1,162 results on '"Dutilh, Bas E."'
Search Results
152. RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Coutinho, Felipe Hernandes, Zaragoza-Solas, Asier, López-Pérez, Mario, Barylski, Jakub, Zielezinski, Andrzej, Dutilh, Bas E, Edwards, Robert, Rodriguez-Valera, Francisco, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Coutinho, Felipe Hernandes, Zaragoza-Solas, Asier, López-Pérez, Mario, Barylski, Jakub, Zielezinski, Andrzej, Dutilh, Bas E, Edwards, Robert, and Rodriguez-Valera, Francisco
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- 2021
153. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Goettsch, Winfried, Beerenwinkel, Niko, Deng, Li, Dölken, Lars, Dutilh, Bas E, Erhard, Florian, Kaderali, Lars, von Kleist, Max, Marquet, Roland, Matthijnssens, Jelle, McCallin, Shawna, McMahon, Dino, Rattei, Thomas, Van Rij, Ronald P, Robertson, David L, Schwemmle, Martin, Stern-Ginossar, Noam, Marz, Manja, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Goettsch, Winfried, Beerenwinkel, Niko, Deng, Li, Dölken, Lars, Dutilh, Bas E, Erhard, Florian, Kaderali, Lars, von Kleist, Max, Marquet, Roland, Matthijnssens, Jelle, McCallin, Shawna, McMahon, Dino, Rattei, Thomas, Van Rij, Ronald P, Robertson, David L, Schwemmle, Martin, Stern-Ginossar, Noam, and Marz, Manja
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- 2021
154. Stability of the human gut virome and effect of gluten-free diet
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Garmaeva, Sanzhima, Gulyaeva, Anastasia, Sinha, Trishla, Shkoporov, Andrey N, Clooney, Adam G, Stockdale, Stephen R, Spreckels, Johanne E, Sutton, Thomas D S, Draper, Lorraine A, Dutilh, Bas E, Wijmenga, Cisca, Kurilshikov, Alexander, Fu, Jingyuan, Hill, Colin, Zhernakova, Alexandra, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Garmaeva, Sanzhima, Gulyaeva, Anastasia, Sinha, Trishla, Shkoporov, Andrey N, Clooney, Adam G, Stockdale, Stephen R, Spreckels, Johanne E, Sutton, Thomas D S, Draper, Lorraine A, Dutilh, Bas E, Wijmenga, Cisca, Kurilshikov, Alexander, Fu, Jingyuan, Hill, Colin, and Zhernakova, Alexandra
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- 2021
155. Optimized bacterial DNA isolation method for microbiome analysis of human tissues
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Garza, Daniel R, Achouiti, Soumia, Mes, Wouter, Dutilh, Bas E, Boleij, Annemarie, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Garza, Daniel R, Achouiti, Soumia, Mes, Wouter, Dutilh, Bas E, and Boleij, Annemarie
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- 2021
156. Perspective on taxonomic classification of uncultivated viruses
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, Sullivan, Matthew B, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Dutilh, Bas E, Varsani, Arvind, Tong, Yigang, Simmonds, Peter, Sabanadzovic, Sead, Rubino, Luisa, Roux, Simon, Muñoz, Alejandro Reyes, Lood, Cédric, Lefkowitz, Elliot J, Kuhn, Jens H, Krupovic, Mart, Edwards, Robert A, Brister, J Rodney, Adriaenssens, Evelien M, and Sullivan, Matthew B
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- 2021
157. The human gut microbiome and health inequities
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, Kuzawa, Christopher W, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, and Kuzawa, Christopher W
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- 2021
158. Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Taddese, Rahwa, Belzer, Clara, Aalvink, Steven, de Jonge, Marien I, Nagtegaal, Iris D, Dutilh, Bas E, Boleij, Annemarie, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Taddese, Rahwa, Belzer, Clara, Aalvink, Steven, de Jonge, Marien I, Nagtegaal, Iris D, Dutilh, Bas E, and Boleij, Annemarie
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- 2021
159. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
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Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, Sheinman, Michael, Arkhipova, Ksenia, Arndt, Peter F., Dutilh, Bas E., Hermsen, Rutger, Massip, Florian, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, Sheinman, Michael, Arkhipova, Ksenia, Arndt, Peter F., Dutilh, Bas E., Hermsen, Rutger, and Massip, Florian
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- 2021
160. Quantifying The Impact Of Human Leukocyte Antigen On The Human Gut Microbiota
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Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, Andeweg, Stijn P., Kesmir, Can, Dutilh, Bas E., Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, Andeweg, Stijn P., Kesmir, Can, and Dutilh, Bas E.
