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PHAGE-2 Study: Supplemental Bacteriophages Extend Bifidobacterium animalis subsp. lactis BL04 Benefits on Gut Health and Microbiota in Healthy Adults. Nutrients 2020; 12:nu12082474. [PMID: 32824480 PMCID: PMC7468981 DOI: 10.3390/nu12082474] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Probiotics are increasingly used by consumers and practitioners to reduce gastrointestinal (GI) distress and improve gut function. Here, we sought to determine whether the addition of supplemental bacteriophages (PreforPro) could enhance the effects of a common probiotic, Bifidobacterium animalis subsp. lactis (B. lactis) on GI health. A total of 68 participants were enrolled in a 4-week, randomized, parallel-arm, double-blind, placebo-controlled trial where primary outcomes included self-assessments of GI health, a daily stool log, and 16s rRNA analysis of gut microbial populations. We observed within-group improvements in GI inflammation (p = 0.01) and a trending improvement in colon pain (p = 0.08) in individuals consuming B. lactis with PreforPro, but not in the group consuming only the probiotic. There was also a larger increase in Lactobacillus and short-chain fatty acid-producing microbial taxa detected in the stool of participants taking PreforPro with B. lactis compared to the probiotic alone. Overall, these results suggest the addition of PreforPro as a combination therapy may alter gut ecology to extend the GI benefits of consuming B. lactis or other probiotics.
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Rasmussen TS, Koefoed AK, Jakobsen RR, Deng L, Castro-Mejía JL, Brunse A, Neve H, Vogensen FK, Nielsen DS. Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations. FEMS Microbiol Rev 2020; 44:507-521. [DOI: 10.1093/femsre/fuaa020] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Rasmus Riemer Jakobsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Josué L Castro-Mejía
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, 2nd floor - 1870, Frederiksberg, Denmark
| | - Horst Neve
- Institute of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1 - 24103, Kiel, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
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Møller-Olsen C, Ross T, Leppard KN, Foisor V, Smith C, Grammatopoulos DK, Sagona AP. Bacteriophage K1F targets Escherichia coli K1 in cerebral endothelial cells and influences the barrier function. Sci Rep 2020; 10:8903. [PMID: 32483257 PMCID: PMC7264188 DOI: 10.1038/s41598-020-65867-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Bacterial neonatal meningitis results in high mortality and morbidity rates for those affected. Although improvements in diagnosis and treatment have led to a decline in mortality rates, morbidity rates have remained relatively unchanged. Bacterial resistance to antibiotics in this clinical setting further underlines the need for developing other technologies, such as phage therapy. We exploited an in vitro phage therapy model for studying bacterial neonatal meningitis based on Escherichia coli (E. coli) EV36, bacteriophage (phage) K1F and human cerebral microvascular endothelial cells (hCMECs). We show that phage K1F is phagocytosed and degraded by constitutive- and PAMP-dependent LC3-assisted phagocytosis and does not induce expression of inflammatory cytokines TNFα, IL-6, IL-8 or IFNβ. Additionally, we observed that phage K1F temporarily decreases the barrier resistance of hCMEC cultures, a property that influences the barrier permeability, which could facilitate the transition of immune cells across the endothelial vessel in vivo. Collectively, we demonstrate that phage K1F can infect intracellular E. coli EV36 within hCMECs without themselves eliciting an inflammatory or defensive response. This study illustrates the potential of phage therapy targeting infections such as bacterial neonatal meningitis and is an important step for the continued development of phage therapy targeting antibiotic-resistant bacterial infections generally.
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Affiliation(s)
| | - Toby Ross
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Keith N Leppard
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Veronica Foisor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Corinne Smith
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Dimitris K Grammatopoulos
- Warwick Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
- Institute of Precision Diagnostics and Translational Medicine, Dept of Pathology, UHCW NHS Trust, Clifford Bridge Road, CV2 2DX, Coventry, UK
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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Rahimi-Midani A, Choi TJ. Transport of Phage in Melon Plants and Inhibition of Progression of Bacterial Fruit Blotch. Viruses 2020; 12:v12040477. [PMID: 32340158 PMCID: PMC7232510 DOI: 10.3390/v12040477] [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: 03/29/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial fruit blotch (BFB) is an economically important disease in melons and watermelons for which no effective control method is available. Application of phytobacterium-infecting phage has been evaluated as an alternative means of preventing bacterial diseases in plants. Coating of seeds with bacteriophages infecting Acidovorax citrulli, the causal agent of BFB, is effective for controlling the disease, as shown in our previous study. We evaluated the transport of bacteriophage ACPWH from soil to the leaves of melon plants, and we also evaluated its effect on BFB. Leaves of melon plants were spray-inoculated with A. citrulli, and bacteriophage ACPWH was added to soil after symptoms had developed. ACPWH was detected by PCR in foliar tissue 8 h after addition to soil. DAPI-stained ACPWH accumulated at the leaf tip after 24 h. Melon treated with ACPWH showed 27% disease severity, compared to 80% for the non-treated control, indicating that ACPWH can be used to control BFB.
