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Meidaninikjeh S, Mohammadi P, Elikaei A. A simplified method of bacteriophage preparation for transmission electron microscope. J Virol Methods 2024; 328:114951. [PMID: 38750823 DOI: 10.1016/j.jviromet.2024.114951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Bacteriophages are viruses that infect bacteria. Researchers use different methods to study the characteristics of bacteriophages. Transmission electron microscope (TEM) is considered the best method to analyze these characteristics. However, the quality of TEM micrographs is significantly influenced by the preparation methods used to prepare the bacteriophages sample. In this study, researchers compared two different methods for preparing the bacteriophage samples. In one method was used SM buffer, while in the other used deionized water. The results were analyzed by TEM and compared with each other. Additionally, the viability of bacteriophage in deionized water and SM buffer at 4°C was determined through plaque assay within 72 hours. TEM micrographs showed that the quality of bacteriophage sample prepared with deionized water is superior to those prepared with SM buffer. Furthermore, the titer of the bacteriophages did not show a significant reduction during 72 hours in both SM and deionized water. In conclusion, the results suggested that preparation method can significantly impact the quality of TEM micrographs. Using sterile deionized water for the preparation of bacteriophages is a simple way to improve the quality of TEM micrographs and it is advisable to send the samples to the laboratory within 72 hours.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran
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2
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Rasmussen TS, Mao X, Forster S, Larsen SB, Von Münchow A, Tranæs KD, Brunse A, Larsen F, Mejia JLC, Adamberg S, Hansen AK, Adamberg K, Hansen CHF, Nielsen DS. Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments. MICROBIOME 2024; 12:119. [PMID: 38951925 PMCID: PMC11218093 DOI: 10.1186/s40168-024-01820-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/19/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases. METHODS To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline. RESULTS FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy. CONCLUSIONS This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
| | - Xiaotian Mao
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sarah Forster
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sabina Birgitte Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Alexandra Von Münchow
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaare Dyekær Tranæs
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg, Denmark
| | - Frej Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Josue Leonardo Castro Mejia
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Camilla Hartmann Friis Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
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3
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Wilde J, Boyes R, Robinson AV, Daisley BA, Botschner AJ, Brettingham DJL, Macpherson CV, Mallory E, Allen-Vercoe E. Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes. Cell Host Microbe 2024; 32:768-778.e9. [PMID: 38653241 DOI: 10.1016/j.chom.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Microbiomes feature complex interactions between diverse bacteria and bacteriophages. Synthetic microbiomes offer a powerful way to study these interactions; however, a major challenge is obtaining a representative bacteriophage population during the bacterial isolation process. We demonstrate that colony isolation reliably excludes virulent viruses from sample sources with low virion-to-bacteria ratios such as feces, creating "virulent virus-free" controls. When the virulent dsDNA virome is reintroduced to a 73-strain synthetic gut microbiome in a bioreactor model of the human colon, virulent viruses target susceptible strains without significantly altering community structure or metabolism. In addition, we detected signals of prophage induction that associate with virulent predation. Overall, our findings indicate that dilution-based isolation methods generate synthetic gut microbiomes that are heavily depleted, if not devoid, of virulent viruses and that such viruses, if reintroduced, have a targeted effect on community assembly, metabolism, and prophage replication.
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Affiliation(s)
- Jacob Wilde
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Randy Boyes
- Queen's University, Department of Community Health and Epidemiology, Kingston, ON K7L 3N6, Canada
| | - Avery V Robinson
- University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7FY, UK
| | - Brendan A Daisley
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Alexander J Botschner
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Dylan J L Brettingham
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Christine V Macpherson
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Mallory
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Emma Allen-Vercoe
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada.
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4
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Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen W, Zhao X. Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305818. [PMID: 38240578 PMCID: PMC10987132 DOI: 10.1002/advs.202305818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/01/2023] [Indexed: 04/04/2024]
Abstract
Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
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Affiliation(s)
- Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Yanqi Dong
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Menglu Jin
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Senying Lai
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Longhao Jia
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Xueyang Zhao
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Huarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Na L. Gao
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Peer Bork
- European Molecular Biology LaboratoryStructural and Computational Biology Unit69117HeidelbergGermany
- Max Delbrück Centre for Molecular Medicine13125BerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei University03722SeoulSouth Korea
- Department of BioinformaticsBiocenterUniversity of Würzburg97070WürzburgGermany
| | - Zhi Liu
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and Technology430074WuhanChina
| | - Wei‐Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
- Institution of Medical Artificial IntelligenceBinzhou Medical UniversityYantai264003China
| | - Xing‐Ming Zhao
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligenceand MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200433China
- State Key Laboratory of Medical NeurobiologyInstitute of Brain ScienceFudan UniversityShanghai200433China
- International Human Phenome Institutes (Shanghai)Shanghai200433China
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5
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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6
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Kosznik-Kwaśnicka K, Topka G, Mantej J, Grabowski Ł, Necel A, Węgrzyn G, Węgrzyn A. Propagation, Purification, and Characterization of Bacteriophages for Phage Therapy. Methods Mol Biol 2024; 2738:357-400. [PMID: 37966610 DOI: 10.1007/978-1-0716-3549-0_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Phage therapy is an alternative approach to combat bacterial infections. In this approach, bacteriophages are used as antimicrobial agents due to their properties to infect specific bacterial cells, to propagate inside their hosts, and to lyse host cell to release progeny phages. However, to introduce bacteriophages to clinical or veterinary practice, it is necessary to construct a large library of precisely characterized phages. Therefore, in this chapter, methods for propagation, purification, and microbiological characterization of bacteriophages are presented in the light of their potential use in phage therapy. Isolation of newly discovered bacteriophages from different habitats is also described as it is a preliminary assessment of their efficacy in combating bacterial biofilms and in the treatment of bacterial infections in a simple insect model-Galleria mellonella.
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Affiliation(s)
| | | | | | - Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
| | - Agnieszka Necel
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Alicja Węgrzyn
- Phage Therapy Laboratory, University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland.
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7
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Shuai X, Zhou Z, Ba X, Lin Y, Lin Z, Liu Z, Yu X, Zhou J, Zeng G, Ge Z, Chen H. Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems? WATER RESEARCH 2024; 248:120833. [PMID: 37952327 DOI: 10.1016/j.watres.2023.120833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.
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Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangshu Zeng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziye Ge
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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8
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Schwarz C, Mathieu J. Isolation of Enterococcus Bacteriophages from Municipal Wastewater Samples Using an Enrichment Step. Methods Mol Biol 2024; 2738:111-123. [PMID: 37966595 DOI: 10.1007/978-1-0716-3549-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Municipal wastewater, as an aggregate mixture of household and industrial effluents, harbors a highly diverse population of bacteria and their associated bacteriophages. Accordingly, it is a commonly used source of bacteriophages against many human-associated bacterial pathogens. Here, we describe a method for bacteriophage isolation from municipal wastewater with several optional enrichment and concentration steps.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
- Sentinel Environmental, Houston, TX, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA.
- Sentinel Environmental, Houston, TX, USA.