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- 2021
161. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, van Vliet, Daan M, von Meijenfeldt, F A Bastiaan, Dutilh, Bas E, Villanueva, Laura, Sinninghe Damsté, Jaap S, Stams, Alfons J M, Sánchez-Andrea, Irene, Theoretical Biology and Bioinformatics, Sub Bioinformatics, van Vliet, Daan M, von Meijenfeldt, F A Bastiaan, Dutilh, Bas E, Villanueva, Laura, Sinninghe Damsté, Jaap S, Stams, Alfons J M, and Sánchez-Andrea, Irene
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- 2021
162. Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids
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Theoretical Biology and Bioinformatics, Organic geochemistry & molecular biogeology, Organic geochemistry, Sub Bioinformatics, Villanueva, Laura, von Meijenfeldt, F. A.Bastiaan, Westbye, Alexander B., Yadav, Subhash, Hopmans, Ellen C., Dutilh, Bas E., Damsté, Jaap S.Sinninghe, Theoretical Biology and Bioinformatics, Organic geochemistry & molecular biogeology, Organic geochemistry, Sub Bioinformatics, Villanueva, Laura, von Meijenfeldt, F. A.Bastiaan, Westbye, Alexander B., Yadav, Subhash, Hopmans, Ellen C., Dutilh, Bas E., and Damsté, Jaap S.Sinninghe
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- 2021
163. OGRE: Overlap Graph-based metagenomic Read clustEring
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, and Dutilh, Bas E
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- 2021
164. Finding functional associations between prokaryotic virus orthologous groups: a proof of concept
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Pappas, Nikolaos, Dutilh, Bas E, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Pappas, Nikolaos, and Dutilh, Bas E
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- 2021
165. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
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UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
- Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
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- 2021
166. Novel high-resolution targeted sequencing of the cervicovaginal microbiome
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Andralojc, Karolina M, Molina, Mariano A, Qiu, Mengjie, Spruijtenburg, Bram, Rasing, Menno, Pater, Bernard, Huynen, Martijn A, Dutilh, Bas E, Ederveen, Thomas H A, Elmelik, Duaa, Siebers, Albert G, Loopik, Diede, Bekkers, Ruud L M, Leenders, William P J, Melchers, Willem J G, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Andralojc, Karolina M, Molina, Mariano A, Qiu, Mengjie, Spruijtenburg, Bram, Rasing, Menno, Pater, Bernard, Huynen, Martijn A, Dutilh, Bas E, Ederveen, Thomas H A, Elmelik, Duaa, Siebers, Albert G, Loopik, Diede, Bekkers, Ruud L M, Leenders, William P J, and Melchers, Willem J G
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- 2021
167. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021
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Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.
- Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
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- 2021
168. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy
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Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Agencia Estatal de Investigación (España), European Research Council, Jahn, Martin T., Lachnit, Tim, Markert, Sebastian M., Stigloher, Christian, Pita, Lucía, Ribes, Marta, Dutilh, Bas E., Hentschel, Ute, Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, Agencia Estatal de Investigación (España), European Research Council, Jahn, Martin T., Lachnit, Tim, Markert, Sebastian M., Stigloher, Christian, Pita, Lucía, Ribes, Marta, Dutilh, Bas E., and Hentschel, Ute
- Abstract
Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach (‘PhageFISH-CLEM‘) localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts
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- 2021
169. OGRE: Overlap Graph-based metagenomic Read clustEring
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Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, Dutilh, Bas E., Balvert, Marleen, Luo, Xiao, Hauptfeld, Ernestina, Schönhuth, Alexander, and Dutilh, Bas E.
- Abstract
Motivation: The microbes that live in an environment can be identified from the combined genomic material, also referred to as the metagenome. Sequencing a metagenome can result in large volumes of sequencing reads. A promising approach to reduce the size of metagenomic datasets is by clustering reads into groups based on their overlaps. Clustering reads are valuable to facilitate downstream analyses, including computationally intensive strain-aware assembly. As current read clustering approaches cannot handle the large datasets arising from high-throughput metagenome sequencing, a novel read clustering approach is needed. In this article, we propose OGRE, an Overlap Graph-based Read clustEring procedure for high-throughput sequencing data, with a focus on shotgun metagenomes. Results: We show that for small datasets OGRE outperforms other read binners in terms of the number of species included in a cluster, also referred to as cluster purity, and the fraction of all reads that is placed in one of the clusters. Furthermore, OGRE is able to process metagenomic datasets that are too large for other read binners into clusters with high cluster purity. Conclusion: OGRE is the only method that can successfully cluster reads in species-specific clusters for large metagenomic datasets without running into computation time- or memory issues. Availabilityand implementation: Code is made available on Github (https://github.com/Marleen1/OGRE).
