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Optimization of microbial DNA extraction from human skin samples for CRISPR typing. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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2
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Rykachevsky A, Stepakov A, Muzyukina P, Medvedeva S, Dobrovolski M, Burnaev E, Severinov K, Savitskaya E. SCRAMBLER: A Tool for De Novo CRISPR Array Reconstruction and Its Application for Analysis of the Structure of Prokaryotic Populations. CRISPR J 2021; 4:673-685. [PMID: 34661428 DOI: 10.1089/crispr.2021.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
CRISPR arrays are prokaryotic genomic loci consisting of repeat sequences alternating with unique spacers acquired from foreign nucleic acids. As one of the fastest-evolving parts of the genome, CRISPR arrays can be used to differentiate closely related prokaryotic lineages and track individual strains in prokaryotic communities. However, the assembly of full-length CRISPR arrays sequences remains a problem. Here, we developed SCRAMBLER, a tool that includes several pipelines for assembling CRISPR arrays from high-throughput short-read sequencing data. We assessed its performance with model data sets (Escherichia coli strains containing different CRISPR arrays and imitating prokaryotic communities of different complexities) and intestinal microbiomes of extant and extinct pachyderms. Evaluation of SCRAMBLER's performance using model data sets demonstrated its ability to assemble CRISPR arrays correctly from reads containing pairs of spacers, yielding a precision rate of >80% and a recall rate of 60-85% when checked against ground-truth data. Likewise, SCRAMBLER successfully assembled CRISPR arrays from the environmental samples, as attested by their matching with database entries. SCRAMBLER, an open-source software (github.com/biolab-tools/SCRAMBLER), can facilitate analysis of the composition and dynamics of CRISPR arrays in complex communities.
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Affiliation(s)
- Anton Rykachevsky
- Center for Computational and Data-Intensive Science and Engineering and Rutgers, State University of New Jersey, Piscataway, USA
| | - Alexander Stepakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Polina Muzyukina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Sofia Medvedeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Mark Dobrovolski
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
| | - Evgeny Burnaev
- Center for Computational and Data-Intensive Science and Engineering and Rutgers, State University of New Jersey, Piscataway, USA
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA.,Laboratory of Genetic Regulation of Prokaryotic Mobile Genetic Elements, Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow, Russia; and Rutgers, State University of New Jersey, Piscataway, USA.,Waksman Institute, Rutgers, State University of New Jersey, Piscataway, USA
| | - Ekaterina Savitskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Rutgers, State University of New Jersey, Piscataway, USA
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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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4
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Abstract
Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. The highly personalized human skin microbiome may serve as a viable marker in personal identification. Amplicon sequencing resolution using 16S rRNA cannot identify bacterial communities sufficiently to discriminate between individuals. Thus, novel higher-resolution genetic markers are required for forensic purposes. The clustered regularly interspaced short palindromic repeats (CRISPRs) are prokaryotic genetic elements that can provide a history of infections encountered by the bacteria. The sequencing of CRISPR spacers may provide phylogenetic information with higher resolution than other markers. However, using spacer sequencing for discrimination of personal skin microbiome is difficult due to limited information on CRISPRs in human skin microbiomes. It remains unclear whether personal microbiome discrimination can be achieved using spacer diversity or which CRISPRs will be forensically relevant. We identified common CRISPRs in the human skin microbiome via metagenomic reconstruction and used amplicon sequencing for deep sequencing of spacers. We successfully reconstructed 24 putative CRISPR arrays using metagenomic data sets. A total of 1,223,462 reads from three CRISPR arrays revealed that spacers in the skin microbiome were highly personalized, and conserved repeats were commonly shared between individuals. These individual specificities observed using CRISPR typing were confirmed by comparing the CRISPR diversity to microbiome diversity assessed using 16S rRNA amplicon sequencing. CRISPR typing achieved 95.2% accuracy in personal classification, whereas 16S rRNA sequencing only achieved 52.6%. These results suggest that sequencing CRISPRs in the skin microbiome may be a more powerful approach for personal identification and ecological studies compared to conventional 16S rRNA sequencing. IMPORTANCE Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. In this study, we identified 24 putative CRISPR arrays using a shotgun metagenome data set of the human skin microbiome. The findings of this study expand our understanding of the nature of CRISPRs by identifying novel CRISPR candidates. We developed a method to efficiently determine the diversity of three CRISPR arrays. Our analysis revealed that the CRISPR spacer diversity in the human skin microbiome is highly personalized compared with the microbiome diversity assessed by 16S rRNA sequencing, providing a new perspective on the study of the skin microbiome.