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9
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Larsen F, Jakobsen RR, Mao X, Castro-Mejia J, Deng L, Nielsen DS. Purification and Up-Concentration of Bacteriophages and Viruses from Fecal Samples. Methods Mol Biol 2024; 2738:105-110. [PMID: 37966594 DOI: 10.1007/978-1-0716-3549-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The viral fraction of human and experimental animal fecal matter is increasingly attracting research interest due to its newfound influence on the gut microbiome and host health. During the past decade, high-throughput sequencing techniques have seen massive improvements, and in recent years, bioinformatics pipelines for virome analysis have also vastly improved with respect to both user-friendliness and output quality. Yet, the shape and quality of such data are highly dependent on how the viruses are isolated and their genomes extracted and processed to build sequencing libraries.Here we describe a simple protocol for virus isolation from fecal samples suitable for further propagation/characterization or sequencing efforts. It is based on two filtration steps: one for removing large particles such as bacteria and one for removing free DNA and up-concentrating phages and other viruses in the solution. The method is highly scalable, adaptable to a long range of sample types including low-input samples, and has a quantifiable output suitable for both plaquing and sequencing.
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Affiliation(s)
- Frej Larsen
- University of Copenhagen, Frederiksberg C, Denmark.
| | | | - Xiaotian Mao
- University of Copenhagen, Frederiksberg C, Denmark
| | | | - Ling Deng
- University of Copenhagen, Frederiksberg C, Denmark
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10
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Larsen F, Offersen SM, Li VR, Deng L, Nielsen DS, Rasmussen TS. Choice of Ultrafilter Affects Recovery Rate of Bacteriophages. Viruses 2023; 15:2051. [PMID: 37896828 PMCID: PMC10612031 DOI: 10.3390/v15102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Studies into the viral fraction of complex microbial communities, like in the mammalian gut, have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of the basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study, we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the extracted viral community. Clinical samples (feces, vaginal swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4, c2, Φ6, Φ29, Φx174, and Φ2972), filtered, and quantified using spot and plaque assays to estimate the loss in recovery. The enveloped Φ6 phage is especially severely affected by the choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that the pore size of ultrafilters may affect the recovery of phages in a strain- and sample-dependent manner, suggesting the need for greater thought when selecting filters for virus extraction.
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Affiliation(s)
- Frej Larsen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Simone Margaard Offersen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (S.M.O.)
| | - Viktoria Rose Li
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (S.M.O.)
| | - Ling Deng
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Dennis Sandris Nielsen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
| | - Torben Sølbeck Rasmussen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark; (L.D.); (D.S.N.)
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Wortelboer K, de Jonge PA, Scheithauer TPM, Attaye I, Kemper EM, Nieuwdorp M, Herrema H. Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety. Nat Commun 2023; 14:5600. [PMID: 37699894 PMCID: PMC10497675 DOI: 10.1038/s41467-023-41329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacteriophages (phages) are bacterial viruses that have been shown to shape microbial communities. Previous studies have shown that faecal virome transplantation can decrease weight gain and normalize blood glucose tolerance in diet-induced obese mice. Therefore, we performed a double-blind, randomised, placebo-controlled pilot study in which 24 individuals with metabolic syndrome were randomised to a faecal filtrate transplantation (FFT) from a lean healthy donor (n = 12) or placebo (n = 12). The primary outcome, change in glucose metabolism, and secondary outcomes, safety and longitudinal changes within the intestinal bacteriome and phageome, were assessed from baseline up to 28 days. All 24 included subjects completed the study and are included in the analyses. While the overall changes in glucose metabolism are not significantly different between both groups, the FFT is well-tolerated and without any serious adverse events. The phage virion composition is significantly altered two days after FFT as compared to placebo, which coincides with more virulent phage-microbe interactions. In conclusion, we provide evidence that gut phages can be safely administered to transiently alter the gut microbiota of recipients.
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Affiliation(s)
- Koen Wortelboer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Patrick A de Jonge
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Torsten P M Scheithauer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Ilias Attaye
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Vascular Medicine, Amsterdam, The Netherlands
| | - E Marleen Kemper
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Pharmacy and Clinical Pharmacology, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam UMC location Vrije University Medical Center, Department of Internal Medicine, Diabetes Center, Amsterdam, The Netherlands
| | - Hilde Herrema
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands.
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands.
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands.
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12
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Zhai X, Castro-Mejía JL, Gobbi A, Aslampaloglou A, Kot W, Nielsen DS, Deng L. The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses. MICROBIOME 2023; 11:193. [PMID: 37635262 PMCID: PMC10463696 DOI: 10.1186/s40168-023-01632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing. RESULTS We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4 °C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100 days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100 days. Prolonged storage time (500 days) at - 80 °C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction. CONCLUSION Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4 °C for the isolation of viruses and at - 80 °C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.
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Affiliation(s)
- Xichuan Zhai
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Josué L Castro-Mejía
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Alex Gobbi
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Antonios Aslampaloglou
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Witold Kot
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Dennis S Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark.
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Santoro F, Pastore G, Fox V, Petit MA, Iannelli F, Pozzi G. Streptococcus pyogenes Φ1207.3 Is a Temperate Bacteriophage Carrying the Macrolide Resistance Gene Pair mef(A)- msr(D) and Capable of Lysogenizing Different Streptococci. Microbiol Spectr 2023; 11:e0421122. [PMID: 36625667 PMCID: PMC9927172 DOI: 10.1128/spectrum.04211-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Streptococcus pyogenes prophage Φ1207.3 (formerly Tn1207.3) carries the mef(A)-msr(D) resistance genes, responsible for type M macrolide resistance. To investigate if Φ1207.3 is a functional bacteriophage, we transferred the element from the original S. pyogenes host in a prophage-free and competence-deficient S. pneumoniae strain. Pneumococcal cultures of the Φ1207.3-carrying lysogen were treated with mitomycin C to assess if Φ1207.3 enters the lytic cycle. Mitomycin C induced a limited phage burst and a growth impairment, resulting in early entrance into the stationary phase. To determine if Φ1207.3 is able to produce mature phage particles, we prepared concentrated supernatants recovered from a mitomycin C-induced pneumococcal culture by sequential centrifugation and ultracentrifugation steps. Negative-staining transmission electron microscopy (TEM) of supernatants revealed the presence of phage particles with an icosahedral, electron-dense capsid and a long, noncontractile tail, typical of a siphovirus. Quantification of Φ1207.3 was performed by quantitative PCR (qPCR) and semiquantitatively by TEM. PCR quantified 3.34 × 104 and 6.06 × 104 excised forms of phage genome per milliliter of supernatant obtained from the untreated and mitomycin C-treated cultures, respectively. By TEM, we estimated 3.02 × 103 and 7.68 × 103 phage particles per milliliter of supernatant. The phage preparations of Φ1207.3 infected and lysogenized pneumococcal recipient strains at a frequency of 7.5 × 10-6 lysogens/recipient but did not show sufficient lytic activity to form plaques. Phage lysogenization efficiently occurred after 30 min of contact of the phages with the recipient cells and required a minimum of 103 phage particles. IMPORTANCE Bacteriophages play an important role in bacterial physiology and genome evolution. The widespread use of genome sequencing revealed that bacterial genomes can contain several different integrated temperate bacteriophages, which can constitute up to 20% of the genome. Most of these bacteriophages are only predicted in silico and are never shown to be functional. In fact, it is often difficult to induce the lytic cycle of temperate bacteriophages. In this work, we show that Φ1207.3, a peculiar bacteriophage originally from Streptococcus pyogenes, which can lysogenize different streptococci and carries the macrolide resistance mef(A)-msr(D) gene pair, is capable of producing mature virions, but only at a low level, while not being able to produce plaques. This temperate phage is probably a partially functional phage, which seems to have lost lytic characteristics to specialize in lysogenization. While we are not used to conceiving phages separately from lysis, this behavior could actually be more frequent than expected.
