1
|
Fernandez-Cassi X, Kohn T. Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09594-3. [PMID: 38647859 DOI: 10.1007/s12560-024-09594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/25/2024]
Abstract
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.
Collapse
Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland.
- Departament of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona, Catalunya, Spain.
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland
| |
Collapse
|
2
|
Hurych J, Vejmelka J, Hlinakova L, Kramna L, Larionov V, Kulich M, Cinek O, Kohout P. Protocol for faecal microbiota transplantation in irritable bowel syndrome: the MISCEAT study - a randomised, double-blind cross-over study using mixed microbiota from healthy donors. BMJ Open 2022; 12:e056594. [PMID: 35760542 PMCID: PMC9237876 DOI: 10.1136/bmjopen-2021-056594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Several studies have demonstrated dysbiosis in irritable bowel syndrome (IBS). Therefore, faecal microbiota transplantation, whose effect and safety have been proven in Clostridioides difficile infections, may hold promise in other conditions, including IBS. Our study will examine the effectiveness of stool transfer with artificially increased microbial diversity in IBS treatment. METHODS AND ANALYSIS A three-group, double-blind,randomised, cross-over, placebo-controlled study of two pairs of gut microbiota transfer will be conducted in 99 patients with diarrhoeal or mixed type of IBS. Patients aged 18-65 will be randomised into three equally sized groups: group A will first receive two enemas of study microbiota mixture (deep-frozen stored stool microbiota mixed from eight healthy donors); after 8 weeks, they will receive two enemas with placebo (autoclaved microbiota mixture), whereas group B will first receive placebo, then microbiota mixture. Finally, group C will receive placebos only. The IBS Severity Symptom Score (IBS-SSS) questionnaires will be collected at baseline and then at weeks 3, 5, 8, 11, 13, 32. Faecal bacteriome will be profiled before and regularly after interventions using 16S rDNA next-generation sequencing. Food records, dietary questionnaires, anthropometry, bioimpedance, biochemistry and haematology workup will be obtained at study visits during the follow-up period. The primary outcome is the change in the IBS-SSS between the baseline and 4 weeks after the intervention for each patient compared with placebo. Secondary outcomes are IBS-SSS at 2 weeks after the intervention and 32 weeks compared with placebo and changes in the number of loose stools, Bristol stool scale, abdominal pain and bloating, anthropometric parameters, psychological evaluation and the gut microbiome composition. ETHICS AND DISSEMINATION The study was approved by the Ethics Committee of Thomayer University Hospital, Czechia (G-18-26); study results will be published in peer-reviewed journals and presented at international conferences and patient group meetings. TRIAL REGISTRATION NUMBER NCT04899869.
Collapse
Affiliation(s)
- Jakub Hurych
- Department of Medical Microbiology, Charles University Second Faculty of Medicine, Prague, Czech Republic
- Department of Paediatrics, Charles University Second Faculty of Medicine, Prague, Czech Republic
| | - Jiri Vejmelka
- Department of Internal Medicine, Charles University Third Faculty of Medicine, Prague, Czech Republic
| | - Lucie Hlinakova
- Department of Paediatrics, Charles University Second Faculty of Medicine, Prague, Czech Republic
| | - Lenka Kramna
- Department of Paediatrics, Charles University Second Faculty of Medicine, Prague, Czech Republic
| | - Vladyslav Larionov
- Department of Paediatrics, Charles University Second Faculty of Medicine, Prague, Czech Republic
| | - Michal Kulich
- Department of Probability and Statistics, Charles University, Prague, Czech Republic
| | - Ondrej Cinek
- Department of Medical Microbiology, Charles University Second Faculty of Medicine, Prague, Czech Republic
- Department of Paediatrics, Charles University Second Faculty of Medicine, Prague, Czech Republic
| | - Pavel Kohout
- Department of Internal Medicine, Charles University Third Faculty of Medicine, Prague, Czech Republic
| |
Collapse
|
3
|
Chen Y, Li HW, Cong F, Lian YX. Avian leukosis virus subgroup J infection alters viral composition in the chicken gut. FEMS Microbiol Lett 2021; 368:6287573. [PMID: 34048535 DOI: 10.1093/femsle/fnab058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
Chicken is one of the economically important poultry species. Avian leucosis virus subgroup J (ALV-J) has emerged as a serious cause of mortality and suboptimal performance of domestic chickens. Changes in virome may contribute to pathogenesis. Thus, it is important to investigate the effects of ALV-J infection on the composition of the virome in chicken. In the study metagenomic sequencing was used to characterize the virome of feces collected from the AVL-J infected chickens and the controls. Our results indicated that the chicken gut virome contained a diverse range of viruses that can be found in mammal, reptile, fish, and frogs. Furthermore, at the order, family and genus levels, AVL-J infection significantly altered the chicken gut virome composition. The predominant order was Herpesvirales, accounting for more than 96% of the chicken gut virome. Furthermore, the relative abundance of Caudovirales in the controls was higher than that in the AVL-J-infected chickens. At the family level, the relative abundance of Herpesviridae, Myoviridae, Alloherpesviridae, and Genomoviridae was significantly altered in the AVL-J-infected chickens compared with that in the controls. Additionally, the relative abundance of 15 genera showed a significant difference between the AVL-J-infected chickens and controls. These results will increase our understanding of the viral diversity and changes in the virome of chicken gut, with implications in chicken health.
