Search

Your search keyword '"Gillece, John D."' showing total 135 results
Start Over Author "Gillece, John D."
135 results on '"Gillece, John D."'

2. The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation.

Author

Costantini, Maria S., Videvall, Elin, Foster, Jeffrey T., Medeiros, Matthew C. I., Gillece, John D., Paxton, Eben H., Crampton, Lisa H., Mounce, Hanna L., Wang, Alex X., Fleischer, Robert C., Campana, Michael G., and Reed, Floyd A.

Subjects
ADAPTIVE radiation, GUT microbiome, GENETIC barcoding, MICROBIAL communities, PHYLOGENY
Abstract

The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

3. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Author

Martínez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura A., Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît J., Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric C., Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., and Wilmes, Paul

Published
2021
Full Text
View/download PDF

4. Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal

Author

Engelthaler, David M, Hicks, Nathan D, Gillece, John D, Roe, Chandler C, Schupp, James M, Driebe, Elizabeth M, Gilgado, Felix, Carriconde, Fabian, Trilles, Luciana, Firacative, Carolina, Ngamskulrungroj, Popchai, Castañeda, Elizabeth, dos Santos Lazera, Marcia, Melhem, Marcia SC, Pérez-Bercoff, Åsa, Huttley, Gavin, Sorrell, Tania C, Voelz, Kerstin, May, Robin C, Fisher, Matthew C, Thompson, George R, Lockhart, Shawn R, Keim, Paul, and Meyer, Wieland

Subjects
Biotechnology, Genetics, Infectious Diseases, Human Genome, 2.2 Factors relating to the physical environment, Aetiology, 2.1 Biological and endogenous factors, Infection, Biological Evolution, Cryptococcus gattii, Genome, Fungal, Northwestern United States, South America, Microbiology
Abstract

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater understanding of C. gattii evolution in North America and support extensive evolution in, and dispersal from, South America. Importance: Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic.

Published
2014

6. CYP8B1 downregulation mediates the metabolic effects of vertical sleeve gastrectomy in mice

Author

Liu, Yanjun, primary, Tu, Jui, additional, Shi, Linsen, additional, Fang, Zhipeng, additional, Fan, Mingjie, additional, Zhang, Jianying, additional, Ding, Lili, additional, Chen, Yiqiang, additional, Wang, Yangmeng, additional, Zhang, Eryun, additional, Xu, Senlin, additional, Sharma, Nisha, additional, Gillece, John D., additional, Reining, Lauren J., additional, Jin, Lihua, additional, and Huang, Wendong, additional

Published
2023
Full Text
View/download PDF

7. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Author

Herold, Malte, Martínez Arbas, Susana, Narayanasamy, Shaman, Sheik, Abdul R., Kleine-Borgmann, Luise A. K., Lebrun, Laura A., Kunath, Benoît J., Roume, Hugo, Bessarab, Irina, Williams, Rohan B. H., Gillece, John D., Schupp, James M., Keim, Paul S., Jäger, Christian, Hoopmann, Michael R., Moritz, Robert L., Ye, Yuzhen, Li, Sujun, Tang, Haixu, Heintz-Buschart, Anna, May, Patrick, Muller, Emilie E. L., Laczny, Cedric C., and Wilmes, Paul

Published
2020
Full Text
View/download PDF

8. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition

Author

Highlander, Sarah K., primary, Wood, Jason M., additional, Gillece, John D., additional, Folkerts, Megan, additional, Fofanov, Viacheslav, additional, Furstenau, Tara, additional, Singh, Nitin K., additional, Guan, Lisa, additional, Seuylemezian, Arman, additional, Benardini, James N., additional, Engelthaler, David M., additional, Venkateswaran, Kasthuri, additional, and Keim, Paul S., additional

Published
2023
Full Text
View/download PDF

9. Characterization of the microbial resistome in a prospective trial of CBM588 in metastatic renal cell carcinoma (mRCC) offers mechanism for interplay between antibiotic (abx) use and immune checkpoint inhibitor (ICI) activity.