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Lopatina A, Medvedeva S, Artamonova D, Kolesnik M, Sitnik V, Ispolatov Y, Severinov K. Natural diversity of CRISPR spacers of Thermus: evidence of local spacer acquisition and global spacer exchange. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180092. [PMID: 30905291 PMCID: PMC6452258 DOI: 10.1098/rstb.2018.0092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We investigated the diversity of CRISPR spacers of Thermus communities from two locations in Italy, two in Chile and one location in Russia. Among the five sampling sites, a total of more than 7200 unique spacers belonging to different CRISPR-Cas systems types and subtypes were identified. Most of these spacers are not found in CRISPR arrays of sequenced Thermus strains. Comparison of spacer sets revealed that samples within the same area (separated by few to hundreds of metres) have similar spacer sets, which appear to be largely stable at least over the course of several years. While at further distances (hundreds of kilometres and more) the similarity of spacer sets is decreased, there are still multiple common spacers in Thermus communities from different continents. The common spacers can be reconstructed in identical or similar CRISPR arrays, excluding their independent appearance and suggesting an extensive migration of thermophilic bacteria over long distances. Several new Thermus phages were isolated in the sampling sites. Mapping of spacers to bacteriophage sequences revealed examples of local acquisition of spacers from some phages and distinct patterns of targeting of phage genomes by different CRISPR-Cas systems. This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.
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Affiliation(s)
- Anna Lopatina
- 1 Institute of Molecular Genetics, Russian Academy of Sciences , Moscow , Russia.,2 Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,7 Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Sofia Medvedeva
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia.,4 Pasteur Institute , Paris , France
| | - Daria Artamonova
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Matvey Kolesnik
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Vasily Sitnik
- 3 Skolkovo Institute of Science and Technology , Skolkovo , Russia
| | - Yaroslav Ispolatov
- 5 Department of Physics, University of Santiago de Chile , Santiago , Chile
| | - Konstantin Severinov
- 1 Institute of Molecular Genetics, Russian Academy of Sciences , Moscow , Russia.,3 Skolkovo Institute of Science and Technology , Skolkovo , Russia.,6 Waksman Institute, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey , Piscataway, NJ , USA.,7 Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 76100 , Israel
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6
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Ghose C, Ly M, Schwanemann LK, Shin JH, Atab K, Barr JJ, Little M, Schooley RT, Chopyk J, Pride DT. The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None. Front Microbiol 2019; 10:2061. [PMID: 31555247 PMCID: PMC6742758 DOI: 10.3389/fmicb.2019.02061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023] Open
Abstract
Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Katayoon Atab
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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7
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Lam TJ, Ye Y. CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis. CRISPR J 2019; 2:41-50. [PMID: 30820491 PMCID: PMC6390457 DOI: 10.1089/crispr.2018.0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/29/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Prokaryotes use these immune systems to defend against invaders, which include phages, plasmids, and other mobile genetic elements. Relying on the integration of spacers derived from invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems are able to store the memory of past immunological encounters. While CRISPR-Cas systems have evolved in response to invading mobile genetic elements, invaders have also developed mechanisms to avoid detection. As a result of an arms race between CRISPR-Cas systems and their targets, CRISPR arrays typically undergo rapid turnover of spacers through the acquisition and loss events. Additionally, microbiomes of different individuals rarely share spacers. Here, we present a computational pipeline, CRISPRtrack, for strain tracking based on CRISPR spacer content, and we applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor-strain tracking in fecal transplantation and as a general purpose tool for quantifying microbiome similarity.
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Affiliation(s)
- Tony J Lam
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana
| | - Yuzhen Ye
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana
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Hidalgo-Cantabrana C, Sanozky-Dawes R, Barrangou R. Insights into the Human Virome Using CRISPR Spacers from Microbiomes. Viruses 2018; 10:v10090479. [PMID: 30205462 PMCID: PMC6165519 DOI: 10.3390/v10090479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 12/21/2022] Open
Abstract
Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USA.
| | - Rosemary Sanozky-Dawes
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USA.
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Campus BOX 7624, Raleigh, NC 27695, USA.
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9
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Pannaraj PS, Ly M, Cerini C, Saavedra M, Aldrovandi GM, Saboory AA, Johnson KM, Pride DT. Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front Microbiol 2018; 9:1162. [PMID: 29910789 PMCID: PMC5992295 DOI: 10.3389/fmicb.2018.01162] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome.
