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McNair K, Salamon P, Edwards RA, Segall AM. PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes. BMC Bioinformatics 2024; 25:82. [PMID: 38389044 PMCID: PMC10885494 DOI: 10.1186/s12859-024-05701-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence and shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain. More importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. RESULTS Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. The code for PRFect is freely available and installs with a single terminal command. CONCLUSION PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.
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Affiliation(s)
- Katelyn McNair
- Computational Science Research Center, San Diego State University, San Diego, CA, USA.
- Department of Computational Science, University of California Irvine, Irvine, CA, USA.
| | - Peter Salamon
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Anca M Segall
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, USA
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Bustamante G, Liebermann E, McNair K, Fontenot HB. Women's perceptions and preferences for cervical cancer screening in light of updated guidelines. J Am Assoc Nurse Pract 2023; 35:699-707. [PMID: 37498967 DOI: 10.1097/jxx.0000000000000923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/13/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Updated risk-based guidelines for cervical cancer screening (CCS) allow for individualized screening that minimizes unnecessary testing. However, these guidelines are complex and may not be easily understandable to patients. PURPOSE To describe women's perceptions and preferences about CCS in light of recent guideline changes. METHODOLOGY This qualitative study conducted in February 2020 used online, text-based focus groups with a sample of US women ( n = 49) ages 27-45. After participants completed a short demographic survey, an experienced moderator used a semistructured guide to solicit participants' perceptions of routine gynecologic care and CCS. We summarized survey data using descriptive statistics. Two authors analyzed transcripts using conventional content analysis and met with other team members to resolve discrepancies and determine final themes. RESULTS Most participants were non-Hispanic White (65%), had health insurance (90%), and reported having a routine gynecologic examination in the past year (70%). We identified four common themes: (1) low perceived risk of human papillomavirus (HPV) coupled with low knowledge about HPV as a causative factor for cervical cancer, (2) confusion about-and mistrust of-recent individual risk-based guidelines that determine the indicated timing and type of CCS test (Pap or HPV testing), (3) mixed opinions about performing a self-swab for HPV testing, and (4) conflicting perceptions of trust toward providers and the health care industry. CONCLUSIONS Findings highlight women's uncertainty and hesitancy about updated CCS guidelines. IMPLICATIONS Provider-patient communication strategies should consider women's gaps in knowledge about HPV, include the rationale for guidelines and types of tests, and build trust between patients and providers.
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Affiliation(s)
- Gabriela Bustamante
- Instituto de Medicina Social & Desafíos Globales, School of Public Health, Universidad San Francisco de Quito, Quito, Ecuador. Dr. Bustamante is previously at the Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Erica Liebermann
- College of Nursing, University of Rhode Island, Providence, Rhode Island
| | - Katelyn McNair
- Beth Israel Deaconess Lahey Health Breast Center, Plymouth, Massachusetts. Dr. McNair is previously at the Boston College, Connell School of Nursing, Chestnut Hill, Massachusetts
| | - Holly B Fontenot
- School of Nursing, University of Hawaii, Honolulu, Hawaii. Dr. Fontenot is previously at the Boston College, Connell School of Nursing, Chestnut Hill, Massachusetts
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Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Fernanda Mora M, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. Microb Genom 2023; 9:001100. [PMID: 37665209 PMCID: PMC10569736 DOI: 10.1099/mgen.0.001100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Alejandro A. Vega
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Cole Souza
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michelle An
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Nicole Jacobson
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Katelyn McNair
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Maria Fernanda Mora
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Karina Pastrana
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Christopher Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Clarice Harker
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Will S. Plewa
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Susanna R. Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Przemysław Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Antoni Luque
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Present address: Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anca M. Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
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Cobián Güemes AG, Le T, Rojas MI, Jacobson NE, Villela H, McNair K, Hung SH, Han L, Boling L, Octavio JC, Dominguez L, Cantú VA, Archdeacon S, Vega AA, An MA, Hajama H, Burkeen G, Edwards RA, Conrad DJ, Rohwer F, Segall AM. Compounding Achromobacter Phages for Therapeutic Applications. Viruses 2023; 15:1665. [PMID: 37632008 PMCID: PMC10457797 DOI: 10.3390/v15081665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Achromobacter species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by Achromobacter xylosoxidans CF418 or Achromobacter ruhlandii CF116 experienced fatal exacerbations. Achromobacter spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of Achromobacter. In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the Achromobacter Kumeyaay phage collection. Six distinct Achromobacter phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available Achromobacter phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 Achromobacter clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in Achromobacter xylosoxidans CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as Achromobacter phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 × 109 plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill Achromobacter spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.