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Kulikov EE, Golomidova AK, Babenko VV, Letarov AV. A Simple Method for Extraction of the Horse Feces Virome DNA, Suitable for Oxford Nanopore Sequencing. Microbiology (Reading) 2020. [DOI: 10.1134/s002626172002006x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Göller PC, Haro-Moreno JM, Rodriguez-Valera F, Loessner MJ, Gómez-Sanz E. Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil. MICROBIOME 2020; 8:17. [PMID: 32046783 PMCID: PMC7014677 DOI: 10.1186/s40168-020-0795-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 01/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only on the yet largely unknown phage diversity, but may also result in novel insights towards their functioning in the global biogeochemical nutrient cycle and their significance in earthbound ecosystems. Unfortunately, information about soil viromes is rather scarce compared to aquatic environments, due to the heterogeneous soil matrix, which rises major technical difficulties in the extraction process. Resolving these technical challenges and establishing a standardized extraction protocol is, therefore, a fundamental prerequisite for replicable results and comparative virome studies. RESULTS We here report the optimization of protocols for the extraction of phage DNA from agricultural soil preceding metagenomic analysis such that the protocol can equally be harnessed for phage isolation. As an optimization strategy, soil samples were spiked with Listeria phage A511 (Myovirus), Staphylococcus phage 2638AΔLCR (Siphovirus) and Escherichia phage T7 (Podovirus) (each 106 PFU/g soil). The efficacy of phage (i) elution, (ii) filtration, (iii) concentration and (iv) DNA extraction methods was tested. Successful extraction routes were selected based on spiked phage recovery and low bacterial 16S rRNA gene contaminants. Natural agricultural soil viromes were then extracted with the optimized methods and shotgun sequenced. Our approach yielded sufficient amounts of inhibitor-free viral DNA for shotgun sequencing devoid of amplification prior library preparation, and low 16S rRNA gene contamination levels (≤ 0.2‰). Compared to previously published protocols, the number of bacterial read contamination was decreased by 65%. In addition, 379 novel putative complete soil phage genomes (≤ 235 kb) were obtained from over 13,000 manually identified viral contigs, promising the discovery of a large, previously inaccessible viral diversity. CONCLUSION We have shown a considerably enhanced extraction of the soil phage community by protocol optimization that has proven robust in both culture-dependent as well as through viromic analyses. Our huge data set of manually curated soil viral contigs substantially increases the amount of currently available soil virome data, and provides insights into the yet largely undescribed soil viral sequence space.
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Affiliation(s)
- Pauline C Göller
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose M Haro-Moreno
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland.
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
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Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles. Food Microbiol 2020; 85:103278. [DOI: 10.1016/j.fm.2019.103278] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 01/12/2023]
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Bekliz M, Brandani J, Bourquin M, Battin TJ, Peter H. Benchmarking protocols for the metagenomic analysis of stream biofilm viromes. PeerJ 2019; 7:e8187. [PMID: 31879573 PMCID: PMC6927355 DOI: 10.7717/peerj.8187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
Viruses drive microbial diversity, function and evolution and influence important biogeochemical cycles in aquatic ecosystems. Despite their relevance, we currently lack an understanding of their potential impacts on stream biofilm structure and function. This is surprising given the critical role of biofilms for stream ecosystem processes. Currently, the study of viruses in stream biofilms is hindered by the lack of an optimized protocol for their extraction, concentration and purification. Here, we evaluate a range of methods to separate viral particles from stream biofilms, and to concentrate and purify them prior to DNA extraction and metagenome sequencing. Based on epifluorescence microscopy counts of viral-like particles (VLP) and DNA yields, we optimize a protocol including treatment with tetrasodium pyrophosphate and ultra-sonication to disintegrate biofilms, tangential-flow filtration to extract and concentrate VLP, followed by ultracentrifugation in a sucrose density gradient to isolate VLP from the biofilm slurry. Viromes derived from biofilms sampled from three different streams were dominated by Siphoviridae, Myoviridae and Podoviridae and provide first insights into the viral diversity of stream biofilms. Our protocol optimization provides an important step towards a better understanding of the ecological role of viruses in stream biofilms.
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Affiliation(s)
- Meriem Bekliz
- Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Jade Brandani
- Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Massimo Bourquin
- Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Tom J. Battin
- Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Hannes Peter
- Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Federale de Lausanne, Lausanne, Switzerland
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Sutton TDS, Hill C. Gut Bacteriophage: Current Understanding and Challenges. Front Endocrinol (Lausanne) 2019; 10:784. [PMID: 31849833 PMCID: PMC6895007 DOI: 10.3389/fendo.2019.00784] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.
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Affiliation(s)
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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60
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Edgar RH, Cook J, Noel C, Minard A, Sajewski A, Fitzpatrick M, Fernandez R, Hempel JD, Kellum JA, Viator JA. Bacteriophage-mediated identification of bacteria using photoacoustic flow cytometry. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-7. [PMID: 31758676 PMCID: PMC6874036 DOI: 10.1117/1.jbo.24.11.115003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/04/2019] [Indexed: 05/26/2023]
Abstract
Infection with resistant bacteria has become an ever increasing problem in modern medical practice. Currently, broad spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take two to three days and is unable to provide quantitative information. To detect and quantify bacteria rapidly in blood samples, we designed a method using labeled bacteriophage in conjunction with photoacoustic flow cytometry (PAFC). PAFC is the generation of ultrasonic waves created by the absorption of laser light in particles under flow. Bacteriophage is a virus that infects bacteria and possesses the ability to discriminate bacterial surface antigens, allowing the bacteriophage to bind only to their target bacteria. Bacteria can be tagged with dyed phage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. We demonstrate that E. coli; can be detected and discriminated from Salmonella; using this method. Our goal is to develop a method to determine bacterial content in blood samples. We hope to develop this technology into future clinical use and decrease the time required to identify bacterial species from 3 to 4 days to less than 1 hour.