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Affiliation(s)
- Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gabiria Pastore
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Valeria Fox
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marie-Agnes Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis, Jouy-en-Josas, France
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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14
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Edgar RH, Samson AP, Kowalski RP, Kellum JA, Hempel J, Viator JA, Jhanji V. Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling. Front Med (Lausanne) 2023; 10:1017192. [PMID: 36910486 PMCID: PMC9995766 DOI: 10.3389/fmed.2023.1017192] [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: 08/11/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection. Methods We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples. Results Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture. Discussion Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.
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Affiliation(s)
- Robert H Edgar
- Swanson School of Engineering, Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Anie-Pier Samson
- Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - Regis P Kowalski
- School of Medicine and Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States
| | - John A Kellum
- Center for Central Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Spectral Medical, Toronto, ON, Canada
| | - John Hempel
- Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - John A Viator
- Swanson School of Engineering, Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - Vishal Jhanji
- School of Medicine and Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States
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15
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Wang Z, Guo K, Liu Y, Huang C, Wu M. Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment. Semin Cancer Biol 2022; 86:943-954. [PMID: 34656791 PMCID: PMC9008076 DOI: 10.1016/j.semcancer.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/20/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
The gut microbiome includes a series of microorganism genomes, such as bacteriome, virome, mycobiome, etc. The gut microbiota is critically involved in intestine immunity and diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC); however, the underlying mechanism remains incompletely understood. Clarifying the relationship between microbiota and inflammation may profoundly improve our understanding of etiology, disease progression, patient management, and the development of prevention and treatment. In this review, we discuss the latest studies of the influence of enteric viruses (i.e., commensal viruses, pathogenic viruses, and bacteriophages) in the initiation, progression, and complication of colitis and colorectal cancer, and their potential for novel preventative approaches and therapeutic application. We explore the interplay between gut viruses and host immune systems for its effects on the severity of inflammatory diseases and cancer, including both direct and indirect interactions between enteric viruses with other microbes and microbial products. Furthermore, the underlying mechanisms of the virome's roles in gut inflammatory response have been explained to infer potential therapeutic targets with examples in specific clinical trials. Given that very limited literature has thus far discussed these various topics with the gut virome, we believe these extensive analyses may provide insight into the understanding of the molecular pathogenesis of IBD and CRC, which could help add the design of improved therapies for these important human diseases.
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Affiliation(s)
- Zhihan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingying Liu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA.
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16
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A Method for Isolation Bacteriophage Particles-Free Genomic DNA, Exemplified by TP-84, Infecting Thermophilic Geobacillus. Microorganisms 2022; 10:microorganisms10091782. [PMID: 36144384 PMCID: PMC9502220 DOI: 10.3390/microorganisms10091782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/25/2022] Open
Abstract
DNA purification methods are indispensable tools of molecular biology, used for many decades. Nevertheless, for certain specialized applications, the currently employed techniques are not sufficiently effective. While examining a number of the existing methods to purify the genomic DNA of the thermophilic bacteriophage TP-84, which infects Geobacillus stearothermophilus (G. stearothermophilus), we have found out that the obtained DNA is contaminated with trace amounts of infectious TP-84 particles. This was detrimental for the bacteriophage genetic manipulation purposes, as finding the recombinant TP-84 clones was essentially impossible due to the appearance of a high background of native bacteriophage plaques. Thus, we have developed a method, which enables the fast and efficient isolation of a bacteriophage genomic DNA from concentrated phage preparations, obtained using CsCl gradient ultracentrifugation, without the need to remove concentrated CsCl solutions. The method employs silica columns and mini-scale isolation of microgram amounts of high quality DNA. It is universal—the silica mini-columns from various manufacturers can be used to conduct the procedure. The purified DNA, free from infectious bacteriophage particles, is ready for further manipulations. This is particularly important for such thermophilic bacteriophages that may partially survive standard isolation procedures and contaminate the final DNA product.
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17
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Li J, George Markowitz RH, Brooks AW, Mallott EK, Leigh BA, Olszewski T, Zare H, Bagheri M, Smith HM, Friese KA, Habibi I, Lawrence WM, Rost CL, Lédeczi Á, Eeds AM, Ferguson JF, Silver HJ, Bordenstein SR. Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes. PLoS Biol 2022; 20:e3001758. [PMID: 35998206 PMCID: PMC9397868 DOI: 10.1371/journal.pbio.3001758] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/14/2022] [Indexed: 11/28/2022] Open
Abstract
Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.
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Affiliation(s)
- Junhui Li
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert H George Markowitz
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew W Brooks
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Stanford University Genetics Department, Stanford University, Palo Alto, California, United States of America
| | - Elizabeth K Mallott
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brittany A Leigh
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Timothy Olszewski
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
| | - Hamid Zare
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Software Integrated Systems, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Minoo Bagheri
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Holly M Smith
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Katie A Friese
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
| | - Ismail Habibi
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - William M Lawrence
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charlie L Rost
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ákos Lédeczi
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Software Integrated Systems, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Angela M Eeds
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jane F Ferguson
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Heidi J Silver
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
- Tennessee Valley Healthcare System, Department of Veterans Affairs, Nashville, Tennessee, United States of America
| | - Seth R Bordenstein
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
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18
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Wang G, Li S, Yan Q, Guo R, Zhang Y, Chen F, Tian X, Lv Q, Jin H, Ma X, Ma Y. Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome. J Adv Res 2022:S2090-1232(22)00192-8. [PMID: 35995413 DOI: 10.1016/j.jare.2022.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 10/15/2022] Open
Abstract
INTRODUCTION Viruses in the human gut have been linked to health and disease. Deciphering the gut virome is dependent on metagenomic sequencing of the virus-like particles (VLPs) purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset. OBJECTIVES To develop an optimal method for viral amplification and metagenomic sequencing for maximizing the recovery of viral genomes. METHODS We performed parallel virus enrichment and DNA extraction to generate ∼ 30 viral DNA samples from each of 5 fresh fecal specimens and conducted the experiments including 1) optimizing the cycle number for high-fidelity enzyme-based PCR amplification, 2) evaluating the reproducibility of the optimally whole viral metagenomic experimental process, 3) evaluating the reliability of multiple displacement amplification (MDA), 4) testing the capability of long-read sequencing for improving viral metagenomic assembly, and 5) comparing the differences between viral metagenomic and bulk metagenomic approaches. RESULTS Our results revealed that the optimal cycle number for PCR amplification is 15. We verified the reliability of MDA and the effectiveness of long-read sequencing. Based on our optimized results, we generated 151 high-quality viruses using the dataset combined from short-read and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we uncovered significant differences in the efficiency and coverage of viral identification between viral metagenomic and bulk metagenomic approaches. CONCLUSIONS Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about the genome-level characterization of complex viral communities.