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- 2021
170. Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity
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Taddese, Rahwa, Belzer, Clara, Aalvink, Steven, de Jonge, Marien I., Nagtegaal, Iris D., Dutilh, Bas E., Boleij, Annemarie, Taddese, Rahwa, Belzer, Clara, Aalvink, Steven, de Jonge, Marien I., Nagtegaal, Iris D., Dutilh, Bas E., and Boleij, Annemarie
- Abstract
There are many approaches available to produce inactive bacteria by termination of growth, each with a different efficacy, impact on cell integrity, and potential for application in standardized inactivation protocols. The aim of this study was to compare these approaches and develop a standardized protocol for generation of inactivated Gram-positive and Gram-negative bacteria, yielding cells that are metabolically dead with retained cellular integrity i.e., preserving the surface and limited leakage of intracellular proteins and DNA. These inactivated bacteria are required for various applications, for instance, when investigating receptor-triggered signaling or bacterial contact-dependent analysis of cell lines requiring long incubation times. We inactivated eight different bacterial strains of different species by treatment with beta-propiolactone, ethanol, formalin, sodium hydroxide, and pasteurization. Inactivation efficacy was determined by culturing, and cell wall integrity assessed by quantifying released DNA, bacterial membrane and intracellular DNA staining, and visualization by scanning electron microscopy. Based on these results, we discuss the bacterial inactivation methods, and their advantages and disadvantages to study host-microbe interactions with inactivated bacteria.
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- 2021
171. Prophages are associated with extensive, tolerated CRISPR-Cas auto-immunity
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Nobrega, Franklin L., Walinga, Hielke, Dutilh, Bas E., and Brouns, Stan J.J.
- Abstract
CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS may reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a gene regulatory mechanism. Here we investigated the incidence, distribution, and evasion of STS in over 100,000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of tolerance to STS by other mechanisms such as anti-CRISPR proteins and target mutations. We propose a scenario where it is common and perhaps beneficial to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects. The mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages, and contribute both to viral dissemination and bacterial diversification.
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- 2020
172. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)
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Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Dempsey, Donald M, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max, Orton, Richard J, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, University of Queensland [Brisbane], University of Bristol [Bristol], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Utrecht University [Utrecht], Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), Humboldt University Of Berlin, The Pirbright Institute, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), MRC - University of Glasgow Centre for Virus Research, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], University of Oxford, Arizona State University [Tempe] (ASU), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), The authors declare no conflicts of interest. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. This work was supported in part through Laulima Government Solutions, LLC’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC under Contract No. HHSN272201800013C. N.J.K. is partially supported by core funding provided by the Biotechnology and Biological Sciences Research Council, UK. B.E.D. is supported by Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 and European Research Council (ERC) Consolidator grant 865694: DiversiPHI. B.H. is partially supported by National Research, Development and Innovation Office – NKFIH, NN128309. S.S. acknowledges partial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. E.M.A. was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. S.J. is supported by the Federal Ministry of Education and Research (BMBF) under project number 01KI1716 as part of the Research Network Zoonotic Infectious Diseases. FMZ is partially supported by CAPES (Finance Code 001). None of the work reported involved research on human participants or animals. All authors have contributed to this work and agreed to its publication. Except for Donald M. Dempsey, R. Curtis Hendrickson, Richard J. Orton and Donald B. Smith, the authors were members of the ICTV Executive Committee during the relevant period., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Sub Bioinformatics, Theoretical Biology and Bioinformatics, Humboldt University of Berlin, Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)
- Subjects
0303 health sciences ,MESH: Terminology as Topic ,030306 microbiology ,education ,General Medicine ,Biology ,no key words ,Virology ,Executive committee ,Statute ,MESH: Viruses ,03 medical and health sciences ,MESH: Classification ,Law ,Taverne ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Classification methods ,Taxonomy (biology) ,Virus classification ,health care economics and organizations ,MESH: Virology ,030304 developmental biology - Abstract
International audience; This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.
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- 2020
173. Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions
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de Jonge, Patrick A, Smit Sibinga, Dieuwke J C, Boright, Oliver A, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Bioinformatics
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bacteriophages ,Maleic acid ,Polymers ,viruses ,Immunology ,Biology ,Microbiology ,Genome ,chemistry.chemical_compound ,All institutes and research themes of the Radboud University Medical Center ,Virology ,phage-host interactions ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,outer membrane proteins ,Receptor ,Host cell surface ,Bacteria ,SMALPs ,Cell Membrane ,Maleates ,Virion ,Membrane Proteins ,Lipid Droplets ,biology.organism_classification ,Virus-Cell Interactions ,Membrane ,Membrane protein ,chemistry ,Biochemistry ,Solubility ,Insect Science ,Host-Pathogen Interactions ,Polystyrenes ,DNA ,Bacterial Outer Membrane Proteins - Abstract
Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions., The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies. IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.
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- 2020
174. Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)
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van Kessel, Maartje AHJ, Dutilh, Bas E, Neveling, Kornelia, Kwint, Michael P, Veltman, Joris A, Flik, Gert, Jetten, Mike SM, Klaren, Peter HM, and Op den Camp, Huub JM
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- 2011
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175. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria
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Ettwig, Katharina F., Butler, Margaret K., Paslier, Denis Le, Pelletier, Eric, Mangenot, Sophie, Kuypers, Marcel M.M., Schreiber, Frank, Dutilh, Bas E., Zedelius, Johannes, de Beer, Dirk, Gloerich, Jolein, Wessels, Hans J.C.T., van Alen, Theo, Luesken, Francisca, Wu, Ming L., van de Pas-Schoonen, Katinka T., Camp, Huub J.M. Op den, Janssen-Megens, Eva M., Francoijs, Kees-Jan, Stunnenberg, Henk, Weissenbach, Jean, Jetten, Mike S.M., and Strous, Marc
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Methane -- Physiological aspects -- Research ,Denitrification -- Physiological aspects -- Research ,Phytochemistry -- Physiological aspects ,Nitrous oxide -- Physiological aspects -- Research ,Oxidation-reduction reaction -- Physiological aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis., With the ubiquitous use of fertilizers in agriculture, nitrate (N[O.sub.3.sup.-]) and nitrite (N[O.sub.2.sup.-]) have become major electron acceptors in freshwater environments (1). The feedback of eutrophication on the atmospheric methane [...]
