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Loney RE, Delesalle VA, Chaudry BE, Czerpak M, Guffey AA, Goubet-McCall L, McCarty M, Strine MS, Tanke NT, Vill AC, Krukonis GP. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023; 15:2267. [PMID: 38005943 PMCID: PMC10674732 DOI: 10.3390/v15112267] [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: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.
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Affiliation(s)
- Rachel E. Loney
- University Program in Genetics and Genomics, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | | | - Megan Czerpak
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Alexandra A. Guffey
- Janssen Scientific Affairs, LLC. 200 Tournament Dr., Horsham, PA 19044, USA;
| | - Leo Goubet-McCall
- Department of Biology, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, PA 16802, USA;
| | - Michael McCarty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Madison S. Strine
- Department of Immunobiology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA;
| | - Natalie T. Tanke
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Albert C. Vill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA;
| | - Greg P. Krukonis
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA;
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2
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Zhong KX, Wirth JF, Chan AM, Suttle CA. Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis. THE ISME JOURNAL 2023; 17:105-116. [PMID: 36209336 PMCID: PMC9751121 DOI: 10.1038/s41396-022-01327-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Abstract
Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Jennifer F Wirth
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada.
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3
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Delesalle VA, Tomko BE, Vill AC, Lichty KB, Krukonis GP. Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative. Viruses 2022; 14:2106. [PMID: 36298661 PMCID: PMC9607348 DOI: 10.3390/v14102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2023] Open
Abstract
SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage-host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more genes than SPP1. We identified a new putative gene in SPP1 based on a conserved sequence found in all phages. Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. Patterns of divergence point to genes or gene domains likely involved in adaptation to diverse hosts or different environments. Ultimately, comparative genomics of related phages provides insight into the long-term selective pressures that affect phage-bacteria interactions and alter phage genome content.
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Affiliation(s)
- Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Brianne E. Tomko
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
| | - Albert C. Vill
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd., Ithaca, NY 14850, USA
| | - Katherine B. Lichty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biological Sciences, University of Delaware, Wolf Hall, Newark, DE 19716, USA
| | - Greg P. Krukonis
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA
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4
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Vill AC, Delesalle VA, Tomko BE, Lichty KB, Strine MS, Guffey AA, Burton EA, Tanke NT, Krukonis GP. Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:171-178. [PMID: 36793550 PMCID: PMC9917325 DOI: 10.1089/phage.2022.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Despite their importance to microbial dynamics involving Bacillus subtilis, we have a limited understanding of the diversity of phages that can lyse this model organism. Materials and Methods Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild B. subtilis strain. Their genomes were assembled, characterized, and bioinformatically compared. Results Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes. Conclusions A comparative approach provides insights into phage evolution, including the role of indels in protein folding.
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Affiliation(s)
- Albert C. Vill
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | - Brianne E. Tomko
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | - Madison S. Strine
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | | | | | - Natalie T. Tanke
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Greg P. Krukonis
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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5
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Spencer L, Olawuni B, Singh P. Gut Virome: Role and Distribution in Health and Gastrointestinal Diseases. Front Cell Infect Microbiol 2022; 12:836706. [PMID: 35360104 PMCID: PMC8960297 DOI: 10.3389/fcimb.2022.836706] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 12/11/2022] Open
Abstract
The study of the intestinal microbiome is an evolving field of research that includes comprehensive analysis of the vast array of microbes – bacterial, archaeal, fungal, and viral. Various gastrointestinal (GI) diseases, such as Crohn’s disease and ulcerative colitis, have been associated with instability of the gut microbiota. Many studies have focused on importance of bacterial communities with relation to health and disease in humans. The role of viruses, specifically bacteriophages, have recently begin to emerge and have profound impact on the host. Here, we comprehensively review the importance of viruses in GI diseases and summarize their influence in the complex intestinal environment, including their biochemical and genetic activities. We also discuss the distribution of the gut virome as it relates with treatment and immunological advantages. In conclusion, we suggest the need for further studies on this critical component of the intestinal microbiome to decipher the role of the gut virome in human health and disease.
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6
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Prussin AJ, Belser JA, Bischoff W, Kelley ST, Lin K, Lindsley WG, Nshimyimana JP, Schuit M, Wu Z, Bibby K, Marr LC. Viruses in the Built Environment (VIBE) meeting report. MICROBIOME 2020; 8:1. [PMID: 31901242 PMCID: PMC6942371 DOI: 10.1186/s40168-019-0777-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled "Viruses in the Built Environment (VIBE)," at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. RESULTS Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. CONCLUSIONS We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi. Video abstract.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jessica A. Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Werner Bischoff
- Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Kaisen Lin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - William G. Lindsley
- Health Effects Laboratory Division (HELD), National Institute for Occupational Safety and Health, Morgantown, WV 26505 USA
| | | | - Michael Schuit
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702 USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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7
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. MICROBIOME 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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8
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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9
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Forde A, Hill C. Phages of life - the path to pharma. Br J Pharmacol 2018; 175:412-418. [PMID: 29266197 PMCID: PMC5773946 DOI: 10.1111/bph.14106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini-review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient-focused pharmaceutical intervention.
