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Kieran TJ, Sun X, Creager HM, Tumpey TM, Maines TR, Belser JA. An aggregated dataset of serial morbidity and titer measurements from influenza A virus-infected ferrets. Sci Data 2024; 11:510. [PMID: 38760422 PMCID: PMC11101425 DOI: 10.1038/s41597-024-03256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/11/2024] [Indexed: 05/19/2024] Open
Abstract
Data from influenza A virus (IAV) infected ferrets provides invaluable information towards the study of novel and emerging viruses that pose a threat to human health. This gold standard model can recapitulate many clinical signs of infection present in IAV-infected humans, support virus replication of human, avian, swine, and other zoonotic strains without prior adaptation, and permit evaluation of virus transmissibility by multiple modes. While ferrets have been employed in risk assessment settings for >20 years, results from this work are typically reported in discrete stand-alone publications, making aggregation of raw data from this work over time nearly impossible. Here, we describe a dataset of 728 ferrets inoculated with 126 unique IAV, conducted by a single research group under a uniform experimental protocol. This collection of morbidity, mortality, and viral titer data represents the largest publicly available dataset to date of in vivo-generated IAV infection outcomes on a per-ferret level.
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Affiliation(s)
- Troy J Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiangjie Sun
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hannah M Creager
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
- University of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Terrence M Tumpey
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taronna R Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Jessica A Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Pulit-Penaloza JA, Brock N, Belser JA, Sun X, Pappas C, Kieran TJ, Thakur PB, Zeng H, Cui D, Frederick J, Fasce R, Tumpey TM, Maines TR. Highly pathogenic avian influenza A(H5N1) virus of clade 2.3.4.4b isolated from a human case in Chile causes fatal disease and transmits between co-housed ferrets. Emerg Microbes Infect 2024:2332667. [PMID: 38494746 DOI: 10.1080/22221751.2024.2332667] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses have caused large outbreaks within avian populations on five continents, with concurrent spillover into a variety of mammalian species. Mutations associated with mammalian adaptation have been sporadically identified in avian isolates, and more frequently among mammalian isolates following infection. Reports of human infection with A(H5N1) viruses following contact with infected wildlife have been reported on multiple continents, highlighting the need for pandemic risk assessment of these viruses. In this study, the pathogenicity and transmissibility of A/Chile/25945/2023 HPAI A(H5N1) virus, a novel reassortment with four gene segments (PB1, PB2, NP, MP) from North America lineage, isolated from a severe human case in Chile, was evaluated in vitro and using the ferret model. This virus possessed a high capacity to cause fatal disease, characterized by high morbidity and extrapulmonary spread in virus-inoculated ferrets. The virus was capable of transmission to naïve contacts in a direct contact setting, with contact animals similarly exhibiting severe disease, but did not exhibit productive transmission in respiratory droplet or fomite transmission models. Our results indicate that the virus would need to acquire an airborne transmissible phenotype in mammals to potentially cause a pandemic. Nonetheless, this work warrants continuous monitoring of mammalian adaptations in avian viruses, especially in strains isolated from humans, to aid pandemic preparedness efforts.
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Affiliation(s)
| | - Nicole Brock
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica A Belser
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Xiangjie Sun
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Claudia Pappas
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Troy J Kieran
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Poulami Basu Thakur
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hui Zeng
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dan Cui
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Julia Frederick
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rodrigo Fasce
- Viral Diseases Sub department, Public Health Institute, ISP, Santiago, Chile
| | - Terrence M Tumpey
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taronna R Maines
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Belser JA, Kieran TJ, Mitchell ZA, Sun X, Mayfield K, Tumpey TM, Spengler JR, Maines TR. Key considerations to improve the normalization, interpretation and reproducibility of morbidity data in mammalian models of viral disease. Dis Model Mech 2024; 17:dmm050511. [PMID: 38440823 PMCID: PMC10941659 DOI: 10.1242/dmm.050511] [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: 09/15/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Viral pathogenesis and therapeutic screening studies that utilize small mammalian models rely on the accurate quantification and interpretation of morbidity measurements, such as weight and body temperature, which can vary depending on the model, agent and/or experimental design used. As a result, morbidity-related data are frequently normalized within and across screening studies to aid with their interpretation. However, such data normalization can be performed in a variety of ways, leading to differences in conclusions drawn and making comparisons between studies challenging. Here, we discuss variability in the normalization, interpretation, and presentation of morbidity measurements for four model species frequently used to study a diverse range of human viral pathogens - mice, hamsters, guinea pigs and ferrets. We also analyze findings aggregated from influenza A virus-infected ferrets to contextualize this discussion. We focus on serially collected weight and temperature data to illustrate how the conclusions drawn from this information can vary depending on how raw data are collected, normalized and measured. Taken together, this work supports continued efforts in understanding how normalization affects the interpretation of morbidity data and highlights best practices to improve the interpretation and utility of these findings for extrapolation to public health contexts.
