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1. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.

Published
2023
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3. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

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.

Published
2021
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6. Meeting Report of the Second Symposium of the Belgian Society for Viruses of Microbes and Launch of the Phage Valley

Author

Desmecht, Salomé, Latka, Agnieszka, Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima Mendez, Gipsi, Matthijnssens, Jelle, Vázquez, Roberto, Venneman, Jolien, Wagemans, Jeroen, Briers, Yves, Thiry, Damien, Desmecht, Salomé, Latka, Agnieszka, Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima Mendez, Gipsi, Matthijnssens, Jelle, Vázquez, Roberto, Venneman, Jolien, Wagemans, Jeroen, Briers, Yves, and Thiry, Damien

Abstract

The second symposium of the Belgian Society for Viruses of Microbes (BSVoM) took place on 8 September 2023 at the University of Liège with 141 participants from 10 countries. The meeting program covered three thematic sessions opened by international keynote speakers: two sessions were devoted to “Fundamental research in phage ecology and biology” and the third one to the “Present and future applications of phages”. During this one day symposium, four invited keynote lectures, nine selected talks and eight student pitches were given along with thirty presented posters. The president of the Belgian Society for Viruses of Microbes, Prof. Yves Briers, took advantage of this symposium to launch the Phage Valley concept that will put the spotlight on the exceptionally high density of researchers investigating viruses of microbes as well as the successful triple helix approach between academia, industry and government in Belgium., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2024

7. Meeting Report of the Second Symposium of the Belgian Society for Viruses of Microbes and Launch of the Phage Valley

Author

Desmecht, Salomé, primary, Latka, Agnieszka, additional, Ceyssens, Pieter-Jan, additional, Garcia-Pino, Abel, additional, Gillis, Annika, additional, Lavigne, Rob, additional, Lima-Mendez, Gipsi, additional, Matthijnssens, Jelle, additional, Vázquez, Roberto, additional, Venneman, Jolien, additional, Wagemans, Jeroen, additional, Briers, Yves, additional, and Thiry, Damien, additional

Published
2024
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8. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

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, Edwards, Rob A., 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., and Krupovic, Mart

Published
2020
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12. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M., Wittmann, Johannes, Kuhn, Jens H., Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E., Jang, Ho Bin, van Zyl, Leonardo J., Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I., Rumnieks, Janis, Edwards, Robert A., Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K., Kropinski, Andrew M., Barylski, Jakub, Gillis, Annika, Clokie, Martha R. C., Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., and Rodney Brister, J.

Published
2018
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13. Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium

Author

Latka, Agnieszka, primary, Aertsen, Abram, additional, Boeckaerts, Dimitri, additional, Blasdel, Bob, additional, Ceyssens, Pieter-Jan, additional, Garcia-Pino, Abel, additional, Gillis, Annika, additional, Lavigne, Rob, additional, Lima-Mendez, Gipsi, additional, Matthijnssens, Jelle, additional, Onsea, Jolien, additional, Peeters, Eveline, additional, Pirnay, Jean-Paul, additional, Thiry, Damien, additional, Vandenheuvel, Dieter, additional, Van Mechelen, Els, additional, Venneman, Jolien, additional, Verbeken, Gilbert, additional, Wagemans, Jeroen, additional, and Briers, Yves, additional

Published
2023
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14. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M.

Abstract

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

Published
2023

15. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Turner, Dann, Shkoporov, Andrey N, Lood, Cédric, Millard, Andrew D, Dutilh, Bas E, Alfenas-Zerbini, Poliane, van Zyl, Leonardo J, Aziz, Ramy K, Oksanen, Hanna M, Poranen, Minna M, Kropinski, Andrew M, Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A, Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, B L, Sullivan, Matthew B, Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, and Adriaenssens, Evelien M

Published
2023

16. Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium

Author

Latka, Agnieszka, Aertsen, Abram, Boeckaerts, Dimitri, Blasdel, Bob B.G., Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima Mendez, Gipsi, Matthijnssens, Jelle, Onsea, Jolien, Peeters, Eveline, Pirnay, Jean-Paul, Thiry, Damien, Vandenheuvel, Dieter, Van Mechelen, Els, Venneman, Jolien, Verbeken, Gilbert, Wagemans, Jeroen, Briers, Yves, Latka, Agnieszka, Aertsen, Abram, Boeckaerts, Dimitri, Blasdel, Bob B.G., Ceyssens, Pieter-Jan, Garcia-Pino, Abel, Gillis, Annika, Lavigne, Rob, Lima Mendez, Gipsi, Matthijnssens, Jelle, Onsea, Jolien, Peeters, Eveline, Pirnay, Jean-Paul, Thiry, Damien, Vandenheuvel, Dieter, Van Mechelen, Els, Venneman, Jolien, Verbeken, Gilbert, Wagemans, Jeroen, and Briers, Yves