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Affiliation(s)
- Amanda Forde
- APC Microbiome InstituteUniversity College CorkCorkIreland
| | - Colin Hill
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome InstituteUniversity College CorkCorkIreland
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10
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Hayes S, Mahony J, Nauta A, van Sinderen D. Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Viruses 2017; 9:v9060127. [PMID: 28538703 PMCID: PMC5490804 DOI: 10.3390/v9060127] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral ‘dark matter’ of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.
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Affiliation(s)
- Stephen Hayes
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
| | - Arjen Nauta
- Friesland Campina, Amersfoort 3800 BN, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
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11
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Genomic exploration of individual giant ocean viruses. ISME JOURNAL 2017; 11:1736-1745. [PMID: 28498373 DOI: 10.1038/ismej.2017.61] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 12/16/2022]
Abstract
Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on 'giant viruses' that are readily distinguishable by flow cytometry. From a single-milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. We discovered a viral metacaspase homolog in one of our sorted virus particles and discussed its implications in rewiring host metabolism to enhance infection. In addition, we demonstrated that viral metacaspases are widespread in the ocean. We also discovered a virus that contains both a reverse transcriptase and a transposase; although highly speculative, we suggest such a genetic complement would potentially allow this virus to exploit a latency propagation mechanism. Application of single virus genomics provides a powerful opportunity to circumvent cultivation of viruses, moving directly to genomic investigation of naturally occurring viruses, with the assurance that the sequence data is virus-specific, non-chimeric and contains no cellular contamination.
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12
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Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol 2017; 15:397-408. [DOI: 10.1038/nrmicro.2017.30] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Ogilvie LA, Jones BV. The human gut virome: a multifaceted majority. Front Microbiol 2015; 6:918. [PMID: 26441861 PMCID: PMC4566309 DOI: 10.3389/fmicb.2015.00918] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022] Open
Abstract
Here, we outline our current understanding of the human gut virome, in particular the phage component of this ecosystem, highlighting progress, and challenges in viral discovery in this arena. We reveal how developments in high-throughput sequencing technologies and associated data analysis methodologies are helping to illuminate this abundant 'biological dark matter.' Current evidence suggests that the human gut virome is a highly individual but temporally stable collective, dominated by phages exhibiting a temperate lifestyle. This viral community also appears to encode a surprisingly rich functional repertoire that confers a range of attributes to their bacterial hosts, ranging from bacterial virulence and pathogenesis to maintaining host-microbiome stability and community resilience. Despite the significant advances in our understanding of the gut virome in recent years, it is clear that we remain in a period of discovery and revelation, as new methods and technologies begin to provide deeper understanding of the inherent ecological characteristics of this viral ecosystem. As our understanding increases, the nature of the multi-partite interactions occurring between host and microbiome will become clearer, helping us to more rationally define the concepts and principles that will underpin approaches to using human gut virome components for medical or biotechnological applications.
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Affiliation(s)
- Lesley A. Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
- Alacris Theranostics GmbHBerlin, Germany
| | - Brian V. Jones
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
- Queen Victoria Hospital NHS Foundation TrustEast Grinstead, UK
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14
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Comparative genomic and morphological analyses of Listeria phages isolated from farm environments. Appl Environ Microbiol 2015; 80:4616-25. [PMID: 24837381 DOI: 10.1128/aem.00720-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large genome (~135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (~66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (~56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.
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Chow CET, Winget DM, White RA, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Front Microbiol 2015; 6:265. [PMID: 25914678 PMCID: PMC4392320 DOI: 10.3389/fmicb.2015.00265] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/17/2015] [Indexed: 11/13/2022] Open
Abstract
Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant “nr” database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.