Author

Dizman, Nazli, primary, Meza, Luis A, additional, Bergerot, Paulo Gustavo, additional, Dorff, Tanya B., additional, Lyou, Yung, additional, Frankel, Paul Henry, additional, Llamas, Marian, additional, Hsu, Joann, additional, Zengin, Zeynep Busra, additional, Malhotra, Jasnoor, additional, Govindarajan, Ameish, additional, Castro, Daniela V., additional, Gillece, John D, additional, Reining, Lauren J, additional, Trent, Jeffrey M., additional, Takahashi, Motomichi, additional, Oka, Kentaro, additional, Higashi, Seiya, additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2022
Full Text
View/download PDF

10. Nivolumab/ipilimumab with or without CBM588 in metastatic renal cell carcinoma: A randomized phase Ib study and the evolution of the functionality of microbial communities with treatment.

Author

Dizman, Nazli, primary, Meza, Luis A, additional, Bergerot, Paulo Gustavo, additional, Alcantara, Marice, additional, Dorff, Tanya B., additional, Lyou, Yung, additional, Frankel, Paul Henry, additional, Llamas, Marian, additional, Hsu, Joann, additional, Zengin, Zeynep Busra, additional, Malhotra, Jasnoor, additional, Gillece, John D, additional, Reining, Lauren J, additional, Trent, Jeffrey M., additional, Takahashi, Motomichi, additional, Oka, Kentaro, additional, Higashi, Seiya, additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2022
Full Text
View/download PDF

11. Intestinal microbiome associated with development of grade 3/4 adverse in patients with metastatic renal cell carcinoma (mRCC) treated with nivolumab plus ipilimumab (N/I) and probiotic support: Results from a phase Ib study.

Author

Meza, Luis A, primary, Dizman, Nazli, additional, Bergerot, Paulo Gustavo, additional, Dorff, Tanya B., additional, Lyou, Yung, additional, Frankel, Paul Henry, additional, Llamas, Marian, additional, Hsu, Joann, additional, Zengin, Zeynep Busra, additional, Salgia, Nicholas, additional, Malhotra, Jasnoor, additional, Chawla, Neal Shiv, additional, Gillece, John D, additional, Reining, Lauren J, additional, Trent, Jeffrey M., additional, Takahashi, Motomichi, additional, Oka, Kentaro, additional, Higashi, Seiya, additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2022
Full Text
View/download PDF

12. A novel circulating diagnostic and prognostic metagenomic signature in esophageal adenocarcinoma: Implications for precision oncology.

Author

Pratama, Muhammad Yogi, primary, Omstead, Ashten, additional, Gillece, John D, additional, Gorbunova, Anastasia, additional, Kreft, Rachael, additional, Highlander, Sarah K, additional, Jobe, Blair Anderson, additional, Wang, David H., additional, Kelly, Ronan Joseph, additional, Zaidi, Ali Hussainy, additional, and Goel, Ajay, additional

Published
2022
Full Text
View/download PDF

13. Francisella tularensis subsp. tularensis group A.I, United States

Author

Birdsell, Dawn N., Johansson, Anders, Ohrman, Caroline, Kaufman, Emily, Molins, Claudia, Pearson, Talima, Gyuranecz, Miklos, Naumann, Amber, Vogler, Amy J., Myrtennas, Kerstin, Larsson, Par, Forsman, Mats, Sjodin, Andreas, Gillece, John D., Schupp, James, Petersen, Jeannine M., Keim, Paul, and Wagner, David M.

Subjects
Francisella tularensis -- Health aspects, Tularemia -- Causes of -- Care and treatment -- Patient outcomes -- Genetic aspects, Phylogeny -- Analysis, Health
Abstract

Tularemia, caused by the bacterium Francisella tularensis, is a potentially severe disease that often causes unspecific symptoms; because of its low infectious dose and ease of dissemination, F. tularensis is [...]

Published
2014
Full Text
View/download PDF

15. First results of a randomized phase IB study comparing nivolumab/ipilimumab with or without CBM-588 in patients with metastatic renal cell carcinoma.