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Affiliation(s)
- Ana Georgina Cobián Güemes
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Tram Le
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Maria Isabel Rojas
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Nicole E. Jacobson
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Helena Villela
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Marine Microbiomes Lab, Red Sea Research Center, King Abdullah University of Science and Technology, Building 2, Level 3, Room 3216 WS03, Thuwal 23955-6900, Saudi Arabia
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Shr-Hau Hung
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Lili Han
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lance Boling
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Jessica Claire Octavio
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Lorena Dominguez
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Vito Adrian Cantú
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Sinéad Archdeacon
- College of Biological Sciences, University of California Davis, Davis, CA 95616, USA
| | - Alejandro A. Vega
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90025, USA
| | - Michelle A. An
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Hamza Hajama
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Gregory Burkeen
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Robert A. Edwards
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
- Flinders Accelerator for Microbiome Exploration, Flinders University, Sturt Road, Bedford Park 5042, Australia
| | - Douglas J. Conrad
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, San Diego, CA 9500, USA
| | - Forest Rohwer
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Anca M. Segall
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
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Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Mora MF, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. bioRxiv 2023:2023.03.05.531146. [PMID: 36945541 PMCID: PMC10028833 DOI: 10.1101/2023.03.05.531146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Impact statement Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. Data summary The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. ' frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Alejandro A. Vega
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Cole Souza
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michelle An
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Nicole Jacobson
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Katelyn McNair
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Maria Fernanda Mora
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Karina Pastrana
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Christopher Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Clarice Harker
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Will S. Plewa
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Susanna R. Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Przemysław Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Antoni Luque
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anca M. Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
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McNair K, Salamon P, Edwards RA, Segall AM. PRFect: A tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes. Res Sq 2023:rs.3.rs-2997217. [PMID: 37333268 PMCID: PMC10274946 DOI: 10.21203/rs.3.rs-2997217/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain, but more importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. Results Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. Conclusion PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.
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McKerral JC, Papudeshi B, Inglis LK, Roach MJ, Decewicz P, McNair K, Luque A, Dinsdale EA, Edwards RA. The Promise and Pitfalls of Prophages. bioRxiv 2023:2023.04.20.537752. [PMID: 37131798 PMCID: PMC10153245 DOI: 10.1101/2023.04.20.537752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell's energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.
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Affiliation(s)
- Jody C. McKerral
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Laura K. Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Antoni Luque
- The Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
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8
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Ecale Zhou CL, Kimbrel J, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: code for functional annotation and comparison of phage genomes. G3 (Bethesda) 2021; 11:jkab074. [PMID: 33734357 PMCID: PMC8104953 DOI: 10.1093/g3journal/jkab074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/25/2021] [Indexed: 11/12/2022]
Abstract
To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.
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Affiliation(s)
- Carol L Ecale Zhou
- Global Security Computing Applications, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jeffrey Kimbrel
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Robert Edwards
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- College of Science and Engineering, Flinders University, Bedford Park, SA 5048, Australia
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Brian A Souza
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Stephanie Malfatti
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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9
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Rojas MI, Cavalcanti GS, McNair K, Benler S, Alker AT, Cobián-Güemes AG, Giluso M, Levi K, Rohwer F, Bailey BA, Beyhan S, Edwards RA, Shikuma NJ. A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes. mSystems 2020; 5:e00648-20. [PMID: 32723799 PMCID: PMC7394362 DOI: 10.1128/msystems.00648-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome.IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.
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Affiliation(s)
- Maria I Rojas
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Giselle S Cavalcanti
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Katelyn McNair
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Sean Benler
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Amanda T Alker
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Ana G Cobián-Güemes
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Melissa Giluso
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Kyle Levi
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Sinem Beyhan
- Department of Biology, San Diego State University, San Diego, California, USA
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
| | - Robert A Edwards
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Nicholas J Shikuma
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
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10
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Boling L, Cuevas DA, Grasis JA, Kang HS, Knowles B, Levi K, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, Rohwer F. Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. Gut Microbes 2020; 11:721-734. [PMID: 31931655 PMCID: PMC7524278 DOI: 10.1080/19490976.2019.1701353] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.