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- 2010
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176. Growth rate is a dominant factor predicting the rhizosphere effect
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López, José L., Fourie, Arista, Poppeliers, Sanne W. M., Pappas, Nikolaos, Sánchez-Gil, Juan J., de Jonge, Ronnie, and Dutilh, Bas E.
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The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.
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- 2023
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177. Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome.
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de Jonge, Patrick A., Wortelboer, Koen, Scheithauer, Torsten P. M., van den Born, Bert-Jan H., Zwinderman, Aeilko H., Nobrega, Franklin L., Dutilh, Bas E., Nieuwdorp, Max, and Herrema, Hilde
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BACTERIOPHAGES ,METABOLIC syndrome ,HEART metabolism disorders ,WHOLE genome sequencing ,CANDIDATUS ,STREPTOCOCCACEAE - Abstract
There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied. Here, we show gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants by combined sequencing of bulk whole genome and virus like particle communities. MetS gut viromes exhibit decreased richness and diversity. They are enriched in phages infecting Streptococcaceae and Bacteroidaceae and depleted in those infecting Bifidobacteriaceae. Differential abundance analysis identifies eighteen viral clusters (VCs) as significantly associated with either MetS or healthy viromes. Among these are a MetS-associated Roseburia VC that is related to healthy control-associated Faecalibacterium and Oscillibacter VCs. Further analysis of these VCs revealed the Candidatus Heliusviridae, a highly widespread gut phage lineage found in 90+% of participants. The identification of the temperate Ca. Heliusviridae provides a starting point to studies of phage effects on gut bacteria and the role that this plays in MetS. Here, the authors characterize gut viromes in a cohort of individuals with metabolic syndrome, which they find associated with a highly widespread family of gut bacteriophages they name Candidatus Heliusviridae. [ABSTRACT FROM AUTHOR]
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- 2022
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178. Author response: Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
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Sheinman, Michael, primary, Arkhipova, Ksenia, additional, Arndt, Peter F, additional, Dutilh, Bas E, additional, Hermsen, Rutger, additional, and Massip, Florian, additional
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- 2021
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179. Members of a highly widespread bacteriophage family are hallmarks of metabolic syndrome gut microbiomes
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de Jonge, Patrick A., primary, Wortelboer, Koen, additional, Scheithauer, Torsten P.M., additional, van den Born, Bert-Jan H., additional, Zwinderman, Aeilko H., additional, Nobrega, Franklin L., additional, Dutilh, Bas E., additional, Nieuwdorp, Max, additional, and Herrema, Hilde, additional
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- 2021
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180. Virus Bioinformatics
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Pappas, Nikolaos, Roux, Simon, Hölzer, Martin, Lamkiewicz, Kevin, Mock, Florian, Marz, Manja, Dutilh, Bas E., Theoretical Biology and Bioinformatics, Sub Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Bioinformatics
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Bioinformatics ,Evolution ,Prevention ,Coronacrisis-Taverne ,Phylogenomics ,Genomics ,Classification ,Vaccine Related ,Computational biology ,Emerging Infectious Diseases ,Infectious Diseases ,Biodefense ,Virus-host association ,Genetics ,2.2 Factors relating to the physical environment ,Immunization ,Viromics ,Metagenomics ,Aetiology ,Infection - Abstract
Since the discovery of computers, bioinformatics and computational biology have been instrumental in a wide range of discoveries in virology. These include early mathematical models of virus-host interaction, and more recently the analysis of viral nucleotide and protein sequences to track their function, epidemiology, and evolution. The genomics revolution has provided an unprecedented amount of sequence information from both viruses and their hosts. In this article, we discuss how bioinformatics allows viral sequence data to be analyzed and interpreted, including an overview of commonly used tools and examples of applications.
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- 2020
181. Evolutionary Study of the Crassphage Virus at Gene Level
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Rossi, Alessandro, Treu, Laura, Toppo, Stefano, Zschach, Henrike, Campanaro, Stefano, Dutilh, Bas E, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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Viral protein ,Population ,lcsh:QR1-502 ,Genome, Viral ,medicine.disease_cause ,Genome ,lcsh:Microbiology ,Article ,Evolution, Molecular ,03 medical and health sciences ,Feces ,Viral Proteins ,All institutes and research themes of the Radboud University Medical Center ,Virology ,medicine ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Humans ,Bacteriophages ,Evolutionary dynamics ,Clade ,education ,Gene ,Phylogeny ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,biology ,Phylogenetic tree ,mirrortree ,030306 microbiology ,DNA Viruses ,crAssphage ,biology.organism_classification ,Gastrointestinal Microbiome ,Infectious Diseases ,Evolutionary biology ,Viruses ,gene evolution ,Metagenome ,Capsid Proteins ,Metagenomics ,metaviromics ,CrAssphage ,Gene evolution ,Human gut ,Metaviromics ,Mirrortree ,human gut - Abstract
crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.