Author

Meza, Luis A, primary, Dizman, Nazli, additional, Bergerot, Paulo Gustavo, additional, Dorff, Tanya B., additional, Lyou, Yung, additional, Frankel, Paul Henry, additional, Mira, Valerie, additional, Llamas, Marian, additional, Hsu, Joann, additional, Zengin, Zeynep Busra, additional, Salgia, Nicholas, additional, Salgia, Sabrina, additional, Malhotra, Jasnoor, additional, Chawla, Neal Shiv, additional, Chehrazi-Raffle, Alex, additional, Gillece, John D, additional, Reining, Lauren J, additional, Trent, Jeffrey M., additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2021
Full Text
View/download PDF

18. First assessment of the stool mycobiome in patients (pts) with metastatic renal cell carcinoma (mRCC) receiving targeted therapy (TT) or immunotherapy (IO).

Author

Dizman, Nazli, primary, Hsu, Joann, additional, Gillece, John D, additional, Folkerts, Megan, additional, Reining, Lauren J, additional, Bergerot, Paulo Gustavo, additional, Meza, Luis A, additional, Zengin, Zeynep Busra, additional, Muddasani, Ramya, additional, Chawla, Neal, additional, Karimi, Misagh, additional, Trent, Jeffrey M., additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2021
Full Text
View/download PDF

20. A Phase II Clinical Trial of Pembrolizumab and Enobosarm in Patients with Androgen Receptor-Positive Metastatic Triple-Negative Breast Cancer

Author

Yuan, Yuan, primary, Lee, Jin Sun, additional, Yost, Susan E., additional, Frankel, Paul H., additional, Ruel, Christopher, additional, Egelston, Colt A., additional, Guo, Weihua, additional, Gillece, John D., additional, Folkerts, Megan, additional, Reining, Lauren, additional, Highlander, Sarah K., additional, Robinson, Kim, additional, Padam, Simran, additional, Martinez, Norma, additional, Tang, Aileen, additional, Schmolze, Daniel, additional, Waisman, James, additional, Sedrak, Mina, additional, Lee, Peter P., additional, and Mortimer, Joanne, additional

Published
2020
Full Text
View/download PDF

21. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Author

Martínez Arbas, Susana, primary, Narayanasamy, Shaman, additional, Herold, Malte, additional, Lebrun, Laura A., additional, Hoopmann, Michael R., additional, Li, Sujun, additional, Lam, Tony J., additional, Kunath, Benoît J., additional, Hicks, Nathan D., additional, Liu, Cindy M., additional, Price, Lance B., additional, Laczny, Cedric C., additional, Gillece, John D., additional, Schupp, James M., additional, Keim, Paul S., additional, Moritz, Robert L., additional, Faust, Karoline, additional, Tang, Haixu, additional, Ye, Yuzhen, additional, Skupin, Alexander, additional, May, Patrick, additional, Muller, Emilie E. L., additional, and Wilmes, Paul, additional

Published
2020
Full Text
View/download PDF

23. Randomized prospective trial assessing Bifidobacterium-containing probiotic supplementation in metastatic renal cell carcinoma (mRCC) patients receiving vascular endothelial growth factor-tyrosine kinase inhibitors (VEGF-TKIs).

Author

Dizman, Nazli, primary, Hsu, Joann, additional, Bergerot, Paulo Gustavo, additional, Gillece, John D, additional, Folkerts, Megan, additional, Reining, Lauren J, additional, Trent, Jeffrey M., additional, Highlander, Sarah K, additional, and Pal, Sumanta K., additional

Published
2020
Full Text
View/download PDF

24. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Author

Martinez Arbas, Susana(*), Narayanasamy, Shaman(*), Herold, Malte, Lebrun, Laura, Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît, Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric Christian, Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., Wilmes, Paul, Martinez Arbas, Susana(*), Narayanasamy, Shaman(*), Herold, Malte, Lebrun, Laura, Hoopmann, Michael R., Li, Sujun, Lam, Tony J., Kunath, Benoît, Hicks, Nathan D., Liu, Cindy M., Price, Lance B., Laczny, Cedric Christian, Gillece, John D., Schupp, James M., Keim, Paul S., Moritz, Robert L., Faust, Karoline, Tang, Haixu, Ye, Yuzhen, Skupin, Alexander, May, Patrick, Muller, Emilie E. L., and Wilmes, Paul

Abstract

Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.