Abstract

The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of microbial virus researchers in Belgium. The sixteen founders are affiliated to fourteen different research entities across academia, industry and government. Its inaugural symposium was held on 23 September 2022 in the Thermotechnical Institute at KU Leuven. The meeting program covered three thematic sessions launched by international keynote speakers: (1) virus–host interactions, (2) viral ecology, evolution and diversity and (3) present and future applications. During the one-day symposium, four invited keynote lectures, ten selected talks and eight student pitches were given along with 41 presented posters. The meeting hosted 155 participants from twelve countries., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2023

19. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

Author

Adriaenssens, Evelien M., Krupovic, Mart, Knezevic, Petar, Ackermann, Hans-Wolfgang, Barylski, Jakub, Brister, J. Rodney, Clokie, Martha R. C., Duffy, Siobain, Dutilh, Bas E., Edwards, Robert A., Enault, Francois, Jang, Ho Bin, Klumpp, Jochen, Kropinski, Andrew M., Lavigne, Rob, Poranen, Minna M., Prangishvili, David, Rumnieks, Janis, Sullivan, Matthew B., Wittmann, Johannes, Oksanen, Hanna M., Gillis, Annika, and Kuhn, Jens H.

Published
2017
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23. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

Author

Krupovic, Mart, Dutilh, Bas E., Adriaenssens, Evelien M., Wittmann, Johannes, Vogensen, Finn K., Sullivan, Mathew B., Rumnieks, Janis, Prangishvili, David, Lavigne, Rob, Kropinski, Andrew M., Klumpp, Jochen, Gillis, Annika, Enault, Francois, Edwards, Rob A., Duffy, Siobain, Clokie, Martha R. C., Barylski, Jakub, Ackermann, Hans-Wolfgang, and Kuhn, Jens H.

Published
2016
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26. Conjugation across Bacillus cereus and kin: A review

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Hinnekens, Pauline, Fayad, Nancy, Gillis, Annika, Mahillon, Jacques, UCL - SST/ELI/ELIM - Applied Microbiology, Hinnekens, Pauline, Fayad, Nancy, Gillis, Annika, and Mahillon, Jacques

Abstract

Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. Bacillus cereus and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of B. cereus sensu lato (s.l.) 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from B. cereus isolates have been reported as conjugative. However, with the increasing number of genomic data available, in silico analyses indicate that more plasmids from B. cereus s.l. genomes present self-transfer potential. B. cereus s.l. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of B. cereus s.l., it is of prime importance to consider the impact of conjugation within this bacterial group.

Published
2022

27. Virtual Proficiency Testing in food microbiology

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Abdel Massih, Marleen, Ferber, Fabienne, Pitchugina, Elena, Mahillon, Jacques, Gillis, Annika, UCL - SST/ELI/ELIM - Applied Microbiology, Abdel Massih, Marleen, Ferber, Fabienne, Pitchugina, Elena, Mahillon, Jacques, and Gillis, Annika

Published
2022

34. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, 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., Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, 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., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, 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.

Published
2021

35. Bacillus cytotoxicus Genomics: Chromosomal Diversity and Plasmidome Versatility

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Fayad, Nancy, Koné, Klèma Marcel, Gillis, Annika, Mahillon, Jacques, UCL - SST/ELI/ELIM - Applied Microbiology, Fayad, Nancy, Koné, Klèma Marcel, Gillis, Annika, and Mahillon, Jacques

Abstract

Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.

Published
2021

36. Bacilysin within the Bacillus subtilis group: gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Nannan, Catherine, Vu, Huong Quynh, Gillis, Annika, Caulier, Simon, Nguyen, Thuy Thanh Thi, Mahillon, Jacques, UCL - SST/ELI/ELIM - Applied Microbiology, Nannan, Catherine, Vu, Huong Quynh, Gillis, Annika, Caulier, Simon, Nguyen, Thuy Thanh Thi, and Mahillon, Jacques

Abstract

The Bacillus subtilis group comprises species known for their ability to produce a wide variety of antimicrobial peptides. This work focuses on bacilysin, a broad-spectrum active dipeptide, and its prevalence in the B. subtilis group. In silico genome analysis of strains from Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus licheniformis, Bacillus pumilus and B. subtilis subspecies inaquosorum, spizizenii and subtilis revealed that the bacilysin gene cluster is present in all species except for B. licheniformis. This observation was corroborated by PCR detection of the bacilysin genetic determinants on a collection of 168 food and environmental strains from the B. subtilis group. Phylogenetic analyses also demonstrated that the bacilysin gene cluster sequence showed more than 80 % identity within each species of the B. subtilis group. An in vitro screening of the strain collection was performed against foodborne pathogens. Twenty-three strains were selected for their ability of their Cell-Free Supernatant to inhibit foodborne pathogens. After an ammonium sulphate precipitation of their supernatant, eight strains, all belonging to B. velezensis, exhibited antimicrobial activity against Gram-negative pathogens. Using Ultra High Performance Liquid Chromatography - Mass Spectrometry, the presence of bacilysin was confirmed in these eight precipitates. These findings provide evidence that bacilysin is a major player in the antagonistic activity of B. velezensis against Gram-negative foodborne pathogens.