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Affiliation(s)
- Cheryl-Emiliane T Chow
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Danielle M Winget
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada
| | - Richard A White
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research Toronto, ON, Canada ; Graduate Program in Bioinformatics, University of British Columbia Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia Vancouver, BC, Canada ; Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada ; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research Toronto, ON, Canada ; Department of Botany, University of British Columbia Vancouver, BC, Canada
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16
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Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F. Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples. J Vis Exp 2014:52117. [PMID: 25549184 PMCID: PMC4354477 DOI: 10.3791/52117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The accessibility of high-throughput sequencing has revolutionized many fields of biology. In order to better understand host-associated viral and microbial communities, a comprehensive workflow for DNA and RNA extraction was developed. The workflow concurrently generates viral and microbial metagenomes, as well as metatranscriptomes, from a single sample for next-generation sequencing. The coupling of these approaches provides an overview of both the taxonomical characteristics and the community encoded functions. The presented methods use Cystic Fibrosis (CF) sputum, a problematic sample type, because it is exceptionally viscous and contains high amount of mucins, free neutrophil DNA, and other unknown contaminants. The protocols described here target these problems and successfully recover viral and microbial DNA with minimal human DNA contamination. To complement the metagenomics studies, a metatranscriptomics protocol was optimized to recover both microbial and host mRNA that contains relatively few ribosomal RNA (rRNA) sequences. An overview of the data characteristics is presented to serve as a reference for assessing the success of the methods. Additional CF sputum samples were also collected to (i) evaluate the consistency of the microbiome profiles across seven consecutive days within a single patient, and (ii) compare the consistency of metagenomic approach to a 16S ribosomal RNA gene-based sequencing. The results showed that daily fluctuation of microbial profiles without antibiotic perturbation was minimal and the taxonomy profiles of the common CF-associated bacteria were highly similar between the 16S rDNA libraries and metagenomes generated from the hypotonic lysis (HL)-derived DNA. However, the differences between 16S rDNA taxonomical profiles generated from total DNA and HL-derived DNA suggest that hypotonic lysis and the washing steps benefit in not only removing the human-derived DNA, but also microbial-derived extracellular DNA that may misrepresent the actual microbial profiles.
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Affiliation(s)
- Yan Wei Lim
- Department of Biology, San Diego State University;
| | | | - Mike Furlan
- Department of Biology, San Diego State University
| | - Charles E Robertson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado
| | - J Kirk Harris
- Department of Pediatrics, School of Medicine, University of Colorado
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Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. mBio 2014; 5:e02145. [PMID: 25467442 PMCID: PMC4324244 DOI: 10.1128/mbio.02145-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Newly emerging human viruses such as Ebola virus, severe acute respiratory syndrome (SARS) virus, and HIV likely originate within an extant population of viruses in nonhuman hosts and acquire the ability to infect and cause disease in humans. Although several mechanisms preventing viral infection of particular hosts have been described, the mechanisms and constraints on viral host expansion are ill defined. We describe here mycobacteriophage Patience, a newly isolated phage recovered using Mycobacterium smegmatis mc(2)155 as a host. Patience has genomic features distinct from its M. smegmatis host, including a much lower GC content (50.3% versus 67.4%) and an abundance of codons that are rarely used in M. smegmatis. Nonetheless, it propagates well in M. smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. We propose that Patience evolved primarily among lower-GC hosts and that the disparities between its genomic profile and that of M. smegmatis presented only a minimal barrier to host expansion. Rapid adaptions to its new host include recent acquisition of higher-GC genes, expression of out-of-frame proteins within predicted genes, and codon selection among highly expressed genes toward the translational apparatus of its new host. IMPORTANCE The mycobacteriophage Patience genome has a notably lower GC content (50.3%) than its Mycobacterium smegmatis host (67.4%) and has markedly different codon usage biases. The viral genome has an abundance of codons that are rare in the host and are decoded by wobble tRNA pairing, although the phage grows well and expression of most of the genes is detected by mass spectrometry. Patience thus has the genomic profile of a virus that evolved primarily in one type of host genetic landscape (moderate-GC bacteria) but has found its way into a distinctly different high-GC environment. Although Patience genes are ill matched to the host expression apparatus, this is of little functional consequence and has not evidently imposed a barrier to migration across the microbial landscape. Interestingly, comparison of expression levels and codon usage profiles reveals evidence of codon selection as the genome evolves and adapts to its new environment.
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18
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Sime-Ngando T. Environmental bacteriophages: viruses of microbes in aquatic ecosystems. Front Microbiol 2014; 5:355. [PMID: 25104950 PMCID: PMC4109441 DOI: 10.3389/fmicb.2014.00355] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022] Open
Abstract
Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.
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Affiliation(s)
- Télesphore Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Clermont Université Blaise Pascal Aubière, France
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Prussin AJ, Marr LC, Bibby KJ. Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols. FEMS Microbiol Lett 2014; 357:1-9. [PMID: 24891293 DOI: 10.1111/1574-6968.12487] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/06/2023] Open
Abstract
Despite the obvious importance of viral transmission and ecology to medicine, epidemiology, ecology, agriculture, and microbiology, the study of viral bioaerosols and community structure has remained a vastly underexplored area, due to both unresolved technical challenges and unrecognized importance. High-throughput, culture-independent techniques such as viral metagenomics are beginning to revolutionize the study of viral ecology. With recent developments in viral metagenomics, characterization of viral bioaerosol communities provides an opportunity for high-impact future research. However, there remain significant challenges for the study of viral bioaerosols compared with viruses in other matrices, such as water, the human gut, and soil. Collecting enough biomass is essential for successful metagenomic analysis, but this is a challenge with viral bioaerosols. Herein, we provide a perspective on the importance of studying viral bioaerosols, the challenges of studying viral community structure, and the potential opportunities for improvements in methods to study viruses in indoor and outdoor air.
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Affiliation(s)
- Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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