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Affiliation(s)
- Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Fang Chen
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiangge Tian
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China; Pharmaceutical Research Center, Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xiaochi Ma
- Pharmaceutical Research Center, Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Yufang Ma
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
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19
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Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, Franz CMAP. Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5. Viruses 2022; 14:v14081598. [PMID: 35893664 PMCID: PMC9394477 DOI: 10.3390/v14081598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
- Correspondence:
| | - Torben S. Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Finn K. Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Dennis S. Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
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20
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Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. MICROBIOME 2022; 10:105. [PMID: 35799219 PMCID: PMC9264660 DOI: 10.1186/s40168-022-01275-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
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Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Yue Li
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, China
| | - Mohammadali Khan Mirzaei
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Michael Shamash
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Rana Samadfam
- Charles River Laboratories, 22022 Transcanadienne, Senneville, QC, H9X 3R3, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
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21
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Johansen J, Plichta DR, Nissen JN, Jespersen ML, Shah SA, Deng L, Stokholm J, Bisgaard H, Nielsen DS, Sørensen SJ, Rasmussen S. Genome binning of viral entities from bulk metagenomics data. Nat Commun 2022; 13:965. [PMID: 35181661 PMCID: PMC8857322 DOI: 10.1038/s41467-022-28581-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/28/2022] [Indexed: 12/26/2022] Open
Abstract
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.
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Affiliation(s)
- Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakob Nybo Nissen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Statens Serum Institut, Viral & Microbial Special diagnostics, Copenhagen, Denmark
| | - Marie Louise Jespersen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ling Deng
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Manrique P, Zhu Y, van der Oost J, Herrema H, Nieuwdorp M, de Vos WM, Young M. Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome. Gut Microbes 2022; 13:1-15. [PMID: 33794724 PMCID: PMC8023239 DOI: 10.1080/19490976.2021.1897217] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Metabolic Syndrome (MetS) is a growing public health concern worldwide. Individuals with MetS have an increased risk for cardiovascular (CV) disease and type 2 diabetes (T2D). These diseases - in part preventable with the treatment of MetS - increase the chances of premature death and pose a great economic burden to health systems. A healthy gut microbiota is associated with a reduction in MetS, T2D, and CV disease. Treatment of MetS with fecal microbiota transplantation (FMT) can be effective, however, its success rate is intermediate and difficult to predict. Because bacteriophages significantly affect the microbiota membership and function, the aim of this pilot study was to explore the dynamics of the gut bacteriophage community after FMT in MetS subjects. We performed a longitudinal study of stool bacteriophages from healthy donors and MetS subjects before and after FMT treatment. Subjects were assigned to either a control group (self-stool transplant, n = 3) or a treatment group (healthy-donor-stool transplant; n-recipients = 6, n-donors = 5). Stool samples were collected over an 18-week period and bacteriophage-like particles were purified and sequenced. We found that FMT from healthy donors significantly alters the gut bacteriophage community. Subjects with better clinical outcome clustered closer to the heathy donor group, suggesting that throughout the treatment, their bacteriophage community was more similar to healthy donors. Finally, we identified bacteriophage groups that could explain these differences and we examined their prevalence in individuals from a larger cohort of MetS FMT trial.Trial information- http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2705; NTR 2705.
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Affiliation(s)
- Pilar Manrique
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
| | - Yifan Zhu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, AZ Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, AZ Amsterdam, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,RPU Human Microbiology, University of Helsinki, Faculty of Medicine, Helsinki, Finland
| | - Mark Young
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA,CONTACT Mark Young Department of Plant Sciences & Plant Pathology, Montana State University, P.O. Box 173150, Bozeman, MT59717-3150, USA
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23
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Young GR, Yew WC, Nelson A, Bridge SH, Berrington JE, Embleton ND, Smith DL. Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut. Front Pediatr 2022; 10:856520. [PMID: 35558373 PMCID: PMC9087270 DOI: 10.3389/fped.2022.856520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Human milk oligosaccharides, proteins, such as lactoferrin, and bacteria represent just some of the bioactive components of mother's breast milk (BM). Bacteriophages (viruses that infect bacteria) are an often-overlooked component of BM that can cause major changes in microbial composition and metabolism. BM bacteriophage composition has been explored in term and healthy infants, suggesting vertical transmission of bacteriophages occurs between mothers and their infants. Several important differences between term and very preterm infants (<30 weeks gestational age) may limit this phenomenon in the latter. To better understand the link between BM bacteriophages and gut microbiomes of very preterm infants in health and disease, standardised protocols are required for isolation and characterisation from BM. In this study, we use isolated nucleic acid content, bacteriophage richness and Shannon diversity to validate several parameters applicable during bacteriophage isolation from precious BM samples. Parameters validated include sample volume required; centrifugal sedimentation of microbes; hydrolysis of milk samples with digestive enzymes; induction of temperate bacteriophages and concentration/purification of isolated bacteriophage particles in donor milk (DM). Our optimised method enables characterisation of bacteriophages from as little as 0.1 mL BM. We identify viral families that were exclusively identified with the inclusion of induction of temperate bacteriophages (Inoviridae) and hydrolysis of milk lipid processes (Iridoviridae and Baculoviridae). Once applied to a small clinical cohort we demonstrate the vertical transmission of bacteriophages from mothers BM to the gut of very preterm infants at the species level. This optimised method will enable future research characterising the bacteriophage composition of BM in very preterm infants to determine their clinical relevance in the development of a healthy preterm infant gut microbiome.
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Affiliation(s)
- Gregory R Young
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wen C Yew
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Janet E Berrington
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Nicholas D Embleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
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24
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Rahimi-Midani A, Lee SW, Choi TJ. Potential Solutions Using Bacteriophages against Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121496. [PMID: 34943708 PMCID: PMC8698741 DOI: 10.3390/antibiotics10121496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are viruses that specifically infect a bacterial host. They play a great role in the modern biotechnology and antibiotic-resistant microbe era. Since the discovery of phages, their application as a control agent has faced challenges that made antibiotics a better fit for combating pathogenic bacteria. Recently, with the novel sequencing technologies providing new insight into the nature of bacteriophages, their application has a second chance to be used. However, novel challenges need to be addressed to provide proper strategies for their practical application. This review focuses on addressing these challenges by initially introducing the nature of bacteriophages and describing the phage-host-dependent strategies for phage application. We also describe the effect of the long-term application of phages in natural environments and other bacterial communities. Overall, this review gathered crucial information for the future application of phages. We predict the use of phages will not be the only control strategy against pathogenic bacteria. Therefore, more studies must be done for low-risk control methods against antimicrobial-resistant bacteria.
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Affiliation(s)
- Aryan Rahimi-Midani
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
- Correspondence:
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25
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Wang M, Sun Y, Zeng Z, Wang Z. Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 222:112552. [PMID: 34325201 DOI: 10.1016/j.ecoenv.2021.112552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.
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Affiliation(s)
- Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China; International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou, Jiangsu 225009, China.