Published
2021

37. Modifications of cell wall polymers in Gram-positive bacteria by multi-component transmembrane glycosylation systems

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Rismondo, Jeanine, Gillis, Annika, Gründling, Angelika, UCL - SST/ELI/ELIM - Applied Microbiology, Rismondo, Jeanine, Gillis, Annika, and Gründling, Angelika

Abstract

Secondary cell wall polymers fulfil diverse and important functions within the cell wall of Gram-positive bacteria. Here, we will provide a brief overview of the principles of teichoic acid and complex secondary cell wall polysaccharide biosynthesis pathways in Firmicutes and summarize the recently revised mechanism for the decoration of teichoic acids with d-alanines. Many cell wall polymers are decorated with glycosyl groups, either intracellularly or extracellularly. The main focus of this review will be on the extracellular glycosylation mechanism and recent advances that have been made in the identification of enzymes involved in this process. Based on the proteins involved, we propose to rename the system to multi-component transmembrane glycosylation system in place of three-component glycosylation system.

Published
2021

38. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

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).

Published
2021

39. Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Gillis, Annika, Hock, Louise, Mahillon, Jacques, UCL - SST/ELI/ELIM - Applied Microbiology, Gillis, Annika, Hock, Louise, and Mahillon, Jacques

Abstract

Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.

Published
2021

40. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021

Author

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).

Published
2021

42. Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M, Sullivan, Matthew B., Knezevic, Petar, van Zyl, Leonardo J., Sarkar, BL, Dutilh, Bas E., Alfenas-Zerbini, Poliane, Lobocka, Malgorzata, Tong, Yigang, Brister, J. Rodney, Moreno Switt, Andrea I., Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Edwards, Rob A, Kropinski, Andrew M., Petty, Nicola K, Clokie, Martha R. C., 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, François, Turner, Dann, Poranen, Minna, Oksanen, Hanna M, Krupovic, Mart, Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Molecular and Translational Virology

Subjects
11832 Microbiology and virology, VIRION, SSDNA, PHAGE, HIS1, CLASSIFICATION
Abstract

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.

Published
2020

43. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo B P, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, Adriaenssens, Evelien M, Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo B P, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, and Adriaenssens, Evelien M

Abstract

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order - Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods - including comparative genomics, core genome analysis, and marker gene phylogenetics - to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae - a new taxon of the same rank. In the process of the taxon evaluation we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone towards much-needed re-classification in the Caudovirales order.

Published
2020

44. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, 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, 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, and Krupovic, Mart

Published
2020

45. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo B P, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, Adriaenssens, Evelien M, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo B P, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, and Adriaenssens, Evelien M

Published
2020

46. Characterization of PlyB221 and PlyP32, Two Novel Endolysins Encoded by Phages Preying on the Bacillus cereus Group

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Leprince, Audrey, Nuytten, Manon, Gillis, Annika, Mahillon, Jacques, UCL - SST/ELI/ELIM - Applied Microbiology, Leprince, Audrey, Nuytten, Manon, Gillis, Annika, and Mahillon, Jacques

Abstract

Endolysins are phage-encoded enzymes implicated in the breaching of the bacterial cell wall at the end of the viral cycle. This study focuses on the endolysins of Deep-Blue (PlyB221) and Deep-Purple (PlyP32), two phages preying on the Bacillus cereus group. Both enzymes exhibit a typical modular organization with an enzymatically active domain (EAD) located in the N-terminal and a cell wall binding domain (CBD) in the C-terminal part of the protein. In silico analysis indicated that the EAD domains of PlyB221 and PlyP32 are endowed with peptidase and muramidase activities, respectively, whereas in both proteins SH3 domains are involved in the CBD. To evaluate their antimicrobial properties and binding specificity, both endolysins were expressed and purified. PlyB221 and PlyP32 efficiently recognized and lysed all the tested strains from the B. cereus group. Biochemical characterization showed that PlyB221 activity was stable under a wide range of pHs (5–9), NaCl concentrations (up to 200 mM), and temperature treatments (up to 50 °C). Although PlyP32 activity was less stable than that of PlyB221, the endolysin displayed high activity at pH 6–7, NaCl concentration up to 100 mM and the temperature treatment up to 45 °C. Overall, PlyB221 and PlyP32 display suitable characteristics for the development of biocontrol and detection tools.

Published
2020

47. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

UCL - SST/ELI/ELIM - Applied Microbiology, 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, Edwards, Rob A., 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, UCL - SST/ELI/ELIM - Applied Microbiology, 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, Edwards, Rob A., 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., and Krupovic, Mart

Abstract

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.

Published
2020

48. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo BP, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, Adriaenssens, Evelien M, UCL - SST/ELI/ELIM - Applied Microbiology, Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo BP, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, and Adriaenssens, Evelien M

Abstract

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.

Published
2020

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