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Affiliation(s)
- Robert H. Edgar
- University of Pittsburgh, Swanson School of Engineering, Department of Bioengineering, Pittsburgh, Pennsylvania, United States
| | - Justin Cook
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Cierra Noel
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Austin Minard
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Andrea Sajewski
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | | | | | - John D. Hempel
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - John A. Kellum
- University of Pittsburgh, Center for Critical Care Nephrology, Department of Critical Care Medicine, Pittsburgh, Pennsylvania, United States
| | - John A. Viator
- University of Pittsburgh, Swanson School of Engineering, Department of Bioengineering, Pittsburgh, Pennsylvania, United States
- Duquesne University, Pittsburgh, Pennsylvania, United States
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Shkoporov AN, Hill C. Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. Cell Host Microbe 2019; 25:195-209. [PMID: 30763534 DOI: 10.1016/j.chom.2019.01.017] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human gut microbiome is a dense and taxonomically diverse consortium of microorganisms. While the bacterial components of the microbiome have received considerable attention, comparatively little is known about the composition and physiological significance of human gut-associated bacteriophage populations (phageome). By extrapolating our knowledge of phage-host interactions from other environments, one could expect that >1012 viruses reside in the human gut, and we can predict that they play important roles in regulating the complex microbial networks operating in this habitat. Before delving into their function, we need to first overcome the challenges associated with studying and characterizing the phageome. In this Review, we summarize the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome. We also discuss the main challenges in the field and identify promising avenues for future research.
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Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Co. Cork, Ireland.
| | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Co. Cork, Ireland
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Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A. Studying the gut virome in the metagenomic era: challenges and perspectives. BMC Biol 2019; 17:84. [PMID: 31660953 PMCID: PMC6819614 DOI: 10.1186/s12915-019-0704-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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McNamara RP, Dittmer DP. Modern Techniques for the Isolation of Extracellular Vesicles and Viruses. J Neuroimmune Pharmacol 2019; 15:459-472. [PMID: 31512168 DOI: 10.1007/s11481-019-09874-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023]
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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Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. MICROBIOME 2019; 7:119. [PMID: 31455406 PMCID: PMC6712665 DOI: 10.1186/s40168-019-0737-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/16/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity. RESULTS Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids. CONCLUSIONS Overall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.
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Affiliation(s)
- Yoshihiko Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Suguru Nishijima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, Tokyo, 169-8555 Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020 Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Wataru Suda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Kenshiro Oshima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Masahira Hattori
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
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d'Humières C, Touchon M, Dion S, Cury J, Ghozlane A, Garcia-Garcera M, Bouchier C, Ma L, Denamur E, P C Rocha E. A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach. Sci Rep 2019; 9:11331. [PMID: 31383878 PMCID: PMC6683287 DOI: 10.1038/s41598-019-47656-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023] Open
Abstract
The microbiota of the human gut is a complex and rich community where bacteria and their viruses, the bacteriophages, are dominant. There are few studies on the phage community and no clear standard for isolating them, sequencing and analysing their genomes. Since this makes comparisons between studies difficult, we aimed at defining an easy, low-cost, and reproducible methodology. We analysed five different techniques to isolate phages from human adult faeces and developed an approach to analyse their genomes in order to quantify contamination and classify phage contigs in terms of taxonomy and lifestyle. We chose the polyethylene glycol concentration method to isolate phages because of its simplicity, low cost, reproducibility, and of the high number and diversity of phage sequences that we obtained. We also tested the reproducibility of this method with multiple displacement amplification (MDA) and showed that MDA severely decreases the phage genetic diversity of the samples and the reproducibility of the method. Lastly, we studied the influence of sequencing depth on the analysis of phage diversity and observed the beginning of a plateau for phage contigs at 20,000,000 reads. This work contributes to the development of methods for the isolation of phages in faeces and for their comparative analysis.
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Affiliation(s)
- Camille d'Humières
- IAME, UMR 1137, INSERM, Université Paris Diderot, 75018, Paris, France. .,AP-HP, Laboratoire de Bactériologie, Hôpital Bichat, 75018, Paris, France. .,Ecole doctorale Frontières du vivant, Université Paris Diderot, 75013, Paris, France. .,Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France.
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France
| | - Sara Dion
- IAME, UMR 1137, INSERM, Université Paris Diderot, 75018, Paris, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Marc Garcia-Garcera
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France
| | - Christiane Bouchier
- Genomics Platform, BIOMICS, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France
| | - Laurence Ma
- Genomics Platform, BIOMICS, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France
| | - Erick Denamur
- IAME, UMR 1137, INSERM, Université Paris Diderot, 75018, Paris, France.,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, 75015, France
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66
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A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples. Viruses 2019; 11:v11070667. [PMID: 31330855 PMCID: PMC6669555 DOI: 10.3390/v11070667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/10/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
The human gut microbiome (GM) plays an important role in human health and diseases. However, while substantial progress has been made in understanding the role of bacterial inhabitants of the gut, much less is known regarding the viral component of the GM. Bacteriophages (phages) are viruses attacking specific host bacteria and likely play important roles in shaping the GM. Although metagenomic approaches have led to the discoveries of many new viruses, they remain largely uncultured as their hosts have not been identified, which hampers our understanding of their biological roles. Existing protocols for isolation of viromes generally require relatively high input volumes and are generally more focused on extracting nucleic acids of good quality and purity for down-stream analysis, and less on purifying viruses with infective capacity. In this study, we report the development of an efficient protocol requiring low sample input yielding purified viromes containing phages that are still infective, which also are of sufficient purity for genome sequencing. We validated the method through spiking known phages followed by plaque assays, qPCR, and metagenomic sequencing. The protocol should facilitate the process of culturing novel viruses from the gut as well as large scale studies on gut viromes.