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- 2020
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182. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts
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de Jonge, Patrick A, von Meijenfeldt, F A Bastiaan, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, Dutilh, Bas E, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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0301 basic medicine ,Techniques in Genetics ,Science ,viruses ,02 engineering and technology ,Microbiology ,Article ,Environmental ,03 medical and health sciences ,chemistry.chemical_compound ,Techniques in ,All institutes and research themes of the Radboud University Medical Center ,Adsorption ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Genetics ,Human virome ,lcsh:Science ,Gel electrophoresis ,Multidisciplinary ,biology ,Ecology ,021001 nanoscience & nanotechnology ,biology.organism_classification ,030104 developmental biology ,Biochemistry ,chemistry ,Environmental Science ,lcsh:Q ,0210 nano-technology ,DNA ,Bacteria - Abstract
Summary An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes., Graphical Abstract, Highlights • AdsorpSeq allows rapid determination of bacteria-bacteriophage interactions • Model phages can be differentially sequenced based on binding ability with AdsorpSeq • With AdsorpSeq 26 new phage-host interactions were determined in hospital wastewater, Ecology; Environmental Science; Microbiology; Techniques in Genetics
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- 2020
183. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia
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Walter, Juline M, Coutinho, Felipe H, Leomil, Luciana, Hargreaves, Paulo I, Campeão, Mariana E, Vieira, Verônica V, Silva, Beatriz S, Fistarol, Giovana O, Salomon, Paulo S, Sawabe, Tomoo, Mino, Sayaka, Hosokawa, Masashi, Miyashita, Hideaki, Maruyama, Fumito, van Verk, Marcel C, Dutilh, Bas E, Thompson, Cristiane C, Thompson, Fabiano L, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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Microbial ecology ,Coral reefs ,Abrolhos Bank ,Secondary metabolites ,Photoacclimation strategies ,Taverne ,Turf ,Cyanobacteria - Abstract
Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
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- 2020
184. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
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Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Civil, Environmental and Geodetic Engineering [Columbus, USA] (CEGE), Ohio State University [Columbus] (OSU), University of Novi Sad, Institute for Microbial Biotechnology and Metagenomics [Cape Town, South Africa] (IMBM), University of the Western Cape (UWC), National Institute of Cholera and Enteric Diseases, Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Beijing University of Chemical Technology, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Universidad Andrés Bello [Santiago] (UNAB), Institute of Food, Nutrition and Health [Zurich, Suisse] (IFNH), Department of Health Sciences and Technology [ETH Zürich] (D-HEST), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Cairo University, Adam Mickiewicz University in Poznań (UAM), Azabu University, San Diego State University (SDSU), University of Guelph, Ontario Veterinary College [Univ. Guelph, Canada], iThree Institute, University of Technology Sydney (UTS), University of Leicester, D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Rutgers University [Newark], Rutgers University System (Rutgers), Imperial College London, Latvian Biomedical Research and Study Centre [Rīga], University of the Sunshine Coast (USC), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Department of Biosystems (BIOSYST), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Faculty of Health and Applied Sciences [Bristol, UK], University of the West of England [Bristol] (UWE Bristol), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, This research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353. B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by Grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the PhageBiotics Research Community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure., The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies of their organizations. E.M.A gratefully acknowledges the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC)., UCL - SST/ELI/ELIM - Applied Microbiology, University of the Western Cape, Universidade Federal de Vicosa (UFV), Universidad Andrés Bello - UNAB (CHILE), Institut Pasteur [Paris], University of Helsinki, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
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06 Biological Sciences, 07 Agricultural and Veterinary Sciences, 11 Medical and Health Sciences ,Archaeal Viruses ,0303 health sciences ,MESH: Bacteriophages/classification ,Bacteria ,030306 microbiology ,MESH: Bacteria/virology ,Coronacrisis-Taverne ,General Medicine ,Classification ,MESH: Archaeal Viruses/classification ,Archaea ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,Virology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Bacteriophages ,MESH: Archaea/virology ,MESH: Classification/methods ,030304 developmental biology - Abstract
International audience; This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
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- 2020
185. Metabolic models predict bacterial passengers in colorectal cancer
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Garza, Daniel R, Taddese, Rahwa, Wirbel, Jakob, Zeller, Georg, Boleij, Annemarie, Huynen, Martijn A, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Bioinformatics
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0301 basic medicine ,Colorectal cancer ,Colorectal cancer metabolome ,Computational biology ,Biology ,Genome ,lcsh:RC254-282 ,Bacterial driver-passenger model ,03 medical and health sciences ,All institutes and research themes of the Radboud University Medical Center ,0302 clinical medicine ,Metabolomics ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,medicine ,Metabolome ,Microbiome ,Genome-scale metabolic models ,neoplasms ,2. Zero hunger ,Research ,Human microbiome ,Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6] ,biology.organism_classification ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,digestive system diseases ,3. Good health ,Psychiatry and Mental health ,030104 developmental biology ,Metagenomics ,030220 oncology & carcinogenesis ,Colorectal cancer microbiome ,Bacteria - Abstract
Background Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found in pathogens, metagenomic studies indicate the existence of a microbiome signature, where particular bacterial taxa are enriched in the metagenomes of CRC patients. Here, we investigate to what extent the abundance of bacterial taxa in CRC metagenomes can be explained by the growth advantage resulting from the presence of specific CRC metabolites in the tumor microenvironment. Methods We composed lists of metabolites and bacteria that are enriched on CRC samples by reviewing metabolomics experimental literature and integrating data from metagenomic case-control studies. We computationally evaluated the growth effect of CRC enriched metabolites on over 1500 genome-based metabolic models of human microbiome bacteria. We integrated the metabolomics data and the mechanistic models by using scores that quantify the response of bacterial biomass production to CRC-enriched metabolites and used these scores to rank bacteria as potential CRC passengers. Results We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome. Conclusion Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome.