Published
2020

25. Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma.

Author

Dizman, Nazli, Hsu, JoAnn, Bergerot, Paulo G., Gillece, John D., Folkerts, Megan, Reining, Lauren, Trent, Jeffrey, Highlander, Sarah K., and Pal, Sumanta K.

Subjects
RENAL cell carcinoma, GUT microbiome, FISHER discriminant analysis, PROBIOTICS, METASTASIS, CANCER hormone therapy
Abstract

Studies suggest a link between the gut microbiome and metastatic renal cell carcinoma (mRCC) outcomes, including evidence that mRCC patients possess a lower abundance of Bifidobacterium spp. compared to healthy adults. We sought to assess if a Bifidobacterium‐containing yogurt product could modulate the gut microbiome and clinical outcome from vascular endothelial growth factor‐tyrosine kinase inhibitors (VEGF‐TKIs). mRCC patients initiating VEGF‐TKIs, regardless of the line of therapy, were randomized to probiotic‐supplemented (two 4 oz. servings of the probiotic yogurt product daily) or probiotic‐restricted arms. Stool samples were collected prior to therapy and at weeks 2, 3, 4, and 12. Microbiome composition was assessed using whole‐metagenome sequencing. A total of 20 patients were randomized. Bifidobacterium animalis, the active ingredient of the probiotic supplement, reached detectable levels in all patients in the probiotic‐supplemented arm versus two patients in the probiotic‐restricted arm. Clinical benefit rate was similar in probiotic‐supplemented versus probiotic‐restricted arms (70% vs. 80%, p = 0.606). Linear discriminant analysis (LDA) effect size analysis of MetaPhIAn2 abundance data predicted 25 enriched species demonstrating an LDA score >3 in either clinical benefit or no clinical benefit. In patients with clinical benefit (vs. no clinical benefit), Barnesiella intestinihominis and Akkermansia muciniphila were significantly more abundant (p = 7.4 × 10−6 and p = 5.6 × 10−3, respectively). This is the first prospective randomized study demonstrating modulation of the gut microbiome with a probiotic in mRCC. Probiotic supplementation successfully increased the Bifidobacterium spp. levels. Analysis of longitudinal stool specimens identified an association between B. intestinihominis, A. muciniphila, and clinical benefit with therapy. Trial Registration: NCT02944617 [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

26. Critical transitions in microbial communities: mobile genetic elements as drivers of the microbial community dynamics within activated sludge of wastewater treatment

Author

Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Lam, Tony, Laczny, Cedric Christian, Ye, Yuzhen, Keim, Paul S., Muller, Emilie E.L., May, Patrick, Wilmes, Paul, Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Lam, Tony, Laczny, Cedric Christian, Ye, Yuzhen, Keim, Paul S., Muller, Emilie E.L., May, Patrick, and Wilmes, Paul

Published
2018

27. A multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community

Author

Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Laczny, Cedric Christian, Keim, Paul S., Muller, Emilie E.L., May, Patrick, Wilmes, Paul, Martinez Arbas, Susana, Narayanasamy, Shaman, Herold, Malte, Lebrun, Laura, Hicks, Nathan D., Price, Lance B., Gillece, John D., Schupp, James M., Laczny, Cedric Christian, Keim, Paul S., Muller, Emilie E.L., May, Patrick, and Wilmes, Paul

Published
2018

29. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis

Author

Price, Erin P., primary, Sarovich, Derek S., additional, Webb, Jessica R., additional, Hall, Carina M., additional, Jaramillo, Sierra A., additional, Sahl, Jason W., additional, Kaestli, Mirjam, additional, Mayo, Mark, additional, Harrington, Glenda, additional, Baker, Anthony L., additional, Sidak-Loftis, Lindsay C., additional, Settles, Erik W., additional, Lummis, Madeline, additional, Schupp, James M., additional, Gillece, John D., additional, Tuanyok, Apichai, additional, Warner, Jeffrey, additional, Busch, Joseph D., additional, Keim, Paul, additional, Currie, Bart J., additional, and Wagner, David M., additional