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67
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Analysis of Bacteriophages with Insulator-Based Dielectrophoresis. MICROMACHINES 2019; 10:mi10070450. [PMID: 31277396 PMCID: PMC6680707 DOI: 10.3390/mi10070450] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023]
Abstract
Bacterial viruses or phages have great potential in the medical and agricultural fields as alternatives to antibiotics to control nuisance populations of pathogenic bacteria. However, current analysis and purification protocols for phages tend to be resource intensive and have numbers of limitations, such as impacting phage viability. The present study explores the potential of employing the electrokinetic technique of insulator-based dielectrophoresis (iDEP) for virus assessment, separation and enrichment. In particular, the application of the parameter "trapping value" (Tv) is explored as a standardized iDEP signature for each phage species. The present study includes mathematical modeling with COMSOL Multiphysics and extensive experimentation. Three related, but genetically and structurally distinct, phages were studied: Salmonella enterica phage SPN3US, Pseudomonas aeruginosa phage ϕKZ and P. chlororaphis phage 201ϕ2-1. This is the first iDEP study on bacteriophages with large and complex virions and the results illustrate their virions can be successfully enriched with iDEP systems and still retain infectivity. In addition, our results indicate that characterization of the negative dielectrophoretic response of a phage in terms of Tv could be used for predicting individual virus behavior in iDEP systems. The findings reported here can contribute to the establishment of protocols to analyze, purify and/or enrich samples of known and unknown phages.
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68
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Yang Z, Liu X, Shi Y, Yin S, Shen W, Chen J, Chen Y, Chen Y, You B, Gong Y, Luo X, Zhang C, Yuan Z, Peng Y. Characterization and genome annotation of a newly detected bacteriophage infecting multidrug-resistant Acinetobacter baumannii. Arch Virol 2019; 164:1527-1533. [PMID: 30900072 PMCID: PMC6526140 DOI: 10.1007/s00705-019-04213-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/20/2019] [Indexed: 12/03/2022]
Abstract
A novel virulent bacteriophage, φAbp2, infecting multidrug-resistant (MDR) Acinetobacter baumannii was isolated from the wastewater of a sewage management centre at Southwest Hospital, China. Transmission electron microscopy and phylogenetic analysis revealed that φAbp2 belongs to the subfamily Peduovirinae. A one-step growth curve demonstrated that φAbp2 had a latent period of 15 min, a lysis period of 35 min, and a burst size of 222 particles per infected host cell. Moreover, φAbp2 showed a relatively broad host range in local A. baumannii, and it also exhibited tolerance over a wider range of thermal and pH conditions. Genomic sequencing revealed that φAbp2 has a circular double-stranded DNA genome with no sequence similarity to our previously isolated φAbp1. Eighty-eight putative open reading frames (ORFs) encoding 41 proteins of known function and 47 of unknown function were identified, and the G/C content was 37.84%. φAbp2 is a new member of the subfamily Peduovirinae of the family Myoviridae. Its genome sequence is very similar to that of the A. baumannii phage LZ35.
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Affiliation(s)
- Zichen Yang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
- Department of microbiology, College of Basic Medicin, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xinzhu Liu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Yunlong Shi
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Supeng Yin
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
- Department of microbiology, College of Basic Medicin, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wei Shen
- Department of microbiology, College of Basic Medicin, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jing Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Yu Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Yajie Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Bo You
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Yali Gong
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Xiaoqiang Luo
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Cheng Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Zhiqiang Yuan
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China
| | - Yizhi Peng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Burn Research, Southwest Hospital, Chongqing, China.
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69
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Rasmussen TS, de Vries L, Kot W, Hansen LH, Castro-Mejía JL, Vogensen FK, Hansen AK, Nielsen DS. Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet. Viruses 2019; 11:E435. [PMID: 31086117 PMCID: PMC6563299 DOI: 10.3390/v11050435] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/01/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022] Open
Abstract
Often physiological studies using mice from one vendor show different outcome when being reproduced using mice from another vendor. These divergent phenotypes between similar mouse strains from different vendors have been assigned to differences in the gut microbiome. During recent years, evidence has mounted that the gut viral community plays a key role in shaping the gut microbiome and may thus also influence mouse phenotype. However, to date inter-vendor variation in the murine gut virome has not been studied. Using a metavirome approach, combined with 16S rRNA gene sequencing, we here compare the composition of the viral and bacterial gut community of C57BL/6N mice from three different vendors exposed to either a chow-based low-fat diet or high-fat diet. Interestingly, both the bacterial and the viral component of the gut community differed significantly between vendors. The different diets also strongly influenced both the viral and bacterial gut community, but surprisingly the effect of vendor exceeded the effect of diet. In conclusion, the vendor effect is substantial not only on the gut bacterial community but also strongly influences viral community composition. Given the effect of GM on mice phenotype, this is essential to consider for increasing reproducibility of mouse studies.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark.
| | - Liv de Vries
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark.
| | | | - Josué L Castro-Mejía
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark.
| | - Finn Kvist Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark.
| | - Axel Kornerup Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark.
| | - Dennis Sandris Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark.