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- 2020
186. Binomial nomenclature for virus species: a consultation
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Siddell, Stuart G, Walker, Peter J, Lefkowitz, Elliot J, Mushegian, Arcady R, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, School of Cellular and Molecular Medicine [Bristol] (CellModMed), University of Bristol [Bristol], School of Biological Sciences [Brisbane], University of Queensland [Brisbane], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Berlin Institute of Health (BIH), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Guelph, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Blavatnik Institute [Boston], Harvard Medical School [Boston] (HMS), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), MRC - University of Glasgow Centre for Virus Research, A.D. is supported by Medical Research Council programme Grant MC_UU_12014/3. B.E.D. is supported by the Netherlands Organization for Scientific Research (NWO) Vidi Grant 864.14.004. B.H. is supported by National Research, Development and Innovation Office–NKFIH, NN128309. N.J.K. is funded by the Department for Environment, Food and Rural Affairs (Defra), UK (Grant no. SE2944), work at the Pirbright Institute is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/E/I/00007035, BB/E/I/00007036 and BBS/E/I/00007037). J.H.K is supported through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I. S.S. acknowledges partial financial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University., The authors acknowledge the contribution of ICTV Life Member, Dr. Mike Adams, to previous discussions on the need for a standard binomial nomenclature for virus species., Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], Universidade Federal de Vicosa (UFV), Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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Library science ,Biology ,MESH: Terminology as Topic ,Binomial species names ,Executive committee ,International committee on taxonomy of viruses (ICTV) ,03 medical and health sciences ,Virology Division News ,Terminology as Topic ,Virology ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Nomenclature ,Virus classification ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Binomial nomenclature ,Virus taxonomy ,Species nomenclature ,General Medicine ,Classification ,MESH: Viruses/classification ,Viruses ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Taxonomy (biology) ,MESH: Classification/methods - Abstract
Erratum in : Correction to: Binomial nomenclature for virus species: a consultation. [Arch Virol. 2020]; International audience; The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) recognizes the need for a standardized nomenclature for virus species. This article sets out the case for establishing a binomial nomenclature and presents the advantages and disadvantages of different naming formats. The Executive Committee understands that adopting a binomial system would have major practical consequences, and invites comments from the virology community before making any decisions to change the existing nomenclature. The Executive Committee will take account of these comments in deciding whether to approve a standardized binomial system at its next meeting in October 2020. Note that this system would relate only to the formal names of virus species and not to the names of viruses.
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- 2020
187. Integrating Computational Methods to Investigate the Macroecology of Microbiomes
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Mascarenhas, Rilquer, Ruziska, Flávia M, Moreira, Eduardo Freitas, Campos, Amanda B, Loiola, Miguel, Reis, Kaike, Trindade-Silva, Amaro E, Barbosa, Felipe A S, Salles, Lucas, Menezes, Rafael, Veiga, Rafael, Coutinho, Felipe H, Dutilh, Bas E, Guimarães, Paulo R, Assis, Ana Paula A, Ara, Anderson, Miranda, José G V, Andrade, Roberto F S, Vilela, Bruno, Meirelles, Pedro Milet, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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machine learning ,microbial community modeling ,microbial macroecology ,co-occurrence networks ,spatial scales - Abstract
Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.