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Affiliation(s)
- Jessica A. Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Troy J. Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Zoë A. Mitchell
- Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Xiangjie Sun
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kristin Mayfield
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Terrence M. Tumpey
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jessica R. Spengler
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Taronna R. Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Kieran TJ, Sun X, Maines TR, Beauchemin CAA, Belser JA. Exploring associations between viral titer measurements and disease outcomes in ferrets inoculated with 125 contemporary influenza A viruses. J Virol 2024; 98:e0166123. [PMID: 38240592 PMCID: PMC10878272 DOI: 10.1128/jvi.01661-23] [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: 10/23/2023] [Accepted: 12/16/2023] [Indexed: 02/21/2024] Open
Abstract
As use of the ferret model to study influenza A virus (IAV) pathogenicity increases, periodic assessment of data generated in this model is warranted, to identify features associated with virus replication throughout the respiratory tract and to refine future analyses. However, protocol-specific differences present between independent laboratories limit easy aggregation of virological data. We compiled viral titer and clinical data from >1,000 ferrets inoculated with 125 contemporary IAV under a consistent experimental protocol (including high- and low-pathogenicity avian, swine-origin, and human viruses, spanning H1, H2, H3, H5, H7, and H9 subtypes) and examined which meaningful and statistically supported associations were present among numerous quantitative measurements. Viral titers correlated positively between ferret nasal turbinate tissue, lung tissue, and nasal wash specimens, though the strength of the associations varied, notably regarding the particular nasal wash summary measure employed and properties of the virus itself. Use of correlation coefficients and mediation analyses further supported the interconnectedness of viral titer measurements taken at different sites throughout the respiratory tract. IAV possessing mammalian host adaptation markers in the HA and PB2 exhibited more rapid growth in the ferret upper respiratory tract early after infection, supported by quantities derived from infectious titer data to capture infection progression, compared with viruses bearing hallmarks of avian IAV. Collectively, this work identifies summary metrics most closely linked with virological and phenotypic outcomes in ferrets, supporting continued refinement of data analyzed from in vivo experimentation, notably from studies conducted to evaluate the public health risk posed by novel and emerging IAV.IMPORTANCEFerrets are frequently employed to study the pandemic potential of novel and emerging influenza A viruses. However, systematic retrospective analyses of data generated from these experiments are rarely performed, limiting our ability to identify trends in this data and explore how analyses can be refined. Using logarithmic viral titer and clinical data aggregated from one research group over 20 years, we assessed which meaningful and statistically supported associations were present among numerous quantitative measurements obtained from influenza A virus (IAV)-infected ferrets, including those capturing viral titers, infection progression, and disease severity. We identified numerous linear correlations between parameters assessing virus replication at discrete sites in vivo, including parameters capturing infection progression not frequently employed in the field, and sought to investigate the interconnected nature of these associations. This work supports continued refinement of data analyzed from in vivo experimentation, notably from studies which evaluate the public health risk posed by IAV.
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Affiliation(s)
- Troy J. Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Xiangjie Sun
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taronna R. Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Catherine A. A. Beauchemin
- Department of Physics, Toronto Metropolitan University, Toronto, Canada
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) at RIKEN, Wako, Japan
| | - Jessica A. Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Sun X, Belser JA, Pulit-Penaloza JA, Brock N, Kieran TJ, Zeng H, Pappas C, Tumpey TM, Maines TR. A naturally occurring HA-stabilizing amino acid (HA1-Y17) in an A(H9N2) low-pathogenic influenza virus contributes to airborne transmission. mBio 2024; 15:e0295723. [PMID: 38112470 PMCID: PMC10790695 DOI: 10.1128/mbio.02957-23] [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: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Despite the accumulation of evidence showing that airborne transmissible influenza A virus (IAV) typically has a lower pH threshold for hemagglutinin (HA) fusion activation, the underlying mechanism for such a link remains unclear. In our study, by using a pair of isogenic recombinant A(H9N2) viruses with a phenotypical difference in virus airborne transmission in a ferret model due to an acid-destabilizing mutation (HA1-Y17H) in the HA, we demonstrate that an acid-stable A(H9N2) virus possesses a multitude of advantages over its less stable counterpart, including better fitness in the ferret respiratory tract, more effective aerosol emission from infected animals, and improved host susceptibility. Our study provides supporting evidence for the requirement of acid stability in efficient airborne transmission of IAV and sheds light on fundamental mechanisms for virus airborne transmission.
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Affiliation(s)
- Xiangjie Sun
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica A. Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joanna A. Pulit-Penaloza
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nicole Brock
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Troy J. Kieran
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hui Zeng
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claudia Pappas
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Terrence M. Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taronna R. Maines
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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6
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Kieran TJ, DaSilva J, Stark TJ, York IA, Pappas C, Barnes JR, Maines TR, Belser JA. Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types. Microbiol Spectr 2023; 11:e0116623. [PMID: 37404140 PMCID: PMC10433845 DOI: 10.1128/spectrum.01166-23] [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: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism. IMPORTANCE Influenza A virus (IAV) can infect tissues both within and beyond the respiratory tract, leading to extrapulmonary complications, such as conjunctivitis or gastrointestinal disease. Selective pressures governing virus replication and induction of host responses can vary based on the anatomical site of infection, yet studies examining within-host assessments of genetic diversity are typically only conducted in cells derived from the respiratory tract. We examined the contribution of influenza virus tropism on these properties two different ways: by using IAV associated with different tropisms in humans, and by infecting human cell types from two different organ systems susceptible to IAV infection. Despite the diversity of cell types and viruses employed, we observed generally similar measures of viral diversity postinfection across all conditions tested; these findings nonetheless contribute to a greater understanding of the role tissue type contributes to the dynamics of virus evolution within a human host.