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70
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Huh H, Wong S, St Jean J, Slavcev R. Bacteriophage interactions with mammalian tissue: Therapeutic applications. Adv Drug Deliv Rev 2019; 145:4-17. [PMID: 30659855 DOI: 10.1016/j.addr.2019.01.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 11/30/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022]
Abstract
The human body is a large reservoir for bacterial viruses known as bacteriophages (phages), which participate in dynamic interactions with their bacterial and human hosts that ultimately affect human health. The current growing interest in human resident phages is paralleled by new uses of phages, including the design of engineered phages for therapeutic applications. Despite the increasing number of clinical trials being conducted, the understanding of the interaction of phages and mammalian cells and tissues is still largely unknown. The presence of phages in compartments within the body previously considered purely sterile, suggests that phages possess a unique capability of bypassing anatomical and physiological barriers characterized by varying degrees of selectivity and permeability. This review will discuss the direct evidence of the accumulation of bacteriophages in various tissues, focusing on the unique capability of phages to traverse relatively impermeable barriers in mammals and its relevance to its current applications in therapy.
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Affiliation(s)
- Haein Huh
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Shirley Wong
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Jesse St Jean
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Roderick Slavcev
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada.
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71
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Clavijo V, Torres-Acosta MA, Vives-Flórez MJ, Rito-Palomares M. Aqueous two-phase systems for the recovery and purification of phage therapy products: Recovery of salmonella bacteriophage ϕSan23 as a case study. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.09.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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72
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Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe 2019; 25:261-272.e5. [PMID: 30763537 PMCID: PMC6411085 DOI: 10.1016/j.chom.2019.01.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/31/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage. Microbiome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns are driven by bacteriophages, not eukaryotic viruses. Collectively, these observations support a strong role of the microbiome in patterning for the virome.
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Affiliation(s)
- J Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Shao-Pei Chou
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
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73
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Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology. Viruses 2019; 11:E76. [PMID: 30669250 PMCID: PMC6356626 DOI: 10.3390/v11010076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
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Affiliation(s)
- Sari Mäntynen
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Lotta-Riina Sundberg
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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74
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Møller-Olsen C, Ho SFS, Shukla RD, Feher T, Sagona AP. Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells. Sci Rep 2018; 8:17559. [PMID: 30510202 PMCID: PMC6277420 DOI: 10.1038/s41598-018-35859-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/09/2018] [Indexed: 01/13/2023] Open
Abstract
Bacterial infections can be treated with bacteriophages that show great specificity towards their bacterial host and can be genetically modified for different applications. However, whether and how bacteriophages can kill intracellular bacteria in human cells remains elusive. Here, using CRISPR/Cas selection, we have engineered a fluorescent bacteriophage specific for E. coli K1, a nosocomial pathogen responsible for urinary tract infections, neonatal meningitis and sepsis. By confocal and live microscopy, we show that engineered bacteriophages K1F-GFP and E. coli EV36-RFP bacteria displaying the K1 capsule, enter human cells via phagocytosis. Importantly, we show that bacteriophage K1F-GFP efficiently kills intracellular E. coli EV36-RFP in T24 human urinary bladder epithelial cells. Finally, we provide evidence that bacteria and bacteriophages are degraded by LC3-associated phagocytosis and xenophagy.
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Affiliation(s)
| | - Siu Fung Stanley Ho
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Ranti Dev Shukla
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamas Feher
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
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75
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Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. MICROBIOME 2018; 6:145. [PMID: 30126456 PMCID: PMC6102903 DOI: 10.1186/s40168-018-0527-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/09/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a "gold standard" protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data. RESULTS Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes. CONCLUSIONS Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Eoghan Casey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Rebecca Moore
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Joanna Kaczorowska
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc, Moorepark Food Research Centre, Fermoy, Co., Cork, Cork, Ireland
| | - Fionnuala M McAuliffe
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe van Sinderen
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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Parras-Moltó M, Rodríguez-Galet A, Suárez-Rodríguez P, López-Bueno A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. MICROBIOME 2018; 6:119. [PMID: 29954453 PMCID: PMC6022446 DOI: 10.1186/s40168-018-0507-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. RESULTS We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. CONCLUSIONS Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.
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Affiliation(s)
- Marcos Parras-Moltó
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Ana Rodríguez-Galet
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Patricia Suárez-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain.
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77
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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78
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Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, McDonnell SA, Nolan JA, Sutton TD, Dalmasso M, McCann A, Ross RP, Hill C. Reproducible protocols for metagenomic analysis of human faecal phageomes. MICROBIOME 2018; 6:68. [PMID: 29631623 PMCID: PMC5892011 DOI: 10.1186/s40168-018-0446-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/13/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. RESULTS Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. CONCLUSIONS The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.