Collapse
Affiliation(s)
- Yuan Chen
- School of Life Science, Huizhou University, No. 46 Yanda road, Huicheng district, Huizhou 516007, China
| | - Hong-Wei Li
- School of Life Science, Huizhou University, No. 46 Yanda road, Huicheng district, Huizhou 516007, China
| | - Feng Cong
- Guangdong laboratory animal monitoring institute and Guangdong provincial key laboratory of laboratory animals, No. 11 fengxian road, Huangpu district, Guangzhou 510633, China
| | - Yue-Xiao Lian
- Guangdong laboratory animal monitoring institute and Guangdong provincial key laboratory of laboratory animals, No. 11 fengxian road, Huangpu district, Guangzhou 510633, China
| |
Collapse
|
4
|
Gut Microbiome, Diabetes, and Obesity: Complex Interplay of Physiology. GUT MICROBIOME-RELATED DISEASES AND THERAPIES 2021. [DOI: 10.1007/978-3-030-59642-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
5
|
François S, Pybus OG. Towards an understanding of the avian virome. J Gen Virol 2020; 101:785-790. [PMID: 32519942 PMCID: PMC7641393 DOI: 10.1099/jgv.0.001447] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
Collapse
Affiliation(s)
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, UK
| |
Collapse
|
6
|
Ansari MH, Ebrahimi M, Fattahi MR, Gardner MG, Safarpour AR, Faghihi MA, Lankarani KB. Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome. BMC Microbiol 2020; 20:123. [PMID: 32429898 PMCID: PMC7236503 DOI: 10.1186/s12866-020-01817-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/10/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Changes in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome. RESULTS A metagenomics analysis on fecal samples of 50 individuals - 30 of whom met the Rome IV criteria for IBS and 20 healthy controls- was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals - where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome. CONCLUSIONS These findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.
Collapse
Affiliation(s)
- Mina Hojat Ansari
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehregan Ebrahimi
- Department of Biology, Shiraz University, Shiraz, Fars Province, Iran
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Mohammad Reza Fattahi
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
| | - Ali Reza Safarpour
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Faghihi
- Persian Bayan Gene Research and Training Center, Dr. Faghihi's Medical Genetics Center, Shiraz, Iran
- Center for Therapeutic Innovation, Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kamran Bagheri Lankarani
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
7
|
Seo SU, Kweon MN. Virome-host interactions in intestinal health and disease. Curr Opin Virol 2019; 37:63-71. [PMID: 31295677 DOI: 10.1016/j.coviro.2019.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023]
Abstract
The enteric virome consists largely of bacteriophages and prophages related to commensal bacteria. Bacteriophages indirectly affect the host immune system by targeting their associated bacteria; however, studies suggest that bacteriophages also have distinct pathways that enable them to interact directly with the host. Eukaryotic viruses are less abundant than bacteriophages but are more efficient in the stimulation of host immune responses. Acute, permanent, and latent viral infections are detected by different types of pattern recognition receptors and induce host immune responses, including the antiviral type I interferon response. Understanding the complex interplay between commensal microorganisms and the host immune system is a prerequisite to elucidating their role in intestinal diseases.
Collapse
Affiliation(s)
- Sang-Uk Seo
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul 05505, South Korea.
| | - Mi-Na Kweon
- Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul 05505, South Korea.
| |
Collapse
|
8
|
Cinek O, Kramna L, Mazankova K, Kunteová K, Chudá K, C J Claas E, Stene LC, Tapia G. Virus genotyping by massive parallel amplicon sequencing: adenovirus and enterovirus in the Norwegian MIDIA study. J Med Virol 2018; 91:606-614. [PMID: 30537228 DOI: 10.1002/jmv.25361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
OBJECTIVES Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types in a sample, or due to varying efficacy of PCR amplifying the capsid gene on the background of foreign nucleic acids. Here we present a simple protocol for virus genotyping using massive parallel amplicon sequencing. METHODS The protocol utilized a set of 16 tailed degenerate primers flanking the seventh hypervariable region of the adenovirus hexon gene and 9 tailed degenerate primers targeted to the proximal portion of the enterovirus VP1 gene. Subsequent addition of dual indices enabled simultaneous sequencing of 384 different samples on an Illumina MiSeq instrument. Downstream bioinformatic analysis was based on remapping to a set of references representative of the presently known repertoire of virus types. RESULTS After validation with known virus types, the sequencing method was applied on 301 adenovirus-positive samples and 350 enterovirus-positive samples from a longitudinally collected series of stools from 83 children aged 3 to 36 months. We detected 7 different adenovirus types and 27 different enterovirus types. There were 37 (6.2%) samples containing more than one genotype of the same viral genus. At least one dual infection was experienced by 23 of 83 (28%) of the children observed over the 3 years' observation period. CONCLUSIONS Amplicon sequencing with a multiplex set of degenerate primers seems to be a rapid and reliable technical solution for genotyping of large collections of samples where simultaneous infections with multiple strains can be expected.
Collapse
Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Kramna
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Kunteová
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Chudá
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lars C Stene
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - German Tapia
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|