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Affiliation(s)
- Troy J. Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ian A. York
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claudia Pappas
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taronna R. Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica A. Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Varian CP, Saldaña A, Calzada JE, Abad‐Franch F, Kieran TJ, Padukone A, Peterson JK, Gottdenker NL. Food web structure and microenvironment affect Chagas disease vector infection and abundance in a rural landscape. Ecosphere 2023. [DOI: 10.1002/ecs2.4347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Christina P. Varian
- Department of Veterinary Pathology College of Veterinary Medicine, University of Georgia Athens Georgia USA
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES) Panama City Panama
- Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Faculty of Medicine University of Panamá Panama City Panama
| | - Jose E. Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES) Panama City Panama
| | - Fernando Abad‐Franch
- Grupo Triatomíneos Instituto René Rachou, Fundação Oswaldo Cruz – Fiocruz Belo Horizonte Minas Gerais Brazil
- Núcleo de Medicina Tropical, Faculdade de Medicina Universidade de Brasília Brasília Distrito Federal Brazil
| | - Troy J. Kieran
- Department of Environmental Health Science College of Public Health, University of Georgia Athens Georgia USA
| | - Anchal Padukone
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee USA
| | | | - Nicole L. Gottdenker
- Department of Veterinary Pathology College of Veterinary Medicine, University of Georgia Athens Georgia USA
- Center for the Ecology of Infectious Diseases, University of Georgia Athens Georgia USA
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Durso AM, Kieran TJ, Glenn TC, Mullin SJ. Comparison of Three Methods for Measuring Dietary Composition of Plains Hog-nosed Snakes. HERPETOLOGICA 2022. [DOI: 10.1655/herpetologica-d-21-00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Andrew M. Durso
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Stephen J. Mullin
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
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Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
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Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
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10
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Beaudry MS, Wang J, Kieran TJ, Thomas J, Bayona-Vásquez NJ, Gao B, Devault A, Brunelle B, Lu K, Wang JS, Rhodes OE, Glenn TC. Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment. Front Microbiol 2021; 12:644662. [PMID: 33986735 PMCID: PMC8110821 DOI: 10.3389/fmicb.2021.644662] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 12/21/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.
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Affiliation(s)
- Megan S. Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jincheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jesse Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | | | | | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jia-Sheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
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11
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Calderón JM, Erazo D, Kieran TJ, Gottdenker NL, León C, Cordovez J, Guhl F, Glenn TC, González C. How microclimatic variables and blood meal sources influence Rhodnius prolixus abundance and Trypanosoma cruzi infection in Attalea butyracea and Elaeis guineensis palms? Acta Trop 2020; 212:105674. [PMID: 32827453 DOI: 10.1016/j.actatropica.2020.105674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
Chagas disease is a zoonosis that affects several million people and is caused by the parasite Trypanosoma cruzi, which is mainly transmitted through the feces of triatomine bugs. Within triatomines, several Rhodnius species have been found inhabiting palms, and certain factors such as palm species and location have been related to the abundance and T. cruzi infection of those insects in palms. In this study, the main goal was to determine if R. prolixus abundances and infection rates in Attalea butyracea and Elaeis guineensis palms are related to ecological factors such as palm species, crown microclimate, and available blood meal sources. Triatomine sampling was performed in two municipalities of Casanare, Colombia, specifically in the intersection of riparian forests and oil palm plantations. For R. prolixus abundance per palm, the predictors showing more relationship were palm species and blood meal species identified in the palm, and for T. cruzi infection per triatomine, they were palm species and nymphal stage. Palm microclimate was very similar in both palm species and did not show a relationship with triatomine abundance. Comparing palm species, A. butyracea showed more blood meal species, including more refractory host species, than E. guineensis, but lower T. cruzi infection rate and parasitaemia. Interestingly, non-arboreal blood meal species were frequently found in the analyzed nymphs, indicating that the blood source for R. prolixus in palms corresponded to all the fauna located in the surrounded landscape and not only in the palm. These results could expose a new ecological scenario to interpret the T. cruzi transmission in sylvatic environments.
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Affiliation(s)
- Johan M Calderón
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C. 111711, Colombia.
| | - Diana Erazo
- Grupo de Investigación en Biología Matemática y Computacional (BIOMAC), Departamento de Ingeniería Biomédica, Universidad de Los Andes, Bogotá D.C. 111711, Colombia
| | - Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602, USA
| | - Nicole L Gottdenker
- Department of Veterinary Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
| | - Cielo León
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C. 111711, Colombia
| | - Juan Cordovez
- Grupo de Investigación en Biología Matemática y Computacional (BIOMAC), Departamento de Ingeniería Biomédica, Universidad de Los Andes, Bogotá D.C. 111711, Colombia
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C. 111711, Colombia
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602, USA
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C. 111711, Colombia
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12
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Kieran TJ. Ultraconserved element bait set for trypanosomatida target enrichment and phylogenetics. Exp Parasitol 2020; 219:108015. [PMID: 33031787 DOI: 10.1016/j.exppara.2020.108015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Lack of knowledge of taxonomic biodiversity and reliable genetic markers in Trypanosomatidae limit our understanding of their phylogenetic relationships. Ultraconserved elements (UCEs) have improved phylogenetic analyses and inferences in many vertebrate and invertebrate taxa. However, it is unknown whether protozoans have these markers, their abundance, and if these could be reliably used for phylogenetics. In this study I design a target enrichment bait set for UCE loci for this group. In silico testing showed good loci recovery rates across 63 taxa and produced consistent, highly supported phylogenetic trees. This bait set adds a new resource of useful genetic markers for Trypanosomatidae phylogenetics.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, 206 Environmental Health Science Building, Athens, GA, 30602, USA.