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Affiliation(s)
| | - Feargal J. Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Amanda Forde
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Karen M. Daly
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - James A. Nolan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Marion Dalmasso
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, EA4651 ABTE, F-14032 Caen, France
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland
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79
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Abstract
Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) (ME/CFS) is a disabling and debilitating disease of unknown aetiology. It is a heterogeneous disease characterized by various inflammatory, immune, viral, neurological and endocrine symptoms. Several microbiome studies have described alterations in the bacterial component of the microbiome (dysbiosis) consistent with a possible role in disease development. However, in focusing on the bacterial components of the microbiome, these studies have neglected the viral constituent known as the virome. Viruses, particularly those infecting bacteria (bacteriophages), have the potential to alter the function and structure of the microbiome via gene transfer and host lysis. Viral-induced microbiome changes can directly and indirectly influence host health and disease. The contribution of viruses towards disease pathogenesis is therefore an important area for research in ME/CFS. Recent advancements in sequencing technology and bioinformatics now allow more comprehensive and inclusive investigations of human microbiomes. However, as the number of microbiome studies increases, the need for greater consistency in study design and analysis also increases. Comparisons between different ME/CFS microbiome studies are difficult because of differences in patient selection and diagnosis criteria, sample processing, genome sequencing and downstream bioinformatics analysis. It is therefore important that microbiome studies adopt robust, reproducible and consistent study design to enable more reliable and valid comparisons and conclusions to be made between studies. This article provides a comprehensive review of the current evidence supporting microbiome alterations in ME/CFS patients. Additionally, the pitfalls and challenges associated with microbiome studies are discussed.
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80
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Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 2018; 554:118-122. [DOI: 10.1038/nature25474] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/28/2017] [Indexed: 02/06/2023]
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81
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Castro-Mejía JL, Deng L, Vogensen FK, Reyes A, Nielsen DS. Extraction and Purification of Viruses from Fecal Samples for Metagenome and Morphology Analyses. Methods Mol Biol 2018; 1838:49-57. [PMID: 30128989 DOI: 10.1007/978-1-4939-8682-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The human enteric virome consists of endogenous retro elements and viruses that infect the host and members of the gut microbiome (GM). Mounting evidence suggests that the gut virome plays a central role in maintaining homeostasis and via the GM influences immunology of the host. To thoroughly characterize the gut virome, it is often very useful to first separate and concentrate extracellular viral-like particles (eVLPs) enabling an integrative characterization of them. Here, we describe a detailed protocol for extraction and concentration of the viral fraction from fecal samples based on a polyethylene glycol precipitation (PEG) approach. These procedures maximize the yields of eVLPs (and their DNA) with high purity well suited for down-stream analysis such as quantification and morphological assessment, determination of phage-host pairs as well as virome sequencing.
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Affiliation(s)
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Finn K Vogensen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
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82
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Methods for Enrichment and Sequencing of Oral Viral Assemblages: Saliva, Oral Mucosa, and Dental Plaque Viromes. Methods Mol Biol 2018; 1838:143-161. [PMID: 30128995 DOI: 10.1007/978-1-4939-8682-8_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The oral cavity is a major portal of entry for human pathogens including viruses. However, metagenomics has revealed that highly personalized and time-persistent bacteriophage assemblages dominate this habitat. Most oral bacteriophages follow lysogenic life cycles, deploying complex strategies to manage bacterial homeostasis. Although bacterial dysbiosis underlies common oral pathologies such as caries and periodontitis, the cause of these bacteria replacements remains obscure, and it is theorized that bacteriophages play an important role. The enormous sensitivity of metagenomics coupled with next-generation sequencing has made technically feasible to address the putative role of bacteriophages in oral dysbiosis and represents a valuable tool to discover new human viruses.This chapter proposes a workflow that consists of a simple viral enrichment protocol, two alternative random amplification methods, and next-generation sequencing to access virome composition in three oral environments: supragingival plaque, saliva, and mucosa. These protocols circumvent some well-known sources of bias, providing genomic information about DNA and RNA viral communities with minimal contamination from human and bacterial sources.
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83
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The human gut virome: form and function. Emerg Top Life Sci 2017; 1:351-362. [PMID: 33525769 DOI: 10.1042/etls20170039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
Abstract
Advances in next-generation sequencing technologies and the application of metagenomic approaches have fuelled an exponential increase in our understanding of the human gut microbiome. These approaches are now also illuminating features of the diverse and abundant collection of viruses (termed the virome) subsisting with the microbial ecosystems residing within the human holobiont. Here, we focus on the current and emerging knowledge of the human gut virome, in particular on viruses infecting bacteria (bacteriophage or phage), which are a dominant component of this viral community. We summarise current insights regarding the form and function of this 'human gut phageome' and highlight promising avenues for future research. In doing so, we discuss the potential for phage to drive ecological functioning and evolutionary change within this important microbial ecosystem, their contribution to modulation of host-microbiome interactions and stability of the community as a whole, as well as the potential role of the phageome in human health and disease. We also consider the emerging concepts of a 'core healthy gut phageome' and the putative existence of 'viral enterotypes' and 'viral dysbiosis'.