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Affiliation(s)
- Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Chiara Cerini
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Monica Saavedra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abdul A Saboory
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Kevin M Johnson
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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10
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Szafrański SP, Winkel A, Stiesch M. The use of bacteriophages to biocontrol oral biofilms. J Biotechnol 2017; 250:29-44. [PMID: 28108235 DOI: 10.1016/j.jbiotec.2017.01.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/15/2022]
Abstract
Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.
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Affiliation(s)
- Szymon P Szafrański
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
| | - Andreas Winkel
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Meike Stiesch
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Stadtfelddamm 34, D-30625 Hannover, Germany; Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School (MHH), Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
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11
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Abeles SR, Ly M, Santiago-Rodriguez TM, Pride DT. Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes. PLoS One 2015; 10:e0134941. [PMID: 26309137 PMCID: PMC4550281 DOI: 10.1371/journal.pone.0134941] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/15/2015] [Indexed: 12/23/2022] Open
Abstract
Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances.
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Affiliation(s)
- Shira R. Abeles
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, United States of America
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, La Jolla, CA, 92093, United States of America
| | | | - David T. Pride
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, United States of America
- Department of Pathology, University of California, San Diego, La Jolla, CA, 92093, United States of America
- * E-mail:
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12
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Santiago-Rodriguez TM, Naidu M, Abeles SR, Boehm TK, Ly M, Pride DT. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics 2015; 16:549. [PMID: 26215258 PMCID: PMC4515923 DOI: 10.1186/s12864-015-1781-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/15/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined. RESULTS Here, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages. CONCLUSIONS As we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Mayuri Naidu
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Shira R Abeles
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Tobias K Boehm
- College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA.
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - David T Pride
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
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13
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Lum AG, Ly M, Santiago-Rodriguez TM, Naidu M, Boehm TK, Pride DT. Global transcription of CRISPR loci in the human oral cavity. BMC Genomics 2015; 16:401. [PMID: 25994215 PMCID: PMC4438527 DOI: 10.1186/s12864-015-1615-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 05/05/2015] [Indexed: 12/26/2022] Open
Abstract
Background Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment. Results We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage. Conclusions These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1615-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Lum
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Tasha M Santiago-Rodriguez
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Mayuri Naidu
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Tobias K Boehm
- College of Dental Medicine, Western University of Health Sciences, 309 E Second Street, Pomona, CA, 91766, USA.
| | - David T Pride
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. .,Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
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Edlund A, Santiago-Rodriguez TM, Boehm TK, Pride DT. Bacteriophage and their potential roles in the human oral cavity. J Oral Microbiol 2015; 7:27423. [PMID: 25861745 PMCID: PMC4393417 DOI: 10.3402/jom.v7.27423] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 12/26/2022] Open
Abstract
The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts.
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Affiliation(s)
- Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,School of Dentistry, University of California, Los Angeles, CA, USA
| | | | - Tobias K Boehm
- Western University College of Dental Medicine, Pomona, CA, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA;
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Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT. The human urine virome in association with urinary tract infections. Front Microbiol 2015; 6:14. [PMID: 25667584 PMCID: PMC4304238 DOI: 10.3389/fmicb.2015.00014] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/06/2015] [Indexed: 01/21/2023] Open
Abstract
While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary tract health status. We recruited and sampled urine from 20 subjects, 10 subjects with urinary tract infections (UTIs) and 10 without UTIs, and found viral communities in the urine of each subject group. Most of the identifiable viruses were bacteriophage, but eukaryotic viruses also were identified in all subjects. We found reads from human papillomaviruses (HPVs) in 95% of the subjects studied, but none were found to be high-risk genotypes that are associated with cervical and rectal cancers. We verified the presence of some HPV genotypes by quantitative PCR. Some of the HPV genotypes identified were homologous to relatively novel and uncharacterized viruses that previously have been detected on skin in association with cancerous lesions, while others may be associated with anal and genital warts. On a community level, there was no association between the membership or diversity of viral communities based on urinary tract health status. While more data are still needed, detection of HPVs as members of the human urinary virome using viral metagenomics represents a non-invasive technique that could augment current screening techniques to detect low-risk HPVs in the genitourinary tracts of humans.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego San Diego, CA, USA
| | - Natasha Bonilla
- Department of Biology, San Diego State University San Diego, CA, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego San Diego, CA, USA ; Department of Medicine, University of California, San Diego San Diego, CA, USA
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