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Affiliation(s)
- Lance Boling
- Department of Biology, San Diego State University, San Diego, CA, USA,CONTACT Lance Boling Department of Biology, San Diego State University, LS301, 5500 Campanile Dr, San Diego, CA92182USA
| | - Daniel A. Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Juris A. Grasis
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Han Suh Kang
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Katelyn McNair
- Department of Biology, San Diego State University, San Diego, CA, USA,Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | | | | | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
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11
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Ecale Zhou CL, Malfatti S, Kimbrel J, Philipson C, McNair K, Hamilton T, Edwards R, Souza B. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates. Bioinformatics 2020; 35:4402-4404. [PMID: 31086982 PMCID: PMC6821344 DOI: 10.1093/bioinformatics/btz258] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 03/15/2019] [Accepted: 05/03/2019] [Indexed: 11/14/2022] Open
Abstract
Summary To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE’s modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system. Availability and implementation multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carol L Ecale Zhou
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Fort Detrick, MD, USA
| | - Stephanie Malfatti
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Fort Detrick, MD, USA
| | - Jeffrey Kimbrel
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Fort Detrick, MD, USA
| | - Casandra Philipson
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA.,Chemical and Biological Research, Defense Threat Reduction Agency, CA, USA
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, CA, USA
| | - Theron Hamilton
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, USA
| | - Robert Edwards
- Computational Sciences Research Center, San Diego State University, CA, USA
| | - Brian Souza
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Fort Detrick, MD, USA
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12
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McNair K, Zhou C, Dinsdale EA, Souza B, Edwards RA. PHANOTATE: a novel approach to gene identification in phage genomes. Bioinformatics 2019; 35:4537-4542. [PMID: 31329826 PMCID: PMC6853651 DOI: 10.1093/bioinformatics/btz265] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/07/2019] [Accepted: 04/15/2019] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. RESULTS We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank's non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. AVAILABILITY AND IMPLEMENTATION https://github.com/deprekate/PHANOTATE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Carol Zhou
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | - Brian Souza
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Robert A Edwards
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
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13
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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14
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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15
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Benler S, Cobián-Güemes AG, McNair K, Hung SH, Levi K, Edwards R, Rohwer F. A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. Microbiome 2018; 6:191. [PMID: 30352623 PMCID: PMC6199706 DOI: 10.1186/s40168-018-0573-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs. RESULTS This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle. The majority of phage-encoded DGRs were identified as prophages in bacterial hosts from the phyla Bacteroidetes, Proteobacteria, and Firmicutes. Sequence reads from these previously unidentified prophages were present in viral metagenomes (viromes), indicating these prophages can produce functional viruses. Five phages possessed hypervariable proteins with structural similarity to the tail fiber of BPP-1, whereas the functions of the remaining DGR target proteins were unknown. A novel temperate phage that harbors a DGR cassette targeting a protein of unknown function was induced from Bacteroides dorei. This phage, here named Bacteroides dorei Hankyphage, lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively. CONCLUSIONS Here, the number of known DGR-containing phages is increased from four to 92. All of these phages exhibit a temperate lifestyle, including a cosmopolitan human-associated phage. Targeted hypervariation by temperate phages may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.
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Affiliation(s)
- Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | | | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Shr-Hau Hung
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Rob Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
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16
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Abstract
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.