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13
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Aguilera-Uribe M, Meza-Lázaro RN, Kieran TJ, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Phylogeny of the North-Central American clade of blood-sucking reduviid bugs of the tribe Triatomini (Hemiptera: Triatominae) based on the mitochondrial genome. Infection, Genetics and Evolution 2020; 84:104373. [DOI: 10.1016/j.meegid.2020.104373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022]
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14
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Kieran TJ, Goodman SJ, Finger JW, Thomas JC, Hamilton MT, Tuberville TD, Glenn TC. Microbiota of Four Tissue Types in American Alligators (Alligator mississippiensis) Following Extended Dietary Selenomethionine Exposure. Bull Environ Contam Toxicol 2020; 105:381-386. [PMID: 32794125 DOI: 10.1007/s00128-020-02961-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Selenium represents an essential trace nutrient that is necessary for biological functions. Deficiencies can induce disease, but excess can induce toxicity. Selenium deficiency is a major concern in underdeveloped countries, while also posing as a toxic pollutant in waterways surrounding landfills, agricultural areas, and fossil fuel production sites. We examined the microbiome of selenomethionine (SeMet) fed American alligators (Alligator mississippiensis) at the beginning and end of a 7-week exposure experiment. Alligators were randomly divided into three groups: control and 1000 or 2000 ppm SeMet. DNA from before exposure (oral and cloaca swabs) and post-exposure (oral, cloaca, small & large intestines) sampling were extracted and amplified for bacterial 16 s rRNA. While treatment did not seem to have much effect, we observed a predominance of Fusobacteriaceae and Porpyromonodaceae across all tissue types. Cetobacterium and Clostridium are the most abundant genera as potential indicators of the aquatic and carrion feeding lifestyle of alligators.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Samantha J Goodman
- Department of Poultry Science, University of Georgia, 30602, Athens, GA, USA
- College of Veterinary Medicine & Biomedical Sciences, Toxicology Program, Texas A&M University, College Station, TX, 77843, USA
| | - John W Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, 29802, Aiken, SC, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Matthew T Hamilton
- Savannah River Ecology Laboratory, University of Georgia, 29802, Aiken, SC, USA
- Department of Forestry and Natural Resources, West Lafayette, IN, 47907, USA
| | - Tracey D Tuberville
- Savannah River Ecology Laboratory, University of Georgia, 29802, Aiken, SC, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.
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15
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Thomas JC, Oladeinde A, Kieran TJ, Finger JW, Bayona‐Vásquez NJ, Cartee JC, Beasley JC, Seaman JC, McArthur JV, Rhodes OE, Glenn TC. Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site. Microb Biotechnol 2020; 13:1179-1200. [PMID: 32363769 PMCID: PMC7264878 DOI: 10.1111/1751-7915.13578] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/20/2023] Open
Abstract
Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.
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Affiliation(s)
- Jesse C. Thomas
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research UnitUnited States Department of AgricultureAthensGA30605USA
| | - Troy J. Kieran
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
| | - John W. Finger
- Department of Biological SciencesAuburn UniversityAuburnAL36849USA
| | - Natalia J. Bayona‐Vásquez
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
- Institute of BioinformaticsUniversity of GeorgiaAthensGA30602USA
| | - John C. Cartee
- Division of STD PreventionCenters for Disease Control and PreventionAtlantaGA30329USA
| | - James C. Beasley
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
- Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGA30602USA
| | - John C. Seaman
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
| | - J Vuan McArthur
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
| | - Olin E. Rhodes
- Savannah River Ecology LaboratoryUniversity of GeorgiaPO Drawer EAikenSC29802USA
- Odum School of EcologyUniversity of GeorgiaAthensGA30602USA
| | - Travis C. Glenn
- Department of Environmental Health ScienceUniversity of GeorgiaAthensGA30602USA
- Institute of BioinformaticsUniversity of GeorgiaAthensGA30602USA
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16
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Ghosh A, Platt RN, Vandewege MW, Tabassum R, Hsu CY, Isberg SR, Peterson DG, Finger JW, Kieran TJ, Glenn TC, Gongora J, Ray DA. Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus. Anal Biochem 2020; 602:113781. [PMID: 32485163 DOI: 10.1016/j.ab.2020.113781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with >78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
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Affiliation(s)
- Arnab Ghosh
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Roy N Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA; Department of Biology, Eastern New Mexico University, Portales, NM, USA
| | | | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA
| | - Sally R Isberg
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia; The Centre for Crocodile Research, Darwin, NT, Australia
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA
| | - John W Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
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17
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Kieran TJ. Mitochondrial, metagenomic, and phylogenetic analysis of the ground beetle Harpalus pensylvanicus (Coleoptera: Carabidae). Gene 2020; 740:144540. [PMID: 32165294 DOI: 10.1016/j.gene.2020.144540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/08/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
Abstract
Harpalus pensylvanicus (Coloptera: Carabidae) is a weed seed predator common throughout the United States. While Carabidae is a very large group of beetles, limited genomic resources exist, especially mitochondrial genomes. This study expands research in this area by assembling and annotating the complete mitochondrial genome of H. pensylvanicus and performs phylogenetic analyses with closely related species. Further use of the metagenomic data was made to characterize microbial taxa and clusters of orthologous groups of proteins. The complete mitochondrial genome is 16,434 bp in length, AT rich, and consist of 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. Phylogenetic analyses were congruent with the Harpalinae and Pterostichinae clade together. Microbial classification shows a predominance of Gamma- (37.77%) and Alpha-proteobacteria (33.97%).
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.