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26
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Brunse A, Deng L, Pan X, Hui Y, Castro-Mejía JL, Kot W, Nguyen DN, Secher JBM, Nielsen DS, Thymann T. Fecal filtrate transplantation protects against necrotizing enterocolitis. ISME JOURNAL 2021; 16:686-694. [PMID: 34552194 PMCID: PMC8857206 DOI: 10.1038/s41396-021-01107-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/20/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
Necrotizing enterocolitis (NEC) is a life-threatening gastrointestinal disorder afflicting preterm infants, which is currently unpreventable. Fecal microbiota transplantation (FMT) is a promising preventive therapy, but the transfer of pathogenic microbes or toxic compounds raise concern. Removal of bacteria from donor feces by micropore filtering may reduce this risk of bacterial infection, while residual bacteriophages could maintain the NEC-preventive effects. We aimed to assess preclinical efficacy and safety of fecal filtrate transplantation (FFT). Using fecal material from healthy suckling piglets, we compared rectal FMT administration (FMT, n = 16) with cognate FFT by either rectal (FFTr, n = 14) or oro-gastric administration (FFTo, n = 13) and saline (CON, n = 16) in preterm, cesarean-delivered piglets as models for preterm infants. We assessed gut pathology and analyzed mucosal and luminal bacterial and viral composition using 16S rRNA gene amplicon and meta-virome sequencing. Finally, we used isolated ileal mucosa, coupled with RNA-Seq, to gauge the host response to the different treatments. Oro-gastric FFT completely prevented NEC, which was confirmed by microscopy, whereas FMT did not perform better than control. Oro-gastric FFT increased viral diversity and reduced Proteobacteria relative abundance in the ileal mucosa relative to control. An induction of mucosal immunity was observed in response to FMT but not FFT. As preterm infants are extremely vulnerable to infections, rational NEC-preventive strategies need incontestable safety profiles. We show in a clinically relevant animal model that FFT, as opposed to FMT, efficiently prevents NEC without any recognizable side effects.
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Affiliation(s)
- Anders Brunse
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ling Deng
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Xiaoyu Pan
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yan Hui
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Josué L Castro-Mejía
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Duc Ninh Nguyen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan Bojsen-Møller Secher
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dennis Sandris Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Thymann
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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27
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Abstract
Viruses are the most abundant biological entity on Earth, infect cellular organisms from all domains of life, and are central players in the global biosphere. Over the last century, the discovery and characterization of viruses have progressed steadily alongside much of modern biology. In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field. Advances in methods for identifying viral sequences in genomic and metagenomic datasets, coupled to the exponential growth of environmental sequencing, have greatly expanded the catalog of known viruses and fueled the tremendous growth of viral sequence databases. Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology, and biogeochemical cycles, leading to new biotechnological innovations across many diverse fields, including environmental, agricultural, and biomedical sciences.
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Affiliation(s)
- Lee Call
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Stephen Nayfach
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; ,
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28
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Abstract
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables an organism to rapidly adapt to changing environmental conditions, provides a competitive edge and potentially alters its relationship with its host. Although the HGT process is routinely exploited in laboratories, there is a surprising disconnect between what we know from laboratory experiments and what we know from natural environments, such as the human gut microbiome. Owing to a suite of newly available computational algorithms and experimental approaches, we have a broader understanding of the genes that are being transferred and are starting to understand the ecology of HGT in natural microbial communities. This Review focuses on these new technologies, the questions they can address and their limitations. As these methods are applied more broadly, we are beginning to recognize the full extent of HGT possible within a microbiome and the punctuated dynamics of HGT, specifically in response to external stimuli. Furthermore, we are better characterizing the complex selective pressures on mobile genetic elements and the mechanisms by which they interact with the bacterial host genome.
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Affiliation(s)
- Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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29
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王 展, 徐 开, 周 宏. [Characteristics of gut virome and microbiome in patients with stroke]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:862-869. [PMID: 34238738 PMCID: PMC8267978 DOI: 10.12122/j.issn.1673-4254.2021.06.08] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the differences in gut virome and microbiome between patients with stroke and healthy volunteers. OBJECTIVE Fifteen patients with acute ischemic stroke treated in the Department of Neurology of Nanfang Hospital between February, 2014 and February, 2016 and 15 healthy volunteers matched for age and sex were enrolled in this study. Virome sequencing and 16S rRNA sequencing were performed on stool samples of all the participants, and the composition and structures of the virome and microbiome were compared between the two groups. OBJECTIVE No significant difference was found in the overall diversity of virome between the stroke patients and the healthy volunteers (alpha diversity: P=0.320; beta diversity: P=0.169, R2=0.037), but virome composition differed significantly between the two groups. The relative abundance of Bacteroides phage B40_8 and Cronobacter phage CS01 increased significantly in patients with stroke. The structures and composition of the microbiome in patients with stroke also differed significantly from those of the healthy volunteers (alpha diversity: P=0.950; beta diversity: P=0.005, R2=0.117). The relative abundance of Megasphaera increased while that of Bifidobacterium decreased in patients with stroke. Correlation analysis showed that in the virome of stroke patients, the relative abundance of the phage preying Streptococcus was positively correlated with that of their hosts (r=0.550, P=0.036), while in the virome of healthy volunteers, the relative abundance of the phage preying Faecalibacterium (r=0.520, P=0.049), Bilophila (r=0.541, P=0.040) and Roseburia (r=0.526, P=0.046) were positively correlated with that of their respective hosts. OBJECTIVE Stroke patients have similar overall diversity of the virome to healthy volunteers but different virome composition and interaction patterns between the virome and microbiome. The gut microbiome also differs between stroke patients and healthy volunteers. The relative abundance of opportunistic pathogens increases but that of symbiotic bacteria decreases in stroke patients.
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Affiliation(s)
- 展强 王
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 开宇 徐
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 宏伟 周
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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30
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Benler S, Koonin EV. Fishing for phages in metagenomes: what do we catch, what do we miss? Curr Opin Virol 2021; 49:142-150. [PMID: 34139668 DOI: 10.1016/j.coviro.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Metagenomics and metatranscriptomics have become the principal approaches for discovery of novel bacteriophages and preliminary characterization of their ecology and biology. Metagenomic sequencing dramatically expanded the known diversity of tailed and non-tailed phages with double-stranded DNA genomes and those with single-stranded DNA genomes, whereas metatranscriptomics led to the discovery of thousands of new single-stranded RNA phages. Apart from expanding phage diversity, metagenomics studies discover major novel groups of phages with unique features of genome organization, expression strategy and virus-host interaction, such as the putative order 'crAssvirales', which includes the most abundant human-associated viruses. The continued success of metagenomics hinges on the combination of the most powerful computational methods for phage genome assembly and analysis including harnessing CRISPR spacers for the discovery of novel phages and host assignment. Together, these approaches could make a comprehensive characterization of the earth phageome a realistic goal.
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Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information, National Institutes of Health, Bethesda MD, United States.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of Health, Bethesda MD, United States.