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Affiliation(s)
- Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.,Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Gordon D Pusch
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Ross Overbeek
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525, Nijmegen, The Netherlands
| | - Robert Edwards
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA. .,Departments of Biology and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
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17
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Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobián-Güemes AG, Coutinho FH, Dinsdale EA, Felts B, Furby KA, George EE, Green KT, Gregoracci GB, Haas AF, Haggerty JM, Hester ER, Hisakawa N, Kelly LW, Lim YW, Little M, Luque A, McDole-Somera T, McNair K, de Oliveira LS, Quistad SD, Robinett NL, Sala E, Salamon P, Sanchez SE, Sandin S, Silva GGZ, Smith J, Sullivan C, Thompson C, Vermeij MJA, Youle M, Young C, Zgliczynski B, Brainard R, Edwards RA, Nulton J, Thompson F, Rohwer F. Erratum: Corrigendum: Lytic to temperate switching of viral communities. Nature 2016; 539:123. [DOI: 10.1038/nature19335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Abstract
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
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Affiliation(s)
- Robert A Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium Laboratory of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bas E Dutilh
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, CEP 21941-902, Brazil Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands
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19
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Forrest CM, McNair K, Pisar M, Khalil OS, Darlington LG, Stone TW. Altered hippocampal plasticity by prenatal kynurenine administration, kynurenine-3-monoxygenase (KMO) deletion or galantamine. Neuroscience 2015; 310:91-105. [PMID: 26365611 PMCID: PMC4642643 DOI: 10.1016/j.neuroscience.2015.09.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/11/2015] [Accepted: 09/07/2015] [Indexed: 11/16/2022]
Abstract
Glutamate receptors sensitive to N-methyl-D-aspartate (NMDA) are involved in embryonic brain development but their activity may be modulated by the kynurenine pathway of tryptophan metabolism which includes an agonist (quinolinic acid) and an antagonist (kynurenic acid) at these receptors. Our previous work has shown that prenatal inhibition of the pathway produces abnormalities of brain development. In the present study kynurenine and probenecid (both 100mg/kg, doses known to increase kynurenic acid levels in the brain) were administered to female Wistar rats on embryonic days E14, E16 and E18 of gestation and the litter was allowed to develop to post-natal day P60. Western blotting revealed no changes in hippocampal expression of several proteins previously found to be altered by inhibition of the kynurenine pathway including the NMDA receptor subunits GluN1, GluN2A and GluN2B, as well as doublecortin, Proliferating Cell Nuclear Antigen (PCNA), sonic hedgehog and unco-ordinated (unc)-5H1 and 5H3. Mice lacking the enzyme kynurenine-3-monoxygenase (KMO) also showed no changes in hippocampal expression of several of these proteins or the 70-kDa and 100-kDa variants of Disrupted in Schizophrenia-1 (DISC1). Electrical excitability of pyramidal neurons in the CA1 region of hippocampal slices was unchanged, as was paired-pulse facilitation and inhibition. Long-term potentiation was decreased in the kynurenine-treated rats and in the KMO(-/-) mice, but galantamine reversed this effect in the presence of nicotinic receptor antagonists, consistent with evidence that it can potentiate glutamate at NMDA receptors. It is concluded that interference with the kynurenine pathway in utero can have lasting effects on brain function of the offspring, implying that the kynurenine pathway is involved in the regulation of early brain development.
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Affiliation(s)
- C M Forrest
- Institute of Neuroscience and Psychology, West Medical Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - K McNair
- Institute of Neuroscience and Psychology, West Medical Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - M Pisar
- Institute of Neuroscience and Psychology, West Medical Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - O S Khalil
- Institute of Neuroscience and Psychology, West Medical Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - L G Darlington
- Ashtead Hospital, The Warren, Ashtead, Surrey KT21 2SB, UK
| | - T W Stone
- Institute of Neuroscience and Psychology, West Medical Building, University of Glasgow, Glasgow G12 8QQ, UK.
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Abstract
As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
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Affiliation(s)
- Katelyn McNair
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA
| | - Robert A Edwards
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA ; Computational Sciences Research Center, San Diego State University , San Diego, CA , USA ; Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL , USA
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21
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Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014; 5:4498. [PMID: 25058116 PMCID: PMC4111155 DOI: 10.1038/ncomms5498] [Citation(s) in RCA: 483] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/25/2014] [Indexed: 01/20/2023] Open
Abstract
Metagenomics, or sequencing of the genetic material from a complete microbial community, is a
promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many
unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present
in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its
~97 kbp genome is six times more abundant in publicly available metagenomes than all other
known phages together; it comprises up to 90% and 22% of all reads in virus-like particle
(VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all
human faecal metagenomic sequencing reads in the public databases. The majority of
crAssphage-encoded proteins match no known sequences in the database, which is why it was not
detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host
for this phage, consistent with Bacteroides-related protein homologues and a unique
carbohydrate-binding domain encoded in the phage genome. Metagenomic studies of microbial communities often report DNA sequences from
unidentified viruses. Here, Dutilh et al. analyse metagenomic data to reveal the complete
genome of an abundant, ubiquitous virus from human faeces, and predict that the virus infects
bacteria of the Bacteroides group.
