Veterinary Biosciences - Research Publications

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    A communal catalogue reveals Earth's multiscale microbial diversity
    Thompson, LR ; Sanders, JG ; McDonald, D ; Amir, A ; Ladau, J ; Locey, KJ ; Prill, RJ ; Tripathi, A ; Gibbons, SM ; Ackermann, G ; Navas-Molina, JA ; Janssen, S ; Kopylova, E ; Vazquez-Baeza, Y ; Gonzalez, A ; Morton, JT ; Mirarab, S ; Xu, ZZ ; Jiang, L ; Haroon, MF ; Kanbar, J ; Zhu, Q ; Song, SJ ; Kosciolek, T ; Bokulich, NA ; Lefler, J ; Brislawn, CJ ; Humphrey, G ; Owens, SM ; Hampton-Marcell, J ; Berg-Lyons, D ; McKenzie, V ; Fierer, N ; Fuhrman, JA ; Clauset, A ; Stevens, RL ; Shade, A ; Pollard, KS ; Goodwin, KD ; Jansson, JK ; Gilbert, JA ; Knight, R ; Rivera, JLA ; Al-Moosawi, L ; Alverdy, J ; Amato, KR ; Andras, J ; Angenent, LT ; Antonopoulos, DA ; Apprill, A ; Armitage, D ; Ballantine, K ; Barta, J ; Baum, JK ; Berry, A ; Bhatnagar, A ; Bhatnagar, M ; Biddle, JF ; Bittner, L ; Boldgiv, B ; Bottos, E ; Boyer, DM ; Braun, J ; Brazelton, W ; Brearley, FQ ; Campbell, AH ; Caporaso, JG ; Cardona, C ; Carroll, J ; Cary, SC ; Casper, BB ; Charles, TC ; Chu, H ; Claar, DC ; Clark, RG ; Clayton, JB ; Clemente, JC ; Cochran, A ; Coleman, ML ; Collins, G ; Colwell, RR ; Contreras, M ; Crary, BB ; Creer, S ; Cristol, DA ; Crump, BC ; Cui, D ; Daly, SE ; Davalos, L ; Dawson, RD ; Defazio, J ; Delsuc, F ; Dionisi, HM ; Dominguez-Bello, MG ; Dowell, R ; Dubinsky, EA ; Dunn, PO ; Ercolini, D ; Espinoza, RE ; Ezenwa, V ; Fenner, N ; Findlay, HS ; Fleming, ID ; Fogliano, V ; Forsman, A ; Freeman, C ; Friedman, ES ; Galindo, G ; Garcia, L ; Alexandra Garcia-Amado, M ; Garshelis, D ; Gasser, RB ; Gerdts, G ; Gibson, MK ; Gifford, I ; Gill, RT ; Giray, T ; Gittel, A ; Golyshin, P ; Gong, D ; Grossart, H-P ; Guyton, K ; Haig, S-J ; Hale, V ; Hall, RS ; Hallam, SJ ; Handley, KM ; Hasan, NA ; Haydon, SR ; Hickman, JE ; Hidalgo, G ; Hofmockel, KS ; Hooker, J ; Hulth, S ; Hultman, J ; Hyde, E ; Ibanez-Alamo, JD ; Jastrow, JD ; Jex, AR ; Johnson, LS ; Johnston, ER ; Joseph, S ; Jurburg, SD ; Jurelevicius, D ; Karlsson, A ; Karlsson, R ; Kauppinen, S ; Kellogg, CTE ; Kennedy, SJ ; Kerkhof, LJ ; King, GM ; Kling, GW ; Koehler, AV ; Krezalek, M ; Kueneman, J ; Lamendella, R ; Landon, EM ; Lane-deGraaf, K ; LaRoche, J ; Larsen, P ; Laverock, B ; Lax, S ; Lentino, M ; Levin, II ; Liancourt, P ; Liang, W ; Linz, AM ; Lipson, DA ; Liu, Y ; Lladser, ME ; Lozada, M ; Spirito, CM ; MacCormack, WP ; MacRae-Crerar, A ; Magris, M ; Martin-Platero, AM ; Martin-Vivaldi, M ; Margarita Martinez, L ; Martinez-Bueno, M ; Marzinelli, EM ; Mason, OU ; Mayer, GD ; McDevitt-Irwin, JM ; McDonald, JE ; McGuire, KL ; McMahon, KD ; McMinds, R ; Medina, M ; Mendelson, JR ; Metcalf, JL ; Meyer, F ; Michelangeli, F ; Miller, K ; Mills, DA ; Minich, J ; Mocali, S ; Moitinho-Silva, L ; Moore, A ; Morgan-Kiss, RM ; Munroe, P ; Myrold, D ; Neufeld, JD ; Ni, Y ; Nicol, GW ; Nielsen, S ; Nissimov, JI ; Niu, K ; Nolan, MJ ; Noyce, K ; O'Brien, SL ; Okamoto, N ; Orlando, L ; Castellano, YO ; Osuolale, O ; Oswald, W ; Parnell, J ; Peralta-Sanchez, JM ; Petraitis, P ; Pfister, C ; Pilon-Smits, E ; Piombino, P ; Pointing, SB ; Pollock, FJ ; Potter, C ; Prithiviraj, B ; Quince, C ; Rani, A ; Ranjan, R ; Rao, S ; Rees, AP ; Richardson, M ; Riebesell, U ; Robinson, C ; Rockne, KJ ; Rodriguezl, SM ; Rohwer, F ; Roundstone, W ; Safran, RJ ; Sangwan, N ; Sanz, V ; Schrenk, M ; Schrenzel, MD ; Scott, NM ; Seger, RL ; Seguin-Orlando, A ; Seldin, L ; Seyler, LM ; Shakhsheer, B ; Sheets, GM ; Shen, C ; Shi, Y ; Shin, H ; Shogan, BD ; Shutler, D ; Siegel, J ; Simmons, S ; Sjoling, S ; Smith, DP ; Soler, JJ ; Sperling, M ; Steinberg, PD ; Stephens, B ; Stevens, MA ; Taghavi, S ; Tai, V ; Tait, K ; Tan, CL ; Tas, N ; Taylor, DL ; Thomas, T ; Timling, I ; Turner, BL ; Urich, T ; Ursell, LK ; van der Lelie, D ; Van Treuren, W ; van Zwieten, L ; Vargas-Robles, D ; Thurber, RV ; Vitaglione, P ; Walker, DA ; Walters, WA ; Wang, S ; Wang, T ; Weaver, T ; Webster, NS ; Wehrle, B ; Weisenhorn, P ; Weiss, S ; Werner, JJ ; West, K ; Whitehead, A ; Whitehead, SR ; Whittingham, LA ; Willerslev, E ; Williams, AE ; Wood, SA ; Woodhams, DC ; Yang, Y ; Zaneveld, J ; Zarraonaindia, I ; Zhang, Q ; Zhao, H (NATURE PORTFOLIO, 2017-11-23)
    Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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    Eukaryote-ConservedMethylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia
    Emery-Corbin, SJ ; Hamey, JJ ; Ansell, BRE ; Balan, B ; Tichkule, S ; Stroehlein, AJ ; Cooper, C ; McInerney, B ; Hediyeh-Zadeh, S ; Vuong, D ; Crombie, A ; Lacey, E ; Davis, MJ ; Wilkins, MR ; Bahlo, M ; Svard, SG ; Gasser, RB ; Jex, AR ; Russo, C (OXFORD UNIV PRESS, 2020-12-01)
    Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis-a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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    A Perspective on Cryptosporidium and Giardia, with an Emphasis on Bovines and Recent Epidemiological Findings
    Abeywardena, H ; Jex, AR ; Gasser, RB ; Rollinson, D ; Stothard, JR (ELSEVIER ACADEMIC PRESS INC, 2015-01-01)
    Cryptosporidium and Giardia are two common aetiological agents of infectious enteritis in humans and animals worldwide. These parasitic protists are usually transmitted by the faecal-oral route, following the ingestion of infective stages (oocysts or cysts). An essential component of the control of these parasitic infections, from a public health perspective, is an understanding of the sources and routes of transmission in different geographical regions. Bovines are considered potential sources of infection for humans, because species and genotypes of Cryptosporidium and Giardia infecting humans have also been isolated from cattle in molecular parasitological studies. However, species and genotypes of Cryptosporidium and Giardia of bovids, and the extent of zoonotic transmission in different geographical regions in the world, are still relatively poorly understood. The purpose of this article is to (1) provide a brief background on Cryptosporidium and Giardia, (2) review some key aspects of the molecular epidemiology of cryptosporidiosis and giardiasis in animals, with an emphasis on bovines, (3) summarize research of Cryptosporidium and Giardia from cattle and water buffaloes in parts of Australasia and Sri Lanka, considering public health aspects and (4) provide a perspective on future avenues of study. Recent studies reinforce that bovines harbour Cryptosporidium and Giardia that likely pose a human health risk and highlight the need for future investigations of the biology, population genetics and transmission dynamics of Cryptosporidium and Giardia in cattle, water buffaloes and other ruminants in different geographical regions, the fate and transport of infective stages following their release into the environment, as well as for improved strategies for the control and prevention of cryptosporidiosis and giardiasis, guided by molecular epidemiological studies.
