The Plasmidome: a Driving Force of Rumen Microbial Evolution from Birth to Adulthood

Project Information

RuMicroPlas

Grant agreement ID: 640384

DOI

10.3030/640384

Project closed

EC signature date 27 August 2015

Start date 1 January 2016

End date 31 December 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 000,00

EU contribution

€ 1 499 000,00

Coordinated by

BEN-GURION UNIVERSITY OF THE NEGEV
Israel

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (32)

Unravelling plasmidome distribution and interaction with its hosting microbiome

Author(s): Brown Kav, Aya; Rozov, Roye; Bogumil, David; Sørensen, Søren Johannes; Hansen, Lars Hestbjerg; Benhar, Itai; Halperin, Eran; Shamir, Ron; Mizrahi, Itzhak
Published in: Environmental Microbiology, Issue 14, 2020, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14813

Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages.

Author(s): Nir Friedman; Elie Jami; Itzhak Mizrahi
Published in: Environmental Microbiology, Issue 1, 2017, ISSN 0000-0000
Publisher: SFAM
DOI: 10.1111/1462-2920.13846

Modeling the temporal dynamics of the gut microbial community in adults and infants.

Author(s): Shenhav, Liat; Furman, Ori; Briscoe, Leah; Thompson, Mike; Silverman, Justin D.; Mizrahi, Itzhak; Halperin, Eran
Published in: PLoS Computational Biology, Issue 20, 2019, ISSN 0000-0000
Publisher: Plos
DOI: 10.1371/journal.pcbi.1006960

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

Author(s): Wallace, R. John; Sasson, Goor; Garnsworthy, Philip C.; Tapio, Ilma; Gregson, Emma; Bani, Paolo; Huhtanen, Pekka; Bayat, Ali R.; Strozzi, Francesco; Biscarini, Filippo; Snelling, Timothy J.; Saunders, Neil; Potterton, Sarah L.; Craigon, James; Minuti, Andrea; Trevisi, Erminio; Callegari, Maria L.; Cappelli, Fiorenzo Piccioli; Cabezas-Garcia, Edward H.; Vilkki, Johanna; Pinares-Patino, Cesar; Flieg
Published in: Sciences Advances, Issue 9, 2019, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.aav8391

Short- and long-term low-salinity acclimation effects on the branchial and intestinal gene expression in the European seabass (Dicentrarchus labrax).

Author(s): Kokou, Fotini; Con, Pazit; Barki, Assaf; Nitzan, Tali; Slosman, Tatiana; Mizrahi, Itzhak; Cnaani, Avner
Published in: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, Issue 8, 2019, ISSN 1095-6433
Publisher: Elsevier BV
DOI: 10.1016/j.cbpa.2019.01.018

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome.

Author(s): Lizi Bensoussan; Sarah Moraïs; Bareket Dassa; Nir Friedman; Bernard Henrissat; Vincent Lombard; Edward A. Bayer; Itzhak Mizrahi
Published in: Environmental Microbiology, Issue 2, 2017, ISSN 0000-0000
Publisher: Wiley
DOI: 10.1111/1462-2920.13561

Segregational drift and the interplay between plasmid copy number and evolvability

Author(s): Judith Ilhan; Anneke Kupczok; Christian Woehle; Tanita Wein; Nils F Huelter; Philip Rosenstiel; Giddy Landan; Itzhak Mizrahi; Tal Dagan
Published in: Molecular Biology and Evolution, Issue 21, 2018, ISSN 1537-1719
Publisher: Oxford Academic
DOI: 10.1093/molbev/msy225

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance.

Author(s): Wein, Tanita; Hülter, Nils F.; Mizrahi, Itzhak; Dagan, Tal
Published in: Nature Communications, Issue 1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-10600-7

SCAPP: an algorithm for improved plasmid assembly in metagenomes

Author(s): Pellow, D., Zorea, A., Probst, M. et al.
Published in: Microbiome, 2021, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-021-01068-z

Rapid adaptation for fibre degradation by changes in plasmid stoichiometry within Lactobacillus plantarum at the synthetic community level

Author(s): Yonit Ben-David; Sarah Moraïs; Sarah Moraïs; Edward A. Bayer; Itzhak Mizrahi
Published in: Microbial Biotechnology, Issue 1, 2020, ISSN 1751-7915
Publisher: Wiley
DOI: 10.1111/1751-7915.13584

The rumen microbiome: balancing food security and environmental impacts

Author(s): Itzhak Mizrahi 1 , R John Wallace 2 , Sarah Moraïs 3
Published in: Nature reviews microbiology, 2021, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-021-00543-6

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Author(s): Derek M. Bickhart, Mikhail Kolmogorov, Elizabeth Tseng, Daniel M. Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, Ivan Liachko, Shawn T. Sullivan, Sung Bong Shin, Alvah Zorea, Victòria Pascal Andreu, Kevin Panke-Buisse, Marnix H. Medema, Itzhak Mizrahi, Pavel A. Pevzner & Timothy P. L. Smith
Published in: Nature Biotechnology, 2021, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-021-01130-z

PlasClass improves plasmid sequence classification

Author(s): David Pellow; Itzik Mizrahi; Ron Shamir
Published in: PLoS Computational Biology, Vol 16, Iss 4, p e1007781 (2020), Issue 4, 2020, ISSN 1553-7358
Publisher: Public Library of Science (PLoS)
DOI: 10.1101/783571

Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow’s Capacity To Harvest Energy from Its Feed

Author(s): Goor Sasson, Sheerli Kruger Ben-Shabat, Eyal Seroussi, Adi Doron-Faigenboim, Naama Shterzer, Shamay Yaacoby, Margret E. Berg Miller, Bryan A. White, Eran Halperin, Itzhak Mizrahi
Published in: mBio, Issue 8/4, 2017, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mBio.00703-17

Insights Into Culturomics of the Rumen Microbiome

Author(s): Tamar Zehavi, Maraike Probst, Itzhak Mizrahi
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.01999

Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission

Author(s): I. Mizrahi, E. Jami
Published in: animal, 2018, Page(s) 1-13, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1017/S1751731118001957

Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Author(s): Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
Published in: Bioinformatics, 2016, Page(s) btw651, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btw651

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

Author(s): Sheerli Kruger Ben Shabat, Goor Sasson, Adi Doron-Faigenboim, Thomer Durman, Shamay Yaacoby, Margret E