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Affiliation(s)
- Bas E Dutilh
- 1] Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands [2] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [3] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil
| | - Noriko Cassman
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2]
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Savannah E Sanchez
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Genivaldo G Z Silva
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Jeremy J Barr
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Victor Seguritan
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Ramy K Aziz
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Ben Felts
- Department of Mathematics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Elizabeth A Dinsdale
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - John L Mokili
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Robert A Edwards
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil [3] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave B109, Argonne, Illinois 60439, USA
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22
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Forrest C, Khalil O, Pisar M, McNair K, Kornisiuk E, Snitcofsky M, Gonzalez N, Jerusalinsky D, Darlington L, Stone T. Changes in synaptic transmission and protein expression in the brains of adult offspring after prenatal inhibition of the kynurenine pathway. Neuroscience 2013; 254:241-59. [DOI: 10.1016/j.neuroscience.2013.09.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
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23
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Dinsdale EA, Edwards RA, Bailey BA, Tuba I, Akhter S, McNair K, Schmieder R, Apkarian N, Creek M, Guan E, Hernandez M, Isaacs K, Peterson C, Regh T, Ponomarenko V. Multivariate analysis of functional metagenomes. Front Genet 2013; 4:41. [PMID: 23579547 PMCID: PMC3619665 DOI: 10.3389/fgene.2013.00041] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022] Open
Abstract
Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven different data mining and statistical analyses by comparing and contrasting the metabolic functions of 212 microbial metagenomes within and between 10 environments. Not all approaches are appropriate for all questions, and researchers should decide which approach addresses their questions. This work demonstrated the use of each approach: for example, random forests provided a robust and enlightening description of both the clustering of metagenomes and the metabolic processes that were important in separating microbial communities from different environments. All analyses identified that the presence of phage genes within the microbial community was a predictor of whether the microbial community was host-associated or free-living. Several analyses identified the subtle differences that occur with environments, such as those seen in different regions of the marine environment.
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Abstract
Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed. Results: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate. Availability and implementation: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library ‘Random Forest’ (Liaw and Weiner, 2010). The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at http://www.phantome.org/PHACTS/. Contact:katelyn@rohan.sdsu.edu; redwards@sciences.sdsu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katelyn McNair
- Computational Science Research Center, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA.
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25
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McNair K, Broad J, Riedel G, Davies CH, Cobb SR. Global changes in the hippocampal proteome following exposure to an enriched environment. Neuroscience 2007; 145:413-22. [PMID: 17261355 DOI: 10.1016/j.neuroscience.2006.12.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 12/08/2006] [Accepted: 12/11/2006] [Indexed: 10/23/2022]
Abstract
Exposure to an enriched environment promotes neurochemical, structural and neurophysiological changes in the brain and is associated with enhanced synaptic plasticity and improved hippocampal-dependent learning. Using a global proteomics-based approach we have now been able to reveal the altered expression of a diverse range of hippocampal proteins following exposure to an enriched environment. Male Hooded Lister rats (8 weeks) were subjected to a 6-week regimen in which they were housed in either non-enriched (open field) or enriched conditions (toys, wheels etc.). Whole protein extracts from stratum pyramidale and stratum radiatum of area CA1 were then isolated and subjected to differential gel electrophoresis [McNair K, Davies CH, Cobb SR (2006) Plasticity-related regulation of the hippocampal proteome. Eur J Neurosci 23(2):575-580]. Of the 2469 resolvable protein spots detected in this study, 42 spots (1.7% of the detectable proteome) derived from predominantly somatic fractions and 32 proteins spots from dendritic fractions (1.3% of detectable proteome) were significantly altered in abundance following exposure to an enriched environment (somatic: 14 increased/28 decreased abundance, range -1.5 to +1.4-fold change; dendritic: 16 increased, 16 decreased abundance, range -1.6 to +3.0-fold change). Following in-gel tryptic digestion and Maldi-Tof/Q-star mass spectrometry, database searching revealed the identity of 50 protein spots displaying environmental enrichment-related modulation of expression. Identified proteins belonged to a variety of functional classes with gene ontology analysis revealing the majority (>70%) of regulated proteins to be part of the energy metabolism, cytoplasmic organization/biogenesis and signal transduction processes.