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84
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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85
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Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures. Appl Environ Microbiol 2017; 83:AEM.00888-17. [PMID: 28754704 DOI: 10.1128/aem.00888-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
Despite being potentially highly useful for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows the removal of the bulk protein from whey and milk samples with losses of less than 50% of spiked phages. The protocol was applied to extract phages from whey in order to test the notion that members of Lactococcus lactis 936 (now Sk1virus), P335, c2 (now C2virus) and Leuconostoc phage groups are the most frequently encountered in the dairy environment. The relative abundance and diversity of phages in eight and four whey mixtures from dairies using undefined mesophilic mixed-strain cultures containing Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc species (i.e., DL starter cultures) and defined cultures, respectively, were assessed. Results obtained from transmission electron microscopy and high-throughput sequence analyses revealed the dominance of Lc. lactis 936 phages (order Caudovirales, family Siphoviridae) in dairies using undefined DL starter cultures and Lc. lactis c2 phages (order Caudovirales, family Siphoviridae) in dairies using defined cultures. The 936 and Leuconostoc phages demonstrated limited diversity. Possible coinduction of temperate P335 prophages and satellite phages in one of the whey mixtures was also observed.IMPORTANCE The method optimized in this study could provide an important basis for understanding the dynamics of the phage community (abundance, development, diversity, evolution, etc.) in dairies with different sizes, locations, and production strategies. It may also enable the discovery of previously unknown phages, which is crucial for the development of rapid molecular biology-based methods for phage burden surveillance systems. The dominance of only a few phage groups in the dairy environment signifies the depth of knowledge gained over the past decades, which served as the basis for designing current phage control strategies. The presence of a correlation between phages and the type of starter cultures being used in dairies might help to improve the selection and/or design of suitable, custom, and cost-efficient phage control strategies.
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86
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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87
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The Human Gut Phage Community and Its Implications for Health and Disease. Viruses 2017; 9:v9060141. [PMID: 28594392 PMCID: PMC5490818 DOI: 10.3390/v9060141] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 06/02/2017] [Indexed: 12/23/2022] Open
Abstract
In this review, we assess our current understanding of the role of bacteriophages infecting the human gut bacterial community in health and disease. In general, bacteriophages contribute to the structure of their microbial communities by driving host and viral diversification, bacterial evolution, and by expanding the functional diversity of ecosystems. Gut bacteriophages are an ensemble of unique and shared phages in individuals, which encompass temperate phages found predominately as prophage in gut bacteria (prophage reservoir) and lytic phages. In healthy individuals, only a small fraction of the prophage reservoir is activated and found as extracellular phages. Phage community dysbiosis is characterized by a shift in the activated prophage community or an increase of lytic phages, and has been correlated with disease, suggesting that a proper balance between lysis and lysogeny is needed to maintain health. Consequently, the concept of microbial dysbiosis might be extended to the phage component of the microbiome as well. Understanding the dynamics and mechanisms to restore balance after dysbiosis is an active area of research. The use of phage transplants to re-establish health suggests that phages can be used as disease treatment. Such advances represent milestones in our understanding of gut phages in human health and should fuel research on their role in health and disease.
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88
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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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89
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Jurtz VI, Villarroel J, Lund O, Voldby Larsen M, Nielsen M. MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLoS One 2016; 11:e0163111. [PMID: 27684958 PMCID: PMC5042410 DOI: 10.1371/journal.pone.0163111] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/04/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are the most abundant biological entity on the planet, but at the same time do not account for much of the genetic material isolated from most environments due to their small genome sizes. They also show great genetic diversity and mosaic genomes making it challenging to analyze and understand them. Here we present MetaPhinder, a method to identify assembled genomic fragments (i.e.contigs) of phage origin in metagenomic data sets. The method is based on a comparison to a database of whole genome bacteriophage sequences, integrating hits to multiple genomes to accomodate for the mosaic genome structure of many bacteriophages. The method is demonstrated to out-perform both BLAST methods based on single hits and methods based on k-mer comparisons. MetaPhinder is available as a web service at the Center for Genomic Epidemiology https://cge.cbs.dtu.dk/services/MetaPhinder/, while the source code can be downloaded from https://bitbucket.org/genomicepidemiology/metaphinder or https://github.com/vanessajurtz/MetaPhinder.