Published
2017
Full Text
View/download PDF

31. A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens

Author

Sahl, Jason W., primary, Pearson, Talima, additional, Okinaka, Richard, additional, Schupp, James M., additional, Gillece, John D., additional, Heaton, Hannah, additional, Birdsell, Dawn, additional, Hepp, Crystal, additional, Fofanov, Viacheslav, additional, Noseda, Ramón, additional, Fasanella, Antonio, additional, Hoffmaster, Alex, additional, Wagner, David M., additional, and Keim, Paul, additional

Published
2016
Full Text
View/download PDF

33. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats

Author

Sahl, Jason W., primary, Lemmer, Darrin, additional, Travis, Jason, additional, Schupp, James M., additional, Gillece, John D., additional, Aziz, Maliha, additional, Driebe, Elizabeth M., additional, Drees, Kevin P., additional, Hicks, Nathan D., additional, Williamson, Charles Hall Davis, additional, Hepp, Crystal M., additional, Smith, David Earl, additional, Roe, Chandler, additional, Engelthaler, David M., additional, Wagner, David M., additional, and Keim, Paul, additional

Published
2016
Full Text
View/download PDF

34. ABacillus anthracisGenome Sequence from the Sverdlovsk 1979 Autopsy Specimens

Author

Sahl, Jason W., primary, Pearson, Talima, additional, Okinaka, Richard, additional, Schupp, James M., additional, Gillece, John D., additional, Heaton, Hannah, additional, Birdsell, Dawn, additional, Hepp, Crystal, additional, Fofanov, Viacheslav, additional, Noseda, Ramón, additional, Fasanella, Antonio, additional, Hoffmaster, Alex, additional, Wagner, David M., additional, and Keim, Paul, additional

Published
2016
Full Text
View/download PDF

35. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study

Author

Colman, Rebecca E., primary, Anderson, Julia, additional, Lemmer, Darrin, additional, Lehmkuhl, Erik, additional, Georghiou, Sophia B., additional, Heaton, Hannah, additional, Wiggins, Kristin, additional, Gillece, John D., additional, Schupp, James M., additional, Catanzaro, Donald G., additional, Crudu, Valeriu, additional, Cohen, Ted, additional, Rodwell, Timothy C., additional, and Engelthaler, David M., additional

Published
2016
Full Text
View/download PDF

36. The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

Author

Sahl, Jason W., primary, Lemmer, Darrin, additional, Travis, Jason, additional, Schupp, James M., additional, Gillece, John D., additional, Aziz, Maliha, additional, Driebe, Elizabeth M., additional, Drees, Kevin, additional, Hicks, Nathan, additional, Williamson, Charles H.D., additional, Hepp, Crystal, additional, Smith, David, additional, Roe, Chandler, additional, Engelthaler, David M., additional, Wagner, David M., additional, and Keim, Paul, additional

Published
2016
Full Text
View/download PDF

37. Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus

Author

Driebe, Elizabeth M., primary, Sahl, Jason W., additional, Roe, Chandler, additional, Bowers, Jolene R., additional, Schupp, James M., additional, Gillece, John D., additional, Kelley, Erin, additional, Price, Lance B., additional, Pearson, Talima R., additional, Hepp, Crystal M., additional, Brzoska, Pius M., additional, Cummings, Craig A., additional, Furtado, Manohar R., additional, Andersen, Paal S., additional, Stegger, Marc, additional, Engelthaler, David M., additional, and Keim, Paul S., additional

Published
2015
Full Text
View/download PDF

38. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

Author

Roume, Hugo, primary, Heintz-Buschart, Anna, additional, Muller, Emilie E L, additional, May, Patrick, additional, Satagopam, Venkata P, additional, Laczny, Cédric C, additional, Narayanasamy, Shaman, additional, Lebrun, Laura A, additional, Hoopmann, Michael R, additional, Schupp, James M, additional, Gillece, John D, additional, Hicks, Nathan D, additional, Engelthaler, David M, additional, Sauter, Thomas, additional, Keim, Paul S, additional, Moritz, Robert L, additional, and Wilmes, Paul, additional

