamics, and may prove crucial for controlling future epidemics and alleviating significant public health burdens. Together, genomic data and bioinformatics methods enable broad-scale investigations of the spread of SARS-CoV-2 at the local, national, and global scales and allow researchers the ability to efficiently track the emergence of novel variants, reconstruct epidemic dynamics, and provide important insights into drug and vaccine development and disease control. Here, we discuss the tremendous opportunities that genomics offers to unlock the effective use of SARS-CoV-2 genomic data for efficient public health surveillance and guiding timely responses to COVID-19.
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Affiliation(s)
- Sergey Knyazev
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Room 618, Atlanta, GA 30303, USA
| | - Karishma Chhugani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Varuni Sarwal
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Ram Ayyala
- Department of Neuroscience, College of Life Sciences, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Harman Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dhrithi Deshpande
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089, USA
| | - Zoia Comarova
- Paradigm Environmental, 3911 Old Lee Highway, Fairfax, VA 22030
| | - Angela Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Yuri Porozov
- World-Class Research Center "Digital biodesign and personalized healthcare", I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Computational Biology, Sirius University of Science and Technology, Sochi, Russia
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Malak S Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, Australia
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089
| | - Pavel Skums
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
| | - Jason Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alex Zelikovsky
- Department of Computer Science, College of Art and Science, Georgia State University, 1 Park Place, Floor 6, Atlanta, GA 30303, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
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