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Affiliation(s)
| | - Julia Villarroel
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mette Voldby Larsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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90
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Bechshøft RL, Reitelseder S, Højfeldt G, Castro-Mejía JL, Khakimov B, Ahmad HFB, Kjær M, Engelsen SB, Johansen SMB, Rasmussen MA, Lassen AJ, Jensen T, Beyer N, Serena A, Perez-Cueto FJA, Nielsen DS, Jespersen AP, Holm L. Counteracting Age-related Loss of Skeletal Muscle Mass: a clinical and ethnological trial on the role of protein supplementation and training load (CALM Intervention Study): study protocol for a randomized controlled trial. Trials 2016; 17:397. [PMID: 27507236 PMCID: PMC4977774 DOI: 10.1186/s13063-016-1512-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022] Open
Abstract
Background Aging is associated with decreased muscle mass and functional capacity, which in turn decrease quality of life. The number of citizens over the age of 65 years in the Western world will increase by 50 % over the next four decades, and this demographic shift brings forth new challenges at both societal and individual levels. Only a few longitudinal studies have been reported, but whey protein supplementation seems to improve muscle mass and function, and its combination with heavy strength training appears even more effective. However, heavy resistance training may reduce adherence to training, thereby attenuating the overall benefits of training. We hypothesize that light load resistance training is more efficient when both adherence and physical improvement are considered longitudinally. We launched the interdisciplinary project on Counteracting Age-related Loss of Skeletal Muscle Mass (CALM) to investigate the impact of lifestyle changes on physical and functional outcomes as well as everyday practices and habits in a qualitative context. Methods We will randomize 205 participants older than 65 years to be given 1 year of two daily nutrient supplements with 10 g of sucrose and 20 g of either collagen protein, carbohydrates, or whey. Further, two groups will perform either heavy progressive resistance training or light load training on top of the whey supplement. Discussion The primary outcome of the CALM Intervention Study is the change in thigh cross-sectional area. Moreover, we will evaluate changes in physical performance, muscle fiber type and acute anabolic response to whey protein ingestion, sensory adaptation, gut microbiome, and a range of other measures, combined with questionnaires on life quality and qualitative interviews with selected subjects. The CALM Intervention Study will generate scientific evidence and recommendations to counteract age-related loss of skeletal muscle mass in elderly individuals. Trial registration ClinicalTrials.gov NCT02034760. Registered on 10 January 2014. ClinicalTrials.gov NCT02115698. Registered on 14 April 2014. Danish regional committee of the Capital Region H-4-2013-070. Registered on 4 July 2013. Danish Data Protection Agency 2012-58-0004 – BBH-2015-001 I-Suite 03432. Registered on 9 January 2015.
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Affiliation(s)
- Rasmus Leidesdorff Bechshøft
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery M, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400, Copenhagen, NV, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Reitelseder
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery M, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400, Copenhagen, NV, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Grith Højfeldt
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery M, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400, Copenhagen, NV, Denmark
| | | | - Bekzod Khakimov
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hajar Fauzan Bin Ahmad
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Michael Kjær
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery M, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400, Copenhagen, NV, Denmark
| | - Søren Balling Engelsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Morten Arendt Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Pediatric Asthma Center, Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Aske Juul Lassen
- SAXO Institute, Faculty of Humanities, University of Copenhagen, Copenhagen, Denmark
| | - Tenna Jensen
- SAXO Institute, Faculty of Humanities, University of Copenhagen, Copenhagen, Denmark
| | - Nina Beyer
- Musculoskeletal Rehabilitation Research Unit, Department of Physical and Occupational Therapy, Bispebjerg Hospital, Copenhagen, Denmark
| | - Anja Serena
- Arla Foods Ingredients Group P/S, Viby J, Denmark
| | | | - Dennis Sandris Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Lars Holm
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery M, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400, Copenhagen, NV, Denmark. .,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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91
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Forbes JD, Van Domselaar G, Bernstein CN. The Gut Microbiota in Immune-Mediated Inflammatory Diseases. Front Microbiol 2016; 7:1081. [PMID: 27462309 PMCID: PMC4939298 DOI: 10.3389/fmicb.2016.01081] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/28/2016] [Indexed: 12/17/2022] Open
Abstract
The collection of microbes and their genes that exist within and on the human body, collectively known as the microbiome has emerged as a principal factor in human health and disease. Humans and microbes have established a symbiotic association over time, and perturbations in this association have been linked to several immune-mediated inflammatory diseases (IMID) including inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis. IMID is a term used to describe a group of chronic, highly disabling diseases that affect different organ systems. Though a cornerstone commonality between IMID is the idiopathic nature of disease, a considerable portion of their pathobiology overlaps including epidemiological co-occurrence, genetic susceptibility loci and environmental risk factors. At present, it is clear that persons with an IMID are at an increased risk for developing comorbidities, including additional IMID. Advancements in sequencing technologies and a parallel explosion of 16S rDNA and metagenomics community profiling studies have allowed for the characterization of microbiomes throughout the human body including the gut, in a myriad of human diseases and in health. The main challenge now is to determine if alterations of gut flora are common between IMID or, if particular changes in the gut community are in fact specific to a single disease. Herein, we review and discuss the relationships between the gut microbiota and IMID.
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Affiliation(s)
- Jessica D. Forbes
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| | - Charles N. Bernstein
- Department of Internal Medicine and the IBD Clinical and Research Centre, University of Manitoba, WinnipegMB, Canada
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Abstract
Recurrent aphthous ulcer (RAU) is the most common oral mucosal disease with complex etiology. Since its pathogenesis is still not completely clear, specific clinical treatment is lacking. With the continuous development of oral micro-ecology, oral microbial population imbalance as an important pathogenesis of RAU is gradually recognized. At present, the research of oral flora imbalance has made some progress, but as the largest member of the oral microbial community, the research of the virome is still under development. In recent years, the rapid development of macro virus genome science and high throughput sequencing technology has led to a breakthrough in oral virome.
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93
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Abstract
Bacteriophage play many varied roles in microbial ecology and evolution. This chapter collates a vast body of knowledge and expertise on Yersinia pestis phages, including the history of their isolation and classical methods for their isolation and identification. The genomic diversity of Y. pestis phage and bacteriophage islands in the Y. pestis genome are also discussed because all phage research represents a branch of genetics. In addition, our knowledge of the receptors that are recognized by Y. pestis phage, advances in phage therapy for Y. pestis infections, the application of phage in the detection of Y. pestis, and clustered regularly interspaced short palindromic repeats (CRISPRs) sequences of Y. pestis from prophage DNA are all reviewed here.
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