Published
2015
Full Text
View/download PDF

39. The In Silico Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

Author

Sahl, Jason W, primary, Beckstrom-Sternberg, Stephen M, additional, Babic-Sternberg, James, additional, Gillece, John D, additional, Hepp, Crystal M, additional, Auerbach, Raymond K, additional, Tembe, Waibhav, additional, Wagner, David M, additional, Keim, Paul S, additional, and Pearson, Talima, additional

Published
2015
Full Text
View/download PDF

40. Francisella tularensis subsp. tularensis group A.I, United States

Author

Birdsell, Dawn N, Johansson, Anders, Öhrman, Caroline, Kaufman, Emily, Molins, Claudia, Pearson, Talima, Gyuranecz, Miklós, Naumann, Amber, Vogler, Amy J, Myrtennäs, Kerstin, Larsson, Pär, Forsman, Mats, Sjödin, Andreas, Gillece, John D, Schupp, James, Petersen, Jeannine M, Keim, Paul, Wagner, David M, Birdsell, Dawn N, Johansson, Anders, Öhrman, Caroline, Kaufman, Emily, Molins, Claudia, Pearson, Talima, Gyuranecz, Miklós, Naumann, Amber, Vogler, Amy J, Myrtennäs, Kerstin, Larsson, Pär, Forsman, Mats, Sjödin, Andreas, Gillece, John D, Schupp, James, Petersen, Jeannine M, Keim, Paul, and Wagner, David M

Abstract

We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was observed for A.I.12, which suggests an adaptive advantage.

Published
2014
Full Text
View/download PDF

41. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

Author

Muller, Emilie E. L., primary, Pinel, Nicolás, additional, Laczny, Cédric C., additional, Hoopmann, Michael R., additional, Narayanasamy, Shaman, additional, Lebrun, Laura A., additional, Roume, Hugo, additional, Lin, Jake, additional, May, Patrick, additional, Hicks, Nathan D., additional, Heintz-Buschart, Anna, additional, Wampach, Linda, additional, Liu, Cindy M., additional, Price, Lance B., additional, Gillece, John D., additional, Guignard, Cédric, additional, Schupp, James M., additional, Vlassis, Nikos, additional, Baliga, Nitin S., additional, Moritz, Robert L., additional, Keim, Paul S., additional, and Wilmes, Paul, additional

Published
2014
Full Text
View/download PDF

42. Whole-Genome Analysis of Exserohilum rostratum from an Outbreak of Fungal Meningitis and Other Infections

Author

Litvintseva, Anastasia P., primary, Hurst, Steven, additional, Gade, Lalitha, additional, Frace, Michael A., additional, Hilsabeck, Remy, additional, Schupp, James M., additional, Gillece, John D., additional, Roe, Chandler, additional, Smith, David, additional, Keim, Paul, additional, Lockhart, Shawn R., additional, Changayil, Shankar, additional, Weil, M. Ryan, additional, MacCannell, Duncan R., additional, Brandt, Mary E., additional, and Engelthaler, David M., additional

Published
2014
Full Text
View/download PDF

43. Francisella tularensissubsp.tularensisGroup A.I, United States

Author

Birdsell, Dawn N., primary, Johansson, Anders, additional, Öhrman, Caroline, additional, Kaufman, Emily, additional, Molins, Claudia, additional, Pearson, Talima, additional, Gyuranecz, Miklós, additional, Naumann, Amber, additional, Vogler, Amy J., additional, Myrtennäs, Kerstin, additional, Larsson, Pär, additional, Forsman, Mats, additional, Sjödin, Andreas, additional, Gillece, John D., additional, Schupp, James, additional, Petersen, Jeannine M., additional, Keim, Paul, additional, and Wagner, David M., additional

Published
2014
Full Text
View/download PDF

44. Genome Sequence of 'Candidatus Microthrix parvicella' Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Muller, Emilie, Pinel, Nicolás, Gillece, John D., Schupp, James M., Price, Lance B., Engelthaler, David M., Levantesi, Caterina, Tandoi, Valter, Luong, Kkai, Baliga, Nitin S., Korlach, Jonas, Keim, Paul S., Wilmes, Paul, Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group) [research center], Muller, Emilie, Pinel, Nicolás, Gillece, John D., Schupp, James M., Price, Lance B., Engelthaler, David M., Levantesi, Caterina, Tandoi, Valter, Luong, Kkai, Baliga, Nitin S., Korlach, Jonas, Keim, Paul S., and Wilmes, Paul

Abstract

Candidatus Microthrix bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: "Candidatus Microthrix parvicella" strain Bio17-1.