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    The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
    Schwarz, EM ; Korhonen, PK ; Campbell, BE ; Young, ND ; Jex, AR ; Jabbar, A ; Hall, RS ; Mondal, A ; Howe, AC ; Pell, J ; Hofmann, A ; Boag, PR ; Zhu, X-Q ; Gregory, TR ; Loukas, A ; Williams, BA ; Antoshechkin, I ; Brown, CT ; Sternberg, PW ; Gasser, RB (BMC, 2013-01-01)
    BACKGROUND: The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites. RESULTS: The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules. CONCLUSIONS: The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.
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    Next-Generation Molecular-Diagnostic Tools for Gastrointestinal Nematodes of Livestock, with an Emphasis on Small Ruminants: A Turning Point?
    Roeber, F ; Jex, AR ; Gasser, RB ; Rollinson, D (ELSEVIER ACADEMIC PRESS INC, 2013-01-01)
    Parasitic nematodes of livestock have major economic impact worldwide. Despite the diseases caused by these nematodes, some advances towards the development of new therapeutic agents and attempts to develop effective vaccines against some of them, there has been limited progress in the development of practical diagnostic methods. The specific and sensitive diagnosis of parasitic nematode infections of livestock underpins effective disease control, which is now particularly important given the problems associated with anthelmintic resistance in parasite populations. Traditional diagnostic methods have major limitations, in terms of sensitivity and specificity. This chapter provides an account of the significance of parasitic nematodes (order Strongylida), reviews conventional diagnostic techniques that are presently used routinely and describes advances in polymerase chain reaction (PCR)-based methods for the specific diagnosis of nematode infections. A particular emphasis is placed on the recent development of a robotic PCR-based platform for high-throughput diagnosis, and its significance and implications for epidemiological investigations and for use in control programmes.
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    Proteomic Analysis of the Excretory-Secretory Products from Larval Stages of Ascaris suum Reveals High Abundance of Glycosyl Hydrolases
    Wang, T ; Van Steendam, K ; Dhaenens, M ; Vlaminck, J ; Deforce, D ; Jex, AR ; Gasser, RB ; Geldhof, P ; Sripa, B (PUBLIC LIBRARY SCIENCE, 2013-10-01)
    BACKGROUND: Ascaris lumbricoides and Ascaris suum are socioeconomically important and widespread parasites of humans and pigs, respectively. The excretory-secretory (ES) molecules produced and presented at the parasite-host interface during the different phases of tissue invasion and migration are likely to play critical roles in the induction and development of protective immune and other host responses. METHODOLOGY/PRINCIPAL FINDINGS: The aim of this study was to identify the ES proteins of the different larval stages (L3-egg, L3-lung and L4) by LC-MS/MS. In total, 106 different proteins were identified, 20 in L3-egg, 45 in L3-lung stage and 58 in L4. Although most of the proteins identified were stage-specific, 15 were identified in the ES products of at least two stages. Two proteins, i.e. a 14-3-3-like protein and a serpin-like protein, were present in the ES products from the three different larval stages investigated. Interestingly, a comparison of ES products from L4 with those of L3-egg and L3-lung showed an abundance of metabolic enzymes, particularly glycosyl hydrolases. Further study indicated that most of these glycolytic enzymes were transcriptionally upregulated from L4 onwards, with a peak in the adult stage, particularly in intestinal tissue. This was also confirmed by enzymatic assays, showing the highest glycosidase activity in protein extracts from adult worms gut. CONCLUSIONS/SIGNIFICANCE: The present proteomic analysis provides important information on the host-parasite interaction and the biology of the migratory stages of A. suum. In particular, the high transcriptional upregulation of glycosyl hydrolases from the L4 stage onwards reveals that the degradation of complex carbohydrates forms an essential part of the energy metabolism of this parasite once it establishes in the small intestine.
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    The mitochondrial genome of Protostrongylus rufescens - implications for population and systematic studies
    Jabbar, A ; Mohandas, N ; Jex, AR ; Gasser, RB (BMC, 2013-09-12)
    BACKGROUND: Protostrongylus rufescens is a metastrongyloid nematode of small ruminants, such as sheep and goats, causing protostrongylosis. In spite of its importance, the ecology and epidemiology of this parasite are not entirely understood. In addition, genetic data are scant for P. rufescens and related metastrongyloids. METHODS: The mt genome was amplified from a single adult worm of P. rufescens (from sheep) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of the mt genomes were concatenated and subjected to phylogenetic analysis using Bayesian inference. RESULTS: The circular mitochondrial genome was 13,619 bp in length and contained two ribosomal RNA, 12 protein-coding and 22 transfer RNA genes, consistent with nematodes of the order Strongylida for which mt genomes have been determined. Phylogenetic analysis of the concatenated amino acid sequence data for the 12 mt proteins showed that P. rufescens was closely related to Aelurostrongylus abstrusus, Angiostrongylus vasorum, Angiostrongylus cantonensis and Angiostrongylus costaricensis. CONCLUSIONS: The mt genome determined herein provides a source of markers for future investigations of P. rufescens. Molecular tools, employing such mt markers, are likely to find applicability in studies of the population biology of this parasite and the systematics of lungworms.