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Affiliation(s)
- K McNair
- Division of Neuroscience and Biomedical Systems, IBLS, University of Glasgow, Glasgow, G12 8QQ, UK
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Fox A, Wotherspoon G, McNair K, Hudson L, Patel S, Gentry C, Winter J. Regulation and function of spinal and peripheral neuronal B1 bradykinin receptors in inflammatory mechanical hyperalgesia. Pain 2003; 104:683-691. [PMID: 12927641 DOI: 10.1016/s0304-3959(03)00141-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Activation of either B1 or B2 bradykinin receptors by kinins released from damaged tissues contributes to the development and maintenance of inflammatory hyperalgesia. Whereas B2 agonists activate sensory neurones directly, B1 agonists were thought only to have indirect actions on sensory neurones. The recent discovery of constitutive B1 receptor expression in the rat nervous system lead us to re-investigate the role of neuronal B1 receptors in inflammatory hyperalgesia. Therefore we have examined B1 bradykinin receptor regulation in rat dorsal root ganglia in a model of inflammatory hyperalgesia, and correlated it with hyperalgesic behaviour. Twenty-four hours after injection of Freund's complete adjuvant into one hindpaw, there was a significant increase in B1 protein expression (measured by immunohistochemistry) in both ipsilateral and contralateral dorsal root ganglion neurones, whereas axotomy resulted in reduction of B1 protein in ipsilateral dorsal root ganglia. In behavioural experiments, the B1 antagonist desArg10HOE140, administered by either intrathecal or systemic routes, attenuated Freund's complete adjuvant-induced mechanical hyperalgesia in the inflamed paw, but did not affect mechanical allodynia. The B1 agonist, desArg9BK, did not affect paw withdrawal thresholds in nai;ve rats following intraplantar administration into the paw, whilst intrathecal administration elicited mechanical hyperalgesia. However, after Freund's complete adjuvant-induced inflammation, desArg9BK caused a marked mechanical hyperalgesia, by either route, of the contralateral, uninflamed hindpaw, correlating with the observed contralateral and ipsilateral increases in receptor levels. Our results suggest a functional role for B1 receptors expressed both in the periphery and in the spinal cord, in mechanical hyperalgesia during inflammation.
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Affiliation(s)
- A Fox
- Novartis Institute for Medical Sciences, 5 Gower Place, London WC1E 6BS, UK
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Fox A, Kesingland A, Gentry C, McNair K, Patel S, Urban L, James I. The role of central and peripheral Cannabinoid1 receptors in the antihyperalgesic activity of cannabinoids in a model of neuropathic pain. Pain 2001; 92:91-100. [PMID: 11323130 DOI: 10.1016/s0304-3959(00)00474-7] [Citation(s) in RCA: 287] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have examined the effects of cannabinoid agonists on hyperalgesia in a model of neuropathic pain in the rat and investigated the possible sites of action. The antihyperalgesic activity of the cannabinoids was compared with their ability to elicit behavioural effects characteristic of central cannabinoid activity. WIN55,212-2 (0.3-10 mg kg(-1)), CP-55,940 (0.03-1 mg kg(-1)) and HU-210 (0.001-0.03 mg kg(-1)) were all active in a 'tetrad' of tests consisting of tail-flick, catalepsy, rotarod and hypothermia following subcutaneous administration, with a rank order of potency in each of HU-210 > CP-55,940 > WIN55,212-2. The effects of WIN55,212-2 in each assay were blocked by the Cannabinoid1 (CB1) antagonist SR141716A. In the partial sciatic ligation model of neuropathic pain WIN55,212-2, CP-55,940 and HU-210 produced complete reversal of mechanical hyperalgesia within 3 h of subcutaneous administration with D50 values of 0.52, 0.08 and 0.005 mg kg(-1), respectively. In this model WIN55,212-2 was also effective against thermal hyperalgesia and mechanical allodynia. WIN55,212-2 produced pronounced reversal of mechanical hyperalgesia following intrathecal administration that was blocked by the CB1 antagonist SR141716A. Following intraplantar administration into the ipsilateral hindpaw, WIN55,212-2 produced up to 70% reversal of mechanical hyperalgesia, although activity was also observed at high doses following injection into the contralateral paw. The antihyperalgesic effect of WIN55,212-2 injected into the ipsilateral paw was blocked by subcutaneously administered SR141716A, but was not affected by intrathecally administered SR141716A. These data show that cannabinoids are highly potent and efficacious antihyperalgesic agents in a model of neuropathic pain. This activity is likely to be mediated via an action in both the CNS and in the periphery.
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Affiliation(s)
- A Fox
- Novartis Institute for Medical Sciences, 5 Gower Place, WC1E 6BN, London, UK.
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