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- 2020
188. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients?: A systematic review and meta-analysis
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Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, Nagtegaal, Iris D, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
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POLYPS ,Male ,endocrine system diseases ,Colorectal cancer ,Review Article ,HEREDITARY ,Gastroenterology ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Genetics (clinical) ,Brain Neoplasms ,Middle Aged ,CANCER ,Lynch syndrome ,DEFICIENCY ,Meta-analysis ,HIGH-GRADE DYSPLASIA ,Cohort ,YOUNG-PATIENTS ,Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis ,Female ,Microsatellite Instability ,DNA mismatch repair ,Biomarkers, Tumor/genetics ,Colorectal Neoplasms ,EXPRESSION ,Adult ,Adenoma ,medicine.medical_specialty ,Coronacrisis-Taverne ,Adenoma/diagnosis ,Context (language use) ,Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9] ,Neoplastic Syndromes, Hereditary ,Internal medicine ,Biomarkers, Tumor ,Genetics ,medicine ,Humans ,GERMLINE MUTATION ,business.industry ,SERRATED LESIONS ,Comment ,Microsatellite instability ,medicine.disease ,Colorectal Neoplasms, Hereditary Nonpolyposis ,digestive system diseases ,stomatognathic diseases ,MISMATCH REPAIR PROTEINS ,business - Abstract
Contains fulltext : 218215pub.pdf (Publisher’s version ) (Closed access) The colorectal cancer spectrum has changed due to population screening programs, with a shift toward adenomas and early cancers. Whether it would be a feasible option to test these adenomas for detection of Lynch syndrome (LS) patients is unclear. Through meta-analysis and systematic review, risk factors for DNA mismatch repair deficiency (dMMR) and microsatellite instability (MSI) in adenomas were identified in LS and unselected patient cohorts. Data were extracted for patient age and MMR variant together with adenoma type, grade, size, and location. A total of 41 studies were included, and contained more than 519 LS patients and 1698 unselected patients with 1142 and 2213 adenomas respectively. dMMR/MSI was present in 69.5% of conventional adenomas in LS patients, compared with 2.8% in unselected patients. In the LS cohort, dMMR/MSI was more frequently present in patients older than 60 years (82% versus 54%). dMMR/MSI was also more common in villous adenomas (84%), adenomas over 1 cm (81%), and adenomas with high grade dysplasia (88%). No significant differences were observed for dMMR/MSI in relation to MMR variants and location of adenomas. In the context of screening, we conclude that detection of dMMR/MSI in conventional adenomas of unselected patients is uncommon and might be considered as indication for LS testing. Within the LS cohort, 69.5% of LS patients could have been detected through dMMR/MSI screening of their conventional adenomas.
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- 2020
189. Growth rate alterations of human colorectal cancer cells by 157 gut bacteria
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Taddese, Rahwa, Garza, Daniel R, Ruiter, Lilian N, de Jonge, Marien I, Belzer, Clara, Aalvink, Steven, Nagtegaal, Iris D, Dutilh, Bas E, Boleij, Annemarie, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Bioinformatics
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0301 basic medicine ,Microbiology (medical) ,secretomes ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,Virulence ,Biology ,Bacterial Physiological Phenomena ,medicine.disease_cause ,Microbiology ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Cell Line, Tumor ,medicine ,Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14] ,Humans ,Microbiome ,MolEco ,lcsh:RC799-869 ,Bacteroidaceae ,VLAG ,MTT assay ,Bacteria ,Cell growth ,Gastroenterology ,Human microbiome ,human microbiome ,biology.organism_classification ,Enterobacteriaceae ,Colorectal cancer ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,030104 developmental biology ,Infectious Diseases ,cell proliferation ,Cancer cell ,lcsh:Diseases of the digestive system. Gastroenterology ,030211 gastroenterology & hepatology ,Colorectal Neoplasms ,Carcinogenesis ,Research Article ,Research Paper - Abstract
Several bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effect on CRC cell growth. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play. Secretomes ofBacteroidaceae,Enterobacteriaceae,andErysipelotrichaceaebacteria enhanced CRC cell growth, while mostFusobacteriaceaecells and secretomes inhibited growth, contrasting prior findings. In some bacteria, the presence of specific functional genes was associated with CRC cell growth rates, including the virulence genes TcdA inClostridialesand FadA inFusobacteriaceae, which both inhibited growth.Bacteroidaceaecells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, whileFusobacteriaceaecells that inhibit growth were enriched for genes of the ethanolamine utilization pathway. Together, our results reveal how different gut bacteria have wide-ranging effects on cancer cells, contribute a better understanding of the effects of the gut microbiome on the human host, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies.
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- 2020
190. Virus Bioinformatics
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Pappas, Nikolaos, Roux, Simon, Hölzer, Martin, Lamkiewicz, Kevin, Mock, Florian, Marz, Manja, Dutilh, Bas E., Theoretical Biology and Bioinformatics, Sub Bioinformatics, Pappas, Nikolaos, Roux, Simon, Hölzer, Martin, Lamkiewicz, Kevin, Mock, Florian, Marz, Manja, and Dutilh, Bas E.