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18
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Kieran TJ, Bayona-Vásquez NJ, Varian CP, Saldaña A, Samudio F, Calzada JE, Gottdenker NL, Glenn TC. Population genetics of two chromatic morphs of the Chagas disease vector Rhodnius pallescens Barber, 1932 in Panamá. Infect Genet Evol 2020; 84:104369. [PMID: 32442632 DOI: 10.1016/j.meegid.2020.104369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022]
Abstract
Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequencing methods such as RADseq and complete mitochondrial DNA (mtDNA) genome sequencing have great potential for examining vector biology across space and time. Here we utilize a RADseq method (3RAD), along with complete mtDNA sequencing, to examine the population structure of the two chromatic morpho types of R. pallescens in Panama. We sequenced 105 R. pallescens samples from five localities in Panama. We generated a 2216 SNP dataset and 6 complete mtDNA genomes. RADseq showed significant differentiation among the five localities (FCT = 0.695; P = .004), but most of this was between localities with the dark vs. light chromatic morphs (Veraguas vs. Panama Oeste). The mtDNA genomes showed a 97-98% similarity between dark and light chromatic morphs across all genes and a 502 bp insert in light morphs. Thus, both the RADseq and mtDNA data showed highly differentiated clades with essentially no gene flow between the dark and light chromatic morphs from Veraguas and central Panama respectively. We discuss the growing evidence showing clear distinctions between these two morpho types with the possibility that these are separate species, an area of research that requires further investigation. Finally, we discuss the cost-effectiveness of 3RAD which is a third of the cost compared to other RADseq methods used recently in Chagas disease vector research.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA
| | - Christina P Varian
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama; Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Facultad de Medicina, Universidad de Panamá, Panama
| | - Franklyn Samudio
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Nicole L Gottdenker
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA; Odum School of Ecology, The University of Georgia, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA.
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19
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Lourenco JM, Kieran TJ, Seidel DS, Glenn TC, da Silveira MF, Callaway TR, Stewart RL. Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate. PLoS One 2020; 15:e0231533. [PMID: 32282837 PMCID: PMC7153887 DOI: 10.1371/journal.pone.0231533] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 08/18/2019] [Accepted: 03/25/2020] [Indexed: 01/02/2023] Open
Abstract
Most of the research efforts involving the bovine gastrointestinal microbiota have focused on cattle’s forestomach, particularly the rumen, so information concerning the bovine fecal microbiota is more scarce, especially in young beef cattle. The present study was performed to evaluate the ruminal and fecal microbiotas of beef calves as they reached the end of their nursing phase. A total of 18 Angus cow/calf pairs were selected and assigned to one of two treatment groups for the last 92 days of the calves’ nursing period, as follows: 1) calves were supplemented with concentrate in a creep feeding system; or 2) control group with no supplementation of calves. After 92 days, ruminal and fecal samples were individually obtained from calves in both groups, and their microbiotas were evaluated using 16S rRNA gene sequencing. Ruminal samples were predominated by Prevotella (18 to 23% of the total bacterial abundance), regardless if calves received supplementation or not; however, in the feces, Prevotella was only the seventh most abundant genus (0.6 to 2.1% of total bacterial abundance). Both the rumen (P = 0.01) and the feces (P = 0.05) of calves that received supplementation had greater abundance of Firmicutes. In addition, calves that were supplemented had lower abundance of Fibrobacteres (P = 0.03) in their rumens. Regardless if the calves were supplemented or not, Faith’s Phylogenetic Diversity index (P ≤ 0.007) and total concentration of short chain fatty acids (P < 0.001) were both greater in the rumen than in the feces of calves. In summary, the ruminal and fecal microbiotas of weanling beef calves were considerably distinct. Additionally, supplementation with creep feed caused some significant changes in the composition of the gastrointestinal microbiota of the calves, especially in the rumen, where supplementation caused an increase in Firmicutes and a decrease in abundance of Fibrobacteres.
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Affiliation(s)
- Jeferson M. Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Darren S. Seidel
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | | | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
| | - R. Lawton Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
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20
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Ibarra Caballero JR, Ata JP, Leddy KA, Glenn TC, Kieran TJ, Klopfenstein NB, Kim MS, Stewart JE. Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates. Fungal Biol 2020; 124:144-154. [PMID: 32008755 DOI: 10.1016/j.funbio.2019.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
Abstract
Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, and Salix) substrates. The assembled genome was 33.92 Mbp with 2954 contigs and 9389 predicted genes. Only small differences were observed in size and gene content in comparison with two other P. noxius genome assemblies (isolates OVT-YTM/97 from Hong Kong, China and FFPRI411160 from Japan, respectively). Genome analysis of P. noxius isolate P919-02W.7 revealed 488 genes encoding proteins related to carbohydrate and lignin metabolism, many of these enzymes are associated with degradation of plant cell wall components. Most of the transcripts expressed by P. noxius isolate P919-02W.7 were similar regardless of wood substrates. This study highlights the vast suite of decomposing enzymes produced by P. noxius, which suggests potential for degrading diverse wood substrates, even from temperate host trees. This information contributes to our understanding of pathogen ecology, mechanisms of wood decomposition, and pathogenic/saprophytic lifestyle.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jessa P Ata
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA; Department of Forest Biological Sciences, University of the Philippines Los Baños, Laguna 4031, Philippines
| | - K A Leddy
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA.