Published
2012

45. Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak

Author

Hendriksen, Rene S., Price, Lance B., Schupp, James M., Gillece, John D., Kaas, Rolf Sommer, Engelthaler, David M., Bortolaia, Valeria, Pearson, Talima, Waters, Andrew E., Prasad Upadhyay, Bishnu, Devi Shrestha, Sirjana, Adhikari, Shailaja, Shakya, Geeta, Keim, Paul S., Aarestrup, Frank Møller, Hendriksen, Rene S., Price, Lance B., Schupp, James M., Gillece, John D., Kaas, Rolf Sommer, Engelthaler, David M., Bortolaia, Valeria, Pearson, Talima, Waters, Andrew E., Prasad Upadhyay, Bishnu, Devi Shrestha, Sirjana, Adhikari, Shailaja, Shakya, Geeta, Keim, Paul S., and Aarestrup, Frank Møller

Abstract

Cholera continues to be an important cause of human infections, and outbreaks are often observed after natural disasters, such as the one following the 2010 earthquake in Haiti. Once the cholera outbreak was confirmed, rumors spread that the disease was brought to Haiti by a battalion of Nepalese soldiers serving as United Nations peacekeepers. This possible connection has never been confirmed. We used whole-genome sequence typing (WGST), pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing to characterize 24 recent Vibrio cholerae isolates from Nepal and evaluate the suggested epidemiological link with the Haitian outbreak. The isolates were obtained from 30 July to 1 November 2010 from five different districts in Nepal. We compared the 24 genomes to 10 previously sequenced V. cholerae isolates, including 3 from the Haitian outbreak (began July 2010). Antimicrobial susceptibility and PFGE patterns were consistent with an epidemiological link between the isolates from Nepal and Haiti. WGST showed that all 24 V. cholerae isolates from Nepal belonged to a single monophyletic group that also contained isolates from Bangladesh and Haiti. The Nepalese isolates were divided into four closely related clusters. One cluster contained three Nepalese isolates and three Haitian isolates that were almost identical, with only 1- or 2-bp differences. Results in this study are consistent with Nepal as the origin of the Haitian outbreak. This highlights how rapidly infectious diseases might be transmitted globally through international travel and how public health officials need advanced molecular tools along with standard epidemiological analyses to quickly determine the sources of outbreaks. IMPORTANCE Cholera is one of the ancient classical diseases and particularly prone to cause major outbreaks following major natural disasters, such as earthquakes and hurricanes, where the normal separation between sewage and drinking water is destroyed.

Published
2011

48. Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

Author

Muller, Emilie E. L., primary, Pinel, Nicolás, additional, Gillece, John D., additional, Schupp, James M., additional, Price, Lance B., additional, Engelthaler, David M., additional, Levantesi, Caterina, additional, Tandoi, Valter, additional, Luong, Khai, additional, Baliga, Nitin S., additional, Korlach, Jonas, additional, Keim, Paul S., additional, and Wilmes, Paul, additional

Published
2012
Full Text
View/download PDF

50. Whole Genome Sequence Analysis of Cryptococcus gattii from the Pacific Northwest Reveals Unexpected Diversity

Author

Gillece, John D., primary, Schupp, James M., additional, Balajee, S. Arunmozhi, additional, Harris, Julie, additional, Pearson, Talima, additional, Yan, Yongpan, additional, Keim, Paul, additional, DeBess, Emilio, additional, Marsden-Haug, Nicola, additional, Wohrle, Ron, additional, Engelthaler, David M., additional, and Lockhart, Shawn R., additional

Published
2011
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results