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31
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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32
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Cieślik M, Bagińska N, Jończyk-Matysiak E, Węgrzyn A, Węgrzyn G, Górski A. Temperate Bacteriophages-The Powerful Indirect Modulators of Eukaryotic Cells and Immune Functions. Viruses 2021; 13:v13061013. [PMID: 34071422 PMCID: PMC8228536 DOI: 10.3390/v13061013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteriophages are natural biological entities that limit the growth and amplification of bacteria. They are important stimulators of evolutionary variability in bacteria, and currently are considered a weapon against antibiotic resistance of bacteria. Nevertheless, apart from their antibacterial activity, phages may act as modulators of mammalian immune responses. In this paper, we focus on temperate phages able to execute the lysogenic development, which may shape animal or human immune response by influencing various processes, including phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
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Affiliation(s)
- Martyna Cieślik
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.C.); (N.B.); (E.J.-M.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
- Correspondence:
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33
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Alanin KWS, Junco LMF, Jørgensen JB, Nielsen TK, Rasmussen MA, Kot W, Hansen LH. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses 2021; 13:959. [PMID: 34064231 PMCID: PMC8224292 DOI: 10.3390/v13060959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
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Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Laura Milena Forero Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Jacob Bruun Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Morten Arendt Rasmussen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark;
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
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34
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João J, Lampreia J, Prazeres DMF, Azevedo AM. Manufacturing of bacteriophages for therapeutic applications. Biotechnol Adv 2021; 49:107758. [PMID: 33895333 DOI: 10.1016/j.biotechadv.2021.107758] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/14/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022]
Abstract
Bacteriophages, or simply phages, are the most abundant biological entities on Earth. One of the most interesting characteristics of these viruses, which infect and use bacteria as their host organisms, is their high level of specificity. Since their discovery, phages became a tool for the comprehension of basic molecular biology and originated applications in a variety of areas such as agriculture, biotechnology, food safety, veterinary, pollution remediation and wastewater treatment. In particular, phages offer a solution to one of the major problems in public health nowadays, i.e. the emergence of multidrug-resistant bacteria. In these situations, the use of virulent phages as therapeutic agents offers an alternative to the classic, antibiotic-based strategies. The development of phage therapies should be accompanied by the improvement of phage biomanufacturing processes, both at laboratory and industrial scales. In this review, we first present some historical and general aspects related with the discovery, usage and biology of phages and provide a brief overview of the most relevant phage therapy applications. Then, we showcase current processes used for the production and purification of phages and future alternatives in development. On the production side, key factors such as the bacterial physiological state, the conditions of phage infection and the operation parameters are described alongside with the different operation modes, from batch to semi-continuous and continuous. Traditional purification methods used in the initial phage isolation steps are then described followed by the presentation of current state-of-the-art purification approaches. Continuous purification of phages is finally presented as a future biomanufacturing trend.
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Affiliation(s)
- Jorge João
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - João Lampreia
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Duarte Miguel F Prazeres
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
| | - Ana M Azevedo
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal.
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35
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Soleimani-Delfan A, Bouzari M, Wang R. A rapid competitive method for bacteriophage genomic DNA extraction. J Virol Methods 2021; 293:114148. [PMID: 33831496 DOI: 10.1016/j.jviromet.2021.114148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The bacteriophage (phage) DNA extraction methods for genomics analysis is a critical and time-consuming process. Hence, a rapid and cost-effective method for DNA extraction of phages is favorable for phage biologists. In the present study, a cost-effective, simple and rapid procedure for phage genome extraction in less than 10 min is introduced. Highly concentrated phage lysates were prepared using acetone precipitation followed by extraction using various methods such as commercial kits, TES lysis buffer, potassium iodide, and sodium iodide. The quality of the extracted DNA was analyzed by agarose gel electrophoresis and UV absorbance of DNA at 260 and 280 nm. Finally, the extracted DNA was subjected to restriction digestion and next-generation sequencing to approve the efficiency of the method. Based on the time, cost, and quality of obtained DNA, the acetone precipitation of phages and extraction by potassium iodide or sodium iodide method was determined to be the best method for phage DNA extraction tested in this study. Moreover, the extracted genomic DNA using this method is suitable for phage genomic analysis such as restriction enzyme studies, preparation of DNA library, and also next-generation sequencing.
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Affiliation(s)
- Abbas Soleimani-Delfan
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJereeb Street, 81746-73441, Isfahan, Iran
| | - Majid Bouzari
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJereeb Street, 81746-73441, Isfahan, Iran.
| | - Ran Wang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China.
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36
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Perlemoine P, Marcoux PR, Picard E, Hadji E, Zelsmann M, Mugnier G, Marchet A, Resch G, O’Connell L, Lacot E. Phage susceptibility testing and infectious titer determination through wide-field lensless monitoring of phage plaque growth. PLoS One 2021; 16:e0248917. [PMID: 33755710 PMCID: PMC7987195 DOI: 10.1371/journal.pone.0248917] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
The growing number of drug-resistant bacterial infections worldwide is driving renewed interest in phage therapy. Based on the use of a personalized cocktail composed of highly specific bacterial viruses, this therapy relies on a range of tests on agar media to determine the most active phage on a given bacterial target (phage susceptibility testing), or to isolate new lytic phages from an environmental sample (enrichment of phage banks). However, these culture-based techniques are still solely interpreted through direct visual detection of plaques. The main objective of this work is to investigate computer-assisted methods in order to ease and accelerate diagnosis in phage therapy but also to study phage plaque growth kinetics. For this purpose, we designed a custom wide-field lensless imaging device, which allows continuous monitoring over a very large area sensor (3.3 cm2). Here we report bacterial susceptibility to Staphylococcus aureus phage in 3 hr and estimation of infectious titer in 8 hr 20 min. These are much shorter time-to-results than the 12 to 24 hours traditionally needed, since naked eye observation and counting of phage plaques is still the most widely used technique for susceptibility testing prior to phage therapy. Moreover, the continuous monitoring of the samples enables the study of plaque growth kinetics, which enables a deeper understanding of the interaction between phage and bacteria. Finally, thanks to the 4.3 μm resolution, we detect phage-resistant bacterial microcolonies of Klebsiella pneumoniae inside the boundaries of phage plaques and thus show that our prototype is also a suitable device to track phage resistance. Lensless imaging is therefore an all-in-one method that could easily be implemented in cost-effective and compact devices in phage laboratories to help with phage therapy diagnosis.
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Affiliation(s)
- Prisca Perlemoine
- Department of Microtechnologies for Biology and Health, LETI, CEA, University Grenoble Alpes, Grenoble, France
| | - Pierre R. Marcoux
- Department of Microtechnologies for Biology and Health, LETI, CEA, University Grenoble Alpes, Grenoble, France
| | - Emmanuel Picard
- SINAPS, PHELIQS, DEPHY, IRIG, DRF, CEA, University Grenoble Alpes, Grenoble, France
| | - Emmanuel Hadji
- SINAPS, PHELIQS, DEPHY, IRIG, DRF, CEA, University Grenoble Alpes, Grenoble, France
| | - Marc Zelsmann
- LTM–Micro and Nanotechnologies for Health, CNRS, CEA, University Grenoble Alpes, Grenoble, France
| | - Grégoire Mugnier
- LTM–Micro and Nanotechnologies for Health, CNRS, CEA, University Grenoble Alpes, Grenoble, France
| | - Aurélie Marchet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Larry O’Connell
- SyMMES, IRIG, DRF, CEA, University Grenoble Alpes, Grenoble, France
| | - Eric Lacot
- Laboratoire Interdisciplinaire de Physique, CNRS UMR 5588, University Grenoble Alpes, St Martin d’Hères, France
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Abstract
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
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Affiliation(s)
- Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Jørgen Slots
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, California, USA
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
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38
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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review. Microorganisms 2021; 9:524. [PMID: 33806607 PMCID: PMC8000950 DOI: 10.3390/microorganisms9030524] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.
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Affiliation(s)
| | | | | | | | | | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (J.C.); (S.R.S.); (A.S.); (L.A.D.); (R.P.R.)