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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21
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Wamucho A, Unrine JM, Kieran TJ, Glenn TC, Schultz CL, Farman M, Svendsen C, Spurgeon DJ, Tsyusko OV. Genomic mutations after multigenerational exposure of Caenorhabditis elegans to pristine and sulfidized silver nanoparticles. Environ Pollut 2019; 254:113078. [PMID: 31479814 DOI: 10.1016/j.envpol.2019.113078] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/31/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
Our previous study showed heritable reproductive toxicity in the nematode Caenorhabditis elegans after multigenerational exposure to AgNO3 and silver nanoparticles (Ag-NPs). The aim of this study was to determine whether such inheritable effects are correlated with induced germline mutations in C. elegans. Individual C. elegans lineages were exposed for 10 generations to equitoxic concentrations at EC30 of AgNO3, Ag-NPs, and sulfidized Ag-NPs (sAg-NPs), a predominant environmentally transformed product of pristine Ag-NPs. The mutations were detected via whole genome DNA sequencing approach by comparing F0 and F10 generations. An increase in the total number of variants, though not statistically significant, was observed for all Ag treatments and the variants were mainly contributed by single nucleotide polymorphisms (SNPs). This potentially contributed towards reproductive as well as growth toxicity shown previously after ten generations of exposure in every Ag treatment. However, despite Ag-NPs and AgNO3 inducing stronger reproductive toxicity than sAg-NPs, exposure to sAg-NPs resulted in higher mutation accumulation with significant increase in the number of transversions. Thus our results suggest that other mechanisms of inheritance, such as epigenetics, may be at play in Ag-NP- and AgNO3-induced multigenerational and transgenerational reproductive toxicity.
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Affiliation(s)
- Anye Wamucho
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Department of Toxicology and Cancer Biology, University of Kentucky, 1095 V.A. Drive, 306 Health Science Research Building, Lexington, KY 40536, USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Department of Toxicology and Cancer Biology, University of Kentucky, 1095 V.A. Drive, 306 Health Science Research Building, Lexington, KY 40536, USA
| | - Troy J Kieran
- Department of Genetics, University of Georgia, 120 Green St., GA 30602-7223, USA
| | - Travis C Glenn
- Department of Genetics, University of Georgia, 120 Green St., GA 30602-7223, USA
| | - Carolin L Schultz
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh-Gifford, Wallingford, Oxon OX10 8BB, UK; Department of Materials, Oxford University, Begbroke Science Park, Begbroke Hill, Yarnton, Oxford OX5 1PF, UK
| | - Mark Farman
- Department of Plant Pathology, 225 Plant Science Building, Lexington, KY 40546, USA
| | - Claus Svendsen
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh-Gifford, Wallingford, Oxon OX10 8BB, UK
| | - David J Spurgeon
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh-Gifford, Wallingford, Oxon OX10 8BB, UK
| | - Olga V Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Department of Toxicology and Cancer Biology, University of Kentucky, 1095 V.A. Drive, 306 Health Science Research Building, Lexington, KY 40536, USA.
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22
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Kieran TJ, Arnold KMH, Thomas JC, Varian CP, Saldaña A, Calzada JE, Glenn TC, Gottdenker NL. Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens. Parasit Vectors 2019; 12:504. [PMID: 31665056 PMCID: PMC6821009 DOI: 10.1186/s13071-019-3761-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/04/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022] Open
Abstract
Background Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. Methods We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. Results We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48–72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. Conclusions We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.
| | - Kaylee M H Arnold
- Odum School of Ecology, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA
| | - Christina P Varian
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Department of Veterinary Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Nicole L Gottdenker
- Odum School of Ecology, University of Georgia, Athens, GA, USA. .,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA. .,Department of Veterinary Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
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23
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Glenn TC, Nilsen RA, Kieran TJ, Sanders JG, Bayona-Vásquez NJ, Finger JW, Pierson TW, Bentley KE, Hoffberg SL, Louha S, Garcia-De Leon FJ, del Rio Portilla MA, Reed KD, Anderson JL, Meece JK, Aggrey SE, Rekaya R, Alabady M, Belanger M, Winker K, Faircloth BC. Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ 2019; 7:e7755. [PMID: 31616586 PMCID: PMC6791352 DOI: 10.7717/peerj.7755] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [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: 05/12/2019] [Accepted: 08/26/2019] [Indexed: 01/02/2023] Open
Abstract
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in (i.e., getting the smallest possible amount of data from a run); and (3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: (1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and (2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Roger A. Nilsen
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Small Animal Medicine, College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Jon G. Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, United States of America
- Current affiliation: Cornell Institute for Host—Microbe Interaction and Disease, Cornell University, Ithaca, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Francisco J. Garcia-De Leon
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional, La Paz, Mexico
| | | | - Kurt D. Reed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jennifer L. Anderson
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, United States of America
| | - Jennifer K. Meece
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, United States of America
| | - Samuel E. Aggrey
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Poultry Science, University of Georgia, Athens, GA, United States of America
| | - Romdhane Rekaya
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
| | - Magdy Alabady
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - Myriam Belanger
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, AK, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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24
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Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 2019; 7:e7724. [PMID: 31616583 PMCID: PMC6791345 DOI: 10.7717/peerj.7724] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 11/24/2022] Open
Abstract
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
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Affiliation(s)
- Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Peter A. Scott
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Nicholas Troendle
