Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk

Mycobacterium avium subsp. paratuberculosis causes Johne’s disease (JD) in cattle, sheep, goats, and other ruminant animals. JD presents as a chronic granulomatous intestinal infection with a worldwide distribution and imposes a significant economic toll on livestock industries (1). M. avium subsp. paratuberculosis has a complex cell wall structure containing mycolic acids and several lipids similar to those of other members of this genus, yet it is the most slowly growing member. This bacterium often requires 8 to 16 weeks before colonies are visible in culture, which is a major hurdle in diagnostics and therefore in the implementation of optimal JD control measures. Although a well-established domestic and wild animal pathogen, it has also been implicated as a causative agent in human Crohn’s disease (2), and even though this link is controversial (3), M. avium subsp. paratuberculosis isolates have been obtained from humans. For instance, M. avium subsp. paratuberculosis 4, the isolate whose sequence we report here, was originally isolated from the breast milk of a Crohn’s disease patient in 2000 (4)

Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk

Mycobacterium avium subsp. paratuberculosis causes Johne’s disease (JD) in cattle, sheep, goats, and other ruminant animals. JD presents as a chronic granulomatous intestinal infection with a worldwide distribution and imposes a significant economic toll on livestock industries (1). M. avium subsp. paratuberculosis has a complex cell wall structure containing mycolic acids and several lipids similar to those of other members of this genus, yet it is the most slowly growing member. This bacterium often requires 8 to 16 weeks before colonies are visible in culture, which is a major hurdle in diagnostics and therefore in the implementation of optimal JD control measures. Although a well-established domestic and wild animal pathogen, it has also been implicated as a causative agent in human Crohn’s disease (2), and even though this link is controversial (3), M. avium subsp. paratuberculosis isolates have been obtained from humans. For instance, M. avium subsp. paratuberculosis 4, the isolate whose sequence we report here, was originally isolated from the breast milk of a Crohn’s disease patient in 2000 (4)

Identification of Novel Seroreactive Antigens in Johne’s Disease Cattle by Using the Mycobacterium tuberculosis Protein Array

Johne’s disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis, is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between M. aviumsubsp. paratuberculosis and the human pathogen Mycobacterium tuberculosis, here, we applied a whole-proteome M. tuberculosis protein array to identify seroreactive and diagnostic M. avium subsp. paratuberculosis antigens. A genome-scale pairwise analysis of amino acid identity levels between orthologous proteins in M. avium subsp. paratuberculosis and M. tuberculosis showed an average of 62% identity, with more than half the orthologous proteins sharing 75% identity. Analysis of the M. tuberculosis protein array probed with sera from M. avium subsp. paratuberculosis- infected cattle showed antibody binding to 729 M. tuberculosis proteins, with 58% of them having 70% identity to M. avium subsp. paratuberculosis orthologs. The results showed that only 4 of the top 40 seroreactive M. tuberculosis antigens were orthologs of previously reported M. avium subsp. paratuberculosis antigens, revealing the existence of a large number of previously unrecognized candidate diagnostic antigens. Enzyme-linked immunosorbent assay (ELISA) testing of 20 M. avium subsp. paratuberculosis recombinant proteins, representing reactive and nonreactive M. tuberculosis orthologs, further confirmed that the M. tuberculosis array has utility as a screening tool for identifying candidate antigens for Johne’s disease diagnostics. Additional ELISA testing of field serum samples collected from dairy herds around the United States revealed that MAP2942c had the strongest seroreactivity with Johne’s disease-positive samples. Collectively, our studies have considerably expanded the number of candidate M. avium subsp. paratuberculosis proteins with potential utility in the next generation of rationally designed Johne’s disease diagnostic assays

The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

Large-scale association analyses identify host factors influencing human gut microbiome composition

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P <5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) <P <5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis

Complete Genome Sequence of Mycobacterium avium subsp. paratuberculosis, Isolated from Human Breast Milk

Mycobacterium avium subsp. paratuberculosis causes Johne’s disease (JD) in cattle, sheep, goats, and other ruminant animals. JD presents as a chronic granulomatous intestinal infection with a worldwide distribution and imposes a significant economic toll on livestock industries (1). M. avium subsp. paratuberculosis has a complex cell wall structure containing mycolic acids and several lipids similar to those of other members of this genus, yet it is the most slowly growing member. This bacterium often requires 8 to 16 weeks before colonies are visible in culture, which is a major hurdle in diagnostics and therefore in the implementation of optimal JD control measures. Although a well-established domestic and wild animal pathogen, it has also been implicated as a causative agent in human Crohn’s disease (2), and even though this link is controversial (3), M. avium subsp. paratuberculosis isolates have been obtained from humans. For instance, M. avium subsp. paratuberculosis 4, the isolate whose sequence we report here, was originally isolated from the breast milk of a Crohn’s disease patient in 2000 (4)

Complete Genome Sequence of SS52, a Strain of \u3ci\u3eEscherichia coli\u3c/i\u3e O157:H7 Recovered from Supershedder Cattle

Shiga toxin-producing Escherichia coli O157:H7 causes foodborne infections, and cattle are the primary reservoir. Some animals, known as supershedders, excrete orders of magnitude more E. coli O157:H7 in the feces than normal. Here, we report the complete genome sequence of the SS52 supershedder strain of E. coli O157:H7

Comparative Analysis of Super-Shedder Strains of \u3ci\u3eEscherichia coli\u3c/i\u3e O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells

Shiga toxin-producing Escherichia coli O157:H7 (O157) are significant foodborne pathogens and pose a serious threat to public health worldwide. The major reservoirs of O157 are asymptomatic cattle which harbor the organism in the terminal recto-anal junction (RAJ). Some colonized animals, referred to as “super-shedders” (SS), are known to shed O157 in exceptionally large numbers (\u3e104 CFU/g of feces). Recent studies suggest that SS cattle play a major role in the prevalence and transmission of O157, but little is known about the molecular mechanisms associated with super-shedding. Whole genome sequence analysis of an SS O157 strain (SS17) revealed a genome of 5,523,849 bp chromosome with 5,430 open reading frames and two plasmids, pO157 and pSS17, of 94,645 bp and 37,446 bp, respectively. Comparative analyses showed that SS17 is clustered with spinach-associated O157 outbreak strains, and belongs to the lineage I/II, clade 8, D group, and genotype 1, a subgroup of O157 with predicted hyper-virulence. A large number of non-synonymous SNPs and other polymorphisms were identified in SS17 as compared with other O157 strains (EC4115, EDL933, Sakai, TW14359), including in key adherence- and virulence-related loci. Phenotypic analyses revealed a distinctive and strongly adherent aggregative phenotype of SS17 on bovine RAJ stratified squamous epithelial (RSE) cells that was conserved amongst other SS isolates. Molecular genetic and functional analyses of defined mutants of SS17 suggested that the strongly adherent aggregative phenotype amongst SS isolates is LEE-independent, and likely results from a novel mechanism. Taken together, our study provides a rational framework for investigating the molecular mechanisms associated with SS, and strong evidence that SS O157 isolates have distinctive features and use a LEE-independent mechanism for hyper-adherence to bovine rectal epithelial cells