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- 2020
191. Evolutionary Study of the Crassphage Virus at Gene Level
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Rossi, Alessandro, Treu, Laura, Toppo, Stefano, Zschach, Henrike, Campanaro, Stefano, Dutilh, Bas E, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Rossi, Alessandro, Treu, Laura, Toppo, Stefano, Zschach, Henrike, Campanaro, Stefano, and Dutilh, Bas E
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- 2020
192. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, de Jonge, Patrick A, von Meijenfeldt, F A Bastiaan, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, Dutilh, Bas E, Sub Bioinformatics, Theoretical Biology and Bioinformatics, de Jonge, Patrick A, von Meijenfeldt, F A Bastiaan, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, and Dutilh, Bas E
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- 2020
193. Growth rate alterations of human colorectal cancer cells by 157 gut bacteria
- Author
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Taddese, Rahwa, Garza, Daniel R, Ruiter, Lilian N, de Jonge, Marien I, Belzer, Clara, Aalvink, Steven, Nagtegaal, Iris D, Dutilh, Bas E, Boleij, Annemarie, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Taddese, Rahwa, Garza, Daniel R, Ruiter, Lilian N, de Jonge, Marien I, Belzer, Clara, Aalvink, Steven, Nagtegaal, Iris D, Dutilh, Bas E, and Boleij, Annemarie
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- 2020
194. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Dempsey, Donald M, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max, Orton, Richard J, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Walker, Peter J, Siddell, Stuart G, Lefkowitz, Elliot J, Mushegian, Arcady R, Adriaenssens, Evelien M, Dempsey, Donald M, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Hendrickson, R Curtis, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max, Orton, Richard J, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J
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- 2020
195. Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering
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Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Plant-Microbe Interactions, Sub Bioinformatics, Klein, Joël, Neilen, Manon, van Verk, Marcel, Dutilh, Bas E, Van den Ackerveken, Guido, Plant Microbe Interactions, Theoretical Biology and Bioinformatics, Sub Plant-Microbe Interactions, Sub Bioinformatics, Klein, Joël, Neilen, Manon, van Verk, Marcel, Dutilh, Bas E, and Van den Ackerveken, Guido
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- 2020
196. Development of styrene maleic acid lipid particles (SMALPs) as a tool for studies of phage-host interactions
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, de Jonge, Patrick A, Smit Sibinga, Dieuwke J C, Boright, Oliver A, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, Dutilh, Bas E, Theoretical Biology and Bioinformatics, Sub Bioinformatics, de Jonge, Patrick A, Smit Sibinga, Dieuwke J C, Boright, Oliver A, Costa, Ana Rita, Nobrega, Franklin L, Brouns, Stan J J, and Dutilh, Bas E
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- 2020
197. Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Walter, Juline M, Coutinho, Felipe H, Leomil, Luciana, Hargreaves, Paulo I, Campeão, Mariana E, Vieira, Verônica V, Silva, Beatriz S, Fistarol, Giovana O, Salomon, Paulo S, Sawabe, Tomoo, Mino, Sayaka, Hosokawa, Masashi, Miyashita, Hideaki, Maruyama, Fumito, van Verk, Marcel C, Dutilh, Bas E, Thompson, Cristiane C, Thompson, Fabiano L, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Walter, Juline M, Coutinho, Felipe H, Leomil, Luciana, Hargreaves, Paulo I, Campeão, Mariana E, Vieira, Verônica V, Silva, Beatriz S, Fistarol, Giovana O, Salomon, Paulo S, Sawabe, Tomoo, Mino, Sayaka, Hosokawa, Masashi, Miyashita, Hideaki, Maruyama, Fumito, van Verk, Marcel C, Dutilh, Bas E, Thompson, Cristiane C, and Thompson, Fabiano L
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- 2020
198. Prophages are associated with extensive CRISPR-Cas auto-immunity
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Luzia de Nobrega, F. (author), Walinga, Hielke (author), Dutilh, Bas E. (author), Brouns, S.J.J. (author), Luzia de Nobrega, F. (author), Walinga, Hielke (author), Dutilh, Bas E. (author), and Brouns, S.J.J. (author)
- Abstract
CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS has been suggested to reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a regulatory mechanism for gene expression. Here we investigated the incidence, distribution, and evasion of STS in over 100 000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of escape from the potentially deleterious effects of STS by other mechanisms such as anti-CRISPR proteins and CRISPR target mutations. We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects as mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages., BN/Stan Brouns Lab
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- 2020
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199. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts
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de Jonge, P.A. (author), von Meijenfeldt, F. A.Bastiaan (author), Martins Costa, A.R. (author), Luzia de Nobrega, F. (author), Brouns, S.J.J. (author), Dutilh, Bas E. (author), de Jonge, P.A. (author), von Meijenfeldt, F. A.Bastiaan (author), Martins Costa, A.R. (author), Luzia de Nobrega, F. (author), Brouns, S.J.J. (author), and Dutilh, Bas E. (author)
- Abstract
An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes., BN/Stan Brouns Lab
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- 2020
- Full Text
- View/download PDF
200. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients?: A systematic review and meta-analysis
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, Nagtegaal, Iris D, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, and Nagtegaal, Iris D
- Published
- 2020
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