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Natural, Health, and Mathematical Sciences, MidAmerica Nazarene University, Olathe, KS, United States of America
| | - Pindaro Diaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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25
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Glenn TC, Pierson TW, Bayona-Vásquez NJ, Kieran TJ, Hoffberg SL, Thomas IV JC, Lefever DE, Finger JW, Gao B, Bian X, Louha S, Kolli RT, Bentley KE, Rushmore J, Wong K, Shaw TI, Rothrock Jr MJ, McKee AM, Guo TL, Mauricio R, Molina M, Cummings BS, Lash LH, Lu K, Gilbert GS, Hubbell SP, Faircloth BC. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ 2019; 7:e7786. [PMID: 31616589 PMCID: PMC6791344 DOI: 10.7717/peerj.7786] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 12/26/2022] Open
Abstract
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Jesse C. Thomas IV
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Daniel E. Lefever
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
- Current affiliation: Integrative Systems Biology and Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Medicine, University of California, San Diego, CA, United States of America
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Ramya T. Kolli
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - Julie Rushmore
- School of Ecology & College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Kelvin Wong
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: California Water Service, 1720 N First St, San Jose, CA, United States of America
| | - Timothy I. Shaw
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: Department of Computational Biology, St. Jude Childrens Research Hospital, Memphis, TN, United States of America
| | | | - Anna M. McKee
- South Atlantic Water Science Center, U.S. Geological Survey, Norcross, GA, United States of America
| | - Tai L. Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Marirosa Molina
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC, United States of America
| | - Brian S. Cummings
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
| | - Lawrence H. Lash
- Department of Pharmacology, Wayne State University, Detroit, MI, United States of America
| | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, United States of America
| | - Gregory S. Gilbert
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Stephen P. Hubbell
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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Lourenco JM, Callaway TR, Kieran TJ, Glenn TC, McCann JC, Stewart RL. Analysis of the Rumen Microbiota of Beef Calves Supplemented During the Suckling Phase. Front Microbiol 2019; 10:1131. [PMID: 31191476 PMCID: PMC6547912 DOI: 10.3389/fmicb.2019.01131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/28/2018] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
A study was conducted to examine the effects of supplementing beef calves during their suckling phase (popularly known as creep feeding) with supplements that contained or did not contain the enzyme xylanase. Forty-two cow-calf pairs were divided into three groups and assigned to one of three treatments for a period of 105 days, as follows: (1) No supplemental feed for calves (control; CON); (2) Corn and soybean meal-based supplement feed for calves (positive control; PCON); and (3) Same feed regimen as PCON with xylanase added to the supplement (enzyme; ENZ). After 105 days, out of the 42 calves participating in the study, 25 male calves were randomly selected (8 from CON, 9 from PCON, and 8 from ENZ) and samples of their forestomach were collected by esophageal tubing. Immediately after this procedure, all calves were weaned, commingled, and placed in a common post-weaning diet for 4 weeks. At the end of this period, ruminal fluid was once again collected from the same 25 calves. All samples were subjected to DNA extraction and 16S rRNA gene sequencing. At weaning, most of the alpha diversity indexes were greater in CON; however, no differences (P ≥ 0.23) in alpha diversity were observed in samples collected 4 weeks after weaning. Regardless of treatment, 2 phyla - Bacteroidetes and Firmicutes - comprised approximately 80% of the total bacterial abundance of samples collected on both days. At the genus level, an effect of diet (P = 0.02) was observed for Prevotella in the samples collected at weaning; however, no differences were detected in the samples collected 4 weeks after weaning. Calf average daily gain (ADG) during the 105-day creep feeding trial tended (P = 0.09) to be greater in the groups that received supplementation, with the greatest numerical value observed in ENZ. Moreover, there was a positive correlation (ρ = 0.43; P = 0.03) between ADG and abundance of Prevotella, indicating the importance of this bacterial group for ruminants. In summary, most of the significant differences found in this study were detected at weaning, and the majority of them disappeared 4 weeks after the calves were weaned and commingled.
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Affiliation(s)
- Jeferson M. Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Joshua C. McCann
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - R. Lawton Stewart
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
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27
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Erazo D, Gottdenker NL, González C, Guhl F, Cuellar M, Kieran TJ, Glenn TC, Umaña JD, Cordovez J. Generalist host species drive Trypanosoma cruzi vector infection in oil palm plantations in the Orinoco region, Colombia. Parasit Vectors 2019; 12:274. [PMID: 31138275 PMCID: PMC6540391 DOI: 10.1186/s13071-019-3519-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/20/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Oil palm plantation establishment in Colombia has the potential to impact Chagas disease transmission by increasing the distribution range of Rhodnius prolixus. In fact, previous studies have reported Trypanosoma cruzi natural infection in R. prolixus captured in oil palms (Elaeis guineensis) in the Orinoco region, Colombia. The aim of this study is to understand T. cruzi infection in vectors in oil palm plantations relative to community composition and host dietary specialization by analyzing vector blood meals and comparing these results to vectors captured in a native palm tree species, Attalea butyracea. METHODS Rhodnius prolixus nymphs (n = 316) were collected from A. butyracea and E. guineensis palms in Tauramena, Casanare, Colombia. Vector blood meals from these nymphs were determined by amplifying and sequencing a vertebrate-specific 12S rRNA gene fragment. RESULTS Eighteen vertebrate species were identified and pigs (Sus scrofa) made up the highest proportion of blood meals in both habitats, followed by house mouse (Mus musculus) and opossum (Didelphis marsupialis). Individual bugs feeding only from generalist mammal species had the highest predicted vector infection rate, suggesting that generalist mammalian species are more competent hosts for T. cruzi infection . CONCLUSIONS Oil palm plantations and A. butyracea palms found in altered areas provide a similar quality habitat for R. prolixus populations in terms of blood meal availability. Both habitats showed similarities in vector infection rate and potential host species, representing a single T. cruzi transmission scenario at the introduced oil palm plantation and native Attalea palm interface.