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39
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Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity. Viruses 2021; 13:v13020328. [PMID: 33672780 PMCID: PMC7924620 DOI: 10.3390/v13020328] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
For decades, bacteriophage purification has followed structured protocols focused on generating high concentrations of phage in manageable volumes. As research moves toward understanding complex phage populations, purification needs have shifted to maximize the amount of phage while maintaining diversity and activity. The effects of standard phage purification procedures such as polyethylene glycol (PEG) precipitation and cesium chloride (CsCl) density gradients on both diversity and activity of a phage population are not known. We have examined the effects of PEG precipitation and CsCl density gradients on a number of known phage (M13, T4, and ΦX 174) of varying structure and size, individually and as mixed sample. Measurement of phage numbers and activity throughout the purification process was performed. We demonstrate that these methods, used routinely to generate "pure" phage samples, are in fact detrimental to retention of phage number and activity; even more so in mixed phage samples. As such, minimal amounts of processing are recommended to introduce less bias and maintain more of a phage population.
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40
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Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T. Taxonomic, functional and expression analysis of viral communities associated with marine sponges. PeerJ 2021; 9:e10715. [PMID: 33604175 PMCID: PMC7863781 DOI: 10.7717/peerj.10715] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.
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Affiliation(s)
- Mary Nguyen
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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41
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Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, Wang J, Cui G, Sun Y, Xiao M, Kang J, Zhang W, Zhang A, Li P, Liu X, Ulllah H, Ma Y, Li S, Ma T. Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis. Virus Evol 2021; 7:veab022. [PMID: 33959381 PMCID: PMC8087960 DOI: 10.1093/ve/veab022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remains unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, for example ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing twenty-four healthy adults and six children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals' gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were not only inherited from that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (P < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.
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Affiliation(s)
- Qiulong Yan
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yu Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- Institute of Translational Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing 210029, China
| | - Xiuli Chen
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Hao Jin
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Saihan District, Hohhot 010018, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Kuiqing Guan
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Yue Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200032, China
| | - Taj Ayaz
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yanshan Liang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Junyi Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Guangyi Cui
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Yuanyuan Sun
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Manchun Xiao
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Jian Kang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Wei Zhang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Aiqin Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Peng Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Xueyang Liu
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Hayan Ulllah
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yufang Ma
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Shenghui Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Tonghui Ma
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
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Massimino L, Lovisa S, Antonio Lamparelli L, Danese S, Ungaro F. Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? Comput Struct Biotechnol J 2020; 19:16-28. [PMID: 33363706 PMCID: PMC7750180 DOI: 10.1016/j.csbj.2020.11.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is composed of bacteria and viruses that might be associated with colorectal cancer (CRC) onset and progression. Indeed, although viral infections have been reported to be the primary trigger in many diseases, the role of eukaryotic viruses populating the gut mucosa during early colorectal carcinogenesis is underinvestigated. Human eukaryotic viruses in the gut were found to induce alterations of the immune homeostasis so that some viral-dependent mechanisms likely able to induce DNA alterations in the bowel wall have been proposed, although no demonstration is available yet. However, thanks to the latest advancements in computational biology and the implementation of the bioinformatic pipelines, the option of establishing a direct causative link between intestinal virome and CRC will be possible soon, hopefully paving the way to innovative therapeutic strategies blocking or reverting the CRC pathogenesis.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Sara Lovisa
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | | | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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Yang J, Zheng P, Li Y, Wu J, Tan X, Zhou J, Sun Z, Chen X, Zhang G, Zhang H, Huang Y, Chai T, Duan J, Liang W, Yin B, Lai J, Huang T, Du Y, Zhang P, Jiang J, Xi C, Wu L, Lu J, Mou T, Xu Y, Perry SW, Wong ML, Licinio J, Hu S, Wang G, Xie P. Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders. SCIENCE ADVANCES 2020; 6:6/49/eaba8555. [PMID: 33268363 PMCID: PMC7710361 DOI: 10.1126/sciadv.aba8555] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 10/16/2020] [Indexed: 05/23/2023]
Abstract
Gut microbiome disturbances have been implicated in major depressive disorder (MDD). However, little is known about how the gut virome, microbiome, and fecal metabolome change, and how they interact in MDD. Here, using whole-genome shotgun metagenomic and untargeted metabolomic methods, we identified 3 bacteriophages, 47 bacterial species, and 50 fecal metabolites showing notable differences in abundance between MDD patients and healthy controls (HCs). Patients with MDD were mainly characterized by increased abundance of the genus Bacteroides and decreased abundance of the genera Blautia and Eubacterium These multilevel omics alterations generated a characteristic MDD coexpression network. Disturbed microbial genes and fecal metabolites were consistently mapped to amino acid (γ-aminobutyrate, phenylalanine, and tryptophan) metabolism. Furthermore, we identified a combinatorial marker panel that robustly discriminated MDD from HC individuals in both the discovery and validation sets. Our findings provide a deep insight into understanding of the roles of disturbed gut ecosystem in MDD.
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Affiliation(s)
- Jian Yang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yifan Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jing Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xunmin Tan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jingjing Zhou
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Zuoli Sun
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Xu Chen
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Guofu Zhang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Hanping Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yu Huang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tingjia Chai
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiajia Duan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Weiwei Liang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Bangmin Yin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- MOE Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jianbo Lai
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- The Key Laboratory of Mental Disorder's Management of Zhejiang Province, No. 79, Qingchun Road, Hangzhou 310003, China
| | - Tingting Huang
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Yanli Du
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Peifen Zhang
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jiajun Jiang
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Caixi Xi
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Lingling Wu
- Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jing Lu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- The Key Laboratory of Mental Disorder's Management of Zhejiang Province, No. 79, Qingchun Road, Hangzhou 310003, China
| | - Tingting Mou
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- The Key Laboratory of Mental Disorder's Management of Zhejiang Province, No. 79, Qingchun Road, Hangzhou 310003, China
| | - Yi Xu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- The Key Laboratory of Mental Disorder's Management of Zhejiang Province, No. 79, Qingchun Road, Hangzhou 310003, China
| | - Seth W Perry
- Department of Psychiatry and Behavioral Sciences, College of Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience & Physiology, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ma-Li Wong
- Department of Psychiatry and Behavioral Sciences, College of Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience & Physiology, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Julio Licinio
- Department of Psychiatry and Behavioral Sciences, College of Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, USA
- Department of Neuroscience & Physiology, College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Shaohua Hu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
- The Key Laboratory of Mental Disorder's Management of Zhejiang Province, No. 79, Qingchun Road, Hangzhou 310003, China
| | - Gang Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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Marônek M, Link R, Monteleone G, Gardlík R, Stolfi C. Viruses in Cancers of the Digestive System: Active Contributors or Idle Bystanders? Int J Mol Sci 2020; 21:ijms21218133. [PMID: 33143318 PMCID: PMC7663754 DOI: 10.3390/ijms21218133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
The human virome, which is a collection of all the viruses that are present in the human body, is increasingly being recognized as an essential part of the human microbiota. The human gastrointestinal tract and related organs (e.g., liver, pancreas, and gallbladder)-composing the gastrointestinal (or digestive) system-contain a huge number of viral particles which contribute to maintaining tissue homeostasis and keeping our body healthy. However, perturbations of the virome steady-state may, both directly and indirectly, ignite/sustain oncogenic mechanisms contributing to the initiation of a dysplastic process and/or cancer progression. In this review, we summarize and discuss the available evidence on the association and role of viruses in the development of cancers of the digestive system.