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    Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective
    Roeber, F ; Jex, AR ; Gasser, RB (BMC, 2013-05-27)
    Parasitic nematodes (roundworms) of small ruminants and other livestock have major economic impacts worldwide. Despite the impact of the diseases caused by these nematodes and the discovery of new therapeutic agents (anthelmintics), there has been relatively limited progress in the development of practical molecular tools to study the epidemiology of these nematodes. Specific diagnosis underpins parasite control, and the detection and monitoring of anthelmintic resistance in livestock parasites, presently a major concern around the world. The purpose of the present article is to provide a concise account of the biology and knowledge of the epidemiology of the gastrointestinal nematodes (order Strongylida), from an Australian perspective, and to emphasize the importance of utilizing advanced molecular tools for the specific diagnosis of nematode infections for refined investigations of parasite epidemiology and drug resistance detection in combination with conventional methods. It also gives a perspective on the possibility of harnessing genetic, genomic and bioinformatic technologies to better understand parasites and control parasitic diseases.
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    A Molecular Diagnostic Tool to Replace Larval Culture in Conventional Faecal Egg Count Reduction Testing in Sheep
    Roeber, F ; Larsen, JWA ; Anderson, N ; Campbell, AJD ; Anderson, GA ; Gasser, RB ; Jex, AR ; Diemert, DJ (PUBLIC LIBRARY SCIENCE, 2012-05-22)
    The accurate diagnosis of parasitic nematode infections in livestock (including sheep and goats) is central to their effective control and the detection of the anthelmintic resistance. Traditionally, the faecal egg count reduction test (FECRT), combined with the technique of larval culture (LC), has been used widely to assess drug-susceptibility/resistance in strongylid nematodes. However, this approach suffers from a lack of specificity, sensitivity and reliability, and is time-consuming and costly to conduct. Here, we critically assessed a specific PCR assay to support FECRT, in a well-controlled experiment on sheep with naturally acquired strongylid infections known to be resistant to benzimidazoles. We showed that the PCR results were in close agreement with those of total worm count (TWC), but not of LC. Importantly, albendazole resistance detected by PCR-coupled FECRT was unequivocally linked to Teladorsagia circumcincta and, to lesser extent, Trichostrongylus colubriformis, a result that was not achievable by LC. The key findings from this study demonstrate that our PCR-coupled FECRT approach has major merit for supporting anthelmintic resistance in nematode populations. The findings also show clearly that our PCR assay can be used as an alternative to LC, and is more time-efficient and less laborious, which has important practical implications for the effective management and control strongylid nematodes of sheep.
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    Assessment of the genetic relationship between Dictyocaulus species from Bos taurus and Cervus elaphus using complete mitochondrial genomic datasets
    Gasser, RB ; Jabbar, A ; Mohandas, N ; Hoglund, J ; Hall, RS ; Littlewood, DTJ ; Jex, AR (BMC, 2012-10-30)
    BACKGROUND: Dictyocaulus species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or "husk"). There has been ongoing controversy surrounding the validity of some Dictyocaulus species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt) genomes of Dictyocaulus viviparus (from Bos taurus) with Dictyocaulus sp. cf. eckerti from red deer (Cervus elaphus), used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies. METHODS: The mt genomes were amplified from single adult males of D. viviparus and Dictyocaulus sp. cf. eckerti (from red deer) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), also employing data for other strongylids for comparative purposes. RESULTS: The circular mt genomes were 13,310 bp (D. viviparus) and 13,296 bp (Dictyocaulus sp. cf. eckerti) in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between D. viviparus and Dictyocaulus sp. cf. eckerti, and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both D. viviparus and Dictyocaulus sp. cf. eckerti were closely related, and grouped to the exclusion of selected members of the superfamilies Metastrongyloidea, Trichostrongyloidea, Ancylostomatoidea and Strongyloidea. CONCLUSIONS: Consistent with previous findings for nuclear ribosomal DNA sequence data, the present analyses indicate that Dictyocaulus sp. cf. eckerti (red deer) and D. viviparus are separate species. Barcodes in the two mt genomes and proteomes should serve as markers for future studies of the population genetics and/or epidemiology of these and related species of Dictyocaulus.