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Affiliation(s)
- Diana Erazo
- Grupo de Investigación en Biología Matemática y Computacional (BIOMAC), Universidad de los Andes, Bogota, Colombia
| | - Nicole L. Gottdenker
- Department of Pathology, School of Veterinary Medicine, The University of Georgia, Athens, GA USA
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Monica Cuellar
- Grupo de Investigación en Ingeniería Biomédica (GIB), Universidad de los Andes, Bogota, Colombia
| | - Troy J. Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA USA
| | - Travis C. Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA USA
| | - Juan D. Umaña
- Grupo de Investigación en Biología Matemática y Computacional (BIOMAC), Universidad de los Andes, Bogota, Colombia
| | - Juan Cordovez
- Grupo de Investigación en Biología Matemática y Computacional (BIOMAC), Universidad de los Andes, Bogota, Colombia
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Kieran TJ, Gordon ER, Forthman M, Hoey-Chamberlain R, Kimball RT, Faircloth BC, Weirauch C, Glenn TC. Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources. Mol Phylogenet Evol 2019; 130:297-303. [DOI: 10.1016/j.ympev.2018.10.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/12/2018] [Accepted: 10/20/2018] [Indexed: 02/05/2023]
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29
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Warren WC, Kuderna L, Alexander A, Catchen J, Pérez-Silva JG, López-Otín C, Quesada V, Minx P, Tomlinson C, Montague MJ, Farias FHG, Walter RB, Marques-Bonet T, Glenn T, Kieran TJ, Wise SS, Wise JP, Waterhouse RM, Wise JP. The Novel Evolution of the Sperm Whale Genome. Genome Biol Evol 2018; 9:3260-3264. [PMID: 28985367 PMCID: PMC5726484 DOI: 10.1093/gbe/evx187] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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] [Accepted: 09/12/2017] [Indexed: 01/21/2023] Open
Abstract
The sperm whale, made famous by Moby Dick, is one of the most fascinating of all ocean-dwelling species given their unique life history, novel physiological adaptations to hunting squid at extreme ocean depths, and their position as one of the earliest branching toothed whales (Odontoceti). We assembled the sperm whale (Physeter macrocephalus) genome and resequenced individuals from multiple ocean basins to identify new candidate genes for adaptation to an aquatic environment and infer demographic history. Genes crucial for skin integrity appeared to be particularly important in both the sperm whale and other cetaceans. We also find sperm whales experienced a steep population decline during the early Pleistocene epoch. These genomic data add new comparative insight into the evolution of whales.
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Affiliation(s)
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana
| | - José G Pérez-Silva
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Spain
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Spain
| | - Patrick Minx
- McDonnell Genome Institute, Washington University, St Louis
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St Louis
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania
| | | | - Ronald B Walter
- Department of Chemistry and Biochemistry, Texas State University
| | | | - Travis Glenn
- Department of Environmental Health Science, University of Georgia, Environmental Health Science Bldg, Athens, Georgia
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Environmental Health Science Bldg, Athens, Georgia
| | - Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, School of Medicine, University of Louisville
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, School of Medicine, University of Louisville
| | | | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, School of Medicine, University of Louisville
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Lourenço JM, Kieran TJ, McCann JC, Glenn TC, Stewart L. 45 Analysis of the Gastrointestinal Tract-Associated Microbiome of Calves Supplemented during the Suckling Phase. J Anim Sci 2018. [DOI: 10.1093/jas/sky027.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J M Lourenço
- Dept. of Animal and Dairy Science, University of Georgia, Athens, GA
| | - T J Kieran
- Univ. of GA Environmental Health Science, Athens, GA
| | | | - T C Glenn
- Univ. of GA Environmental Health Science, Athens, GA
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31
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Platt RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE, Baker RJ, Stevens RD, Ray DA. Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats. Syst Biol 2018; 67:236-249. [PMID: 28945862 PMCID: PMC5837689 DOI: 10.1093/sysbio/syx070] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 01/05/2023] Open
Abstract
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Science Building, Baton Rouge, LA, USA
| | - Kevin A M Sullivan
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Thomas E Lee
- Department of Biology, Abilene Christian University, 1600 Campus Ct. Abilene, TX, USA
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Richard D Stevens
- Natural Resource Management, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
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32
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Kieran TJ, Gottdenker NL, Varian CP, Saldaña A, Means N, Owens D, Calzada JE, Glenn TC. Blood Meal Source Characterization Using Illumina Sequencing in the Chagas Disease Vector Rhodnius pallescens (Hemiptera: Reduviidae) in Panamá. J Med Entomol 2017; 54:1786-1789. [PMID: 29029145 DOI: 10.1093/jme/tjx170] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Accurate blood meal identification is critical to understand hematophagous vector-host relationships. This study describes a customizable Next-Generation Sequencing (NGS) approach to identify blood meals from Rhodnius pallescens (Hemiptera: Reduviidae) triatomines using multiple barcoded primers and existing software to pick operational taxonomic units and match sequences for blood meal identification. We precisely identified all positive control samples using this method and further examined 74 wild-caught R. pallescens samples. With this novel blood meal identification method, we detected 13 vertebrate species in the blood meals, as well as single and multiple blood meals in individual bugs. Our results demonstrate the reliability and descriptive uses of our method.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA
| | - Nicole L Gottdenker
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA
| | - Christina P Varian
- Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA
| | - Azael Saldaña
- Department of Parasitology, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panamá
| | - Nicolas Means
- University of Oklahoma Health Sciences Center, University of Oklahoma, Oklahoma City, OK
| | - Darlisha Owens
- Department of Biology, Grambling State University, Grambling, LA
| | - Jose E Calzada
- Department of Parasitology, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panamá
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA
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33
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Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC. RAD
cap: sequence capture of dual‐digest
RAD
seq libraries with identifiable duplicates and reduced missing data. Mol Ecol Resour 2016; 16:1264-78. [DOI: 10.1111/1755-0998.12566] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Troy J. Kieran
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois Urbana IL 61801 USA
| | | | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Rodney Mauricio
- Department of Genetics University of Georgia Athens GA 30602 USA
| | - Travis C. Glenn
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
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