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Affiliation(s)
- Martin Marônek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (M.M.); (R.G.)
| | - René Link
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia;
| | - Giovanni Monteleone
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Roman Gardlík
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (M.M.); (R.G.)
| | - Carmine Stolfi
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy;
- Division of Clinical Biochemistry and Clinical Molecular Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-06-72596163
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Saladié M, Caparrós-Martín JA, Agudelo-Romero P, Wark PAB, Stick SM, O'Gara F. Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. Front Microbiol 2020; 11:572504. [PMID: 33123104 PMCID: PMC7573210 DOI: 10.3389/fmicb.2020.572504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years the study of the commensal microbiota is driving a remarkable paradigm shift in our understanding of human physiology. However, intrinsic technical difficulties associated with investigating the Microbiomics of some body niches are hampering the development of new knowledge. This is particularly the case when investigating the functional role played by the human microbiota in modulating the physiology of key organ systems. A major hurdle in investigating specific Microbiome communities is linked to low bacterial density and susceptibility to bias caused by environmental contamination. To prevent such inaccuracies due to background processing noise, harmonized tools for Microbiomic and bioinformatics practices have been recommended globally. The fact that the impact of this undesirable variability is negatively correlated with the DNA concentration in the sample highlights the necessity to improve existing DNA isolation protocols. In this report, we developed and tested a protocol to more efficiently recover bacterial DNA from low volumes of bronchoalveolar lavage fluid obtained from infants and adults. We have compared the efficiency of the described method with that of a commercially available kit for microbiome analysis in body fluids. We show that this new methodological approach performs better in terms of extraction efficiency. As opposed to commercial kits, the DNA extracts obtained with this new protocol were clearly distinguishable from the negative extraction controls in terms of 16S copy number and Microbiome community profiles. Altogether, we described a cost-efficient protocol that can facilitate microbiome research in low-biomass human niches.
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Affiliation(s)
- Montserrat Saladié
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Jose Antonio Caparrós-Martín
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Patricia Agudelo-Romero
- Telethon Kids Institute, Perth, WA, Australia.,ARC Centre for Plant Energy Biology, Faculty of Science, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Peter A B Wark
- Centre of Excellence in Severe Asthma and Priority Research, Centre for Healthy Lungs, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, WA, Australia
| | - Fergal O'Gara
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Telethon Kids Institute, Perth, WA, Australia.,BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
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47
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Miller-Ensminger T, Garretto A, Stark N, Putonti C. Mimicking prophage induction in the body: induction in the lab with pH gradients. PeerJ 2020; 8:e9718. [PMID: 32944418 PMCID: PMC7469935 DOI: 10.7717/peerj.9718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of bacteria within the human body are lysogens, often harboring multiple bacteriophage sequences (prophages) within their genomes. While several different types of environmental stresses can trigger or induce prophages to enter into the lytic cycle, they have yet to be fully explored and understood in the human microbiota. In the laboratory, the most common induction method is the DNA damaging chemical Mitomycin C. Although pH has been listed in the literature as an induction method, it is not widely used. Here, we detail a protocol for prophage induction by culture under different pH conditions. We explored the effects of pH on prophage induction in bacterial isolates from the bladder, where the pH is well documented to vary significantly between individuals as well as between healthy individuals and individuals with urinary tract symptoms or disease. Using this protocol, we successfully induced phages from seven bladder E. coli strains. Testing conditions and stressors appropriate to the environment from which a lysogen is isolated may provide insight into community dynamics of the human microbiota.
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Affiliation(s)
| | - Andrea Garretto
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology & Immunology, University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America
| | - Nicole Stark
- Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Indiana University at Bloomington, Bloomington, IN, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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48
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Rotman SG, Sumrall E, Ziadlou R, Grijpma DW, Richards RG, Eglin D, Moriarty TF. Local Bacteriophage Delivery for Treatment and Prevention of Bacterial Infections. Front Microbiol 2020; 11:538060. [PMID: 33072008 PMCID: PMC7531225 DOI: 10.3389/fmicb.2020.538060] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
As viruses with high specificity for their bacterial hosts, bacteriophages (phages) are an attractive means to eradicate bacteria, and their potential has been recognized by a broad range of industries. Against a background of increasing rates of antibiotic resistance in pathogenic bacteria, bacteriophages have received much attention as a possible "last-resort" strategy to treat infections. The use of bacteriophages in human patients is limited by their sensitivity to acidic pH, enzymatic attack and short serum half-life. Loading phage within a biomaterial can shield the incorporated phage against many of these harmful environmental factors, and in addition, provide controlled release for prolonged therapeutic activity. In this review, we assess the different classes of biomaterials (i.e., biopolymers, synthetic polymers, and ceramics) that have been used for phage delivery and describe the processing methodologies that are compatible with phage embedding or encapsulation. We also elaborate on the clinical or pre-clinical data generated using these materials. While a primary focus is placed on the application of phage-loaded materials for treatment of infection, we also include studies from other translatable fields such as food preservation and animal husbandry. Finally, we summarize trends in the literature and identify current barriers that currently prevent clinical application of phage-loaded biomaterials.
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Affiliation(s)
- Stijn Gerard Rotman
- AO Research Institute Davos, AO Foundation, Davos, Switzerland.,MIRA Institute for Biomedical Engineering and Technical Medicine, Department of Biomaterials Science and Technology, University of Twente, Enschede, Netherlands
| | - Eric Sumrall
- AO Research Institute Davos, AO Foundation, Davos, Switzerland
| | - Reihane Ziadlou
- AO Research Institute Davos, AO Foundation, Davos, Switzerland.,Department of Biomedical Engineering, Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Dirk W Grijpma
- MIRA Institute for Biomedical Engineering and Technical Medicine, Department of Biomaterials Science and Technology, University of Twente, Enschede, Netherlands
| | | | - David Eglin
- AO Research Institute Davos, AO Foundation, Davos, Switzerland.,MIRA Institute for Biomedical Engineering and Technical Medicine, Department of Biomaterials Science and Technology, University of Twente, Enschede, Netherlands
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49
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Guerin E, Hill C. Shining Light on Human Gut Bacteriophages. Front Cell Infect Microbiol 2020; 10:481. [PMID: 33014897 PMCID: PMC7511551 DOI: 10.3389/fcimb.2020.00481] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022] Open
Abstract
The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.
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Affiliation(s)
- Emma Guerin
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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McNamara RP, Dittmer DP. Modern Techniques for the Isolation of Extracellular Vesicles and Viruses. J Neuroimmune Pharmacol 2020. [PMID: 31512168 DOI: 10.1007/s11481-%20019-09874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Extracellular signaling is pivotal to maintain organismal homeostasis. A quickly emerging field of interest within extracellular signaling is the study of extracellular vesicles (EV), which act as messaging vehicles for nucleic acids, proteins, metabolites, lipids, etc. from donor cells to recipient cells. This transfer of biologically active material within a vesicular body is similar to the infection of a cell through a virus particle, which transfers genetic material from one cell to another to preserve an infection state, and viruses are known to modulate EV. Although considerable heterogeneity exists within EV and viruses, this review focuses on those that are small (< 200 nm in diameter) and of relatively low density (< 1.3 g/mL). A multitude of isolation methods for EV and virus particles exist. In this review, we present an update on methods for their isolation, purification, and phenotypic characterization. We hope that the information we provide will be of use to basic science and clinical investigators, as well as biotechnologists in this emerging field. Graphical Abstract.
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Affiliation(s)
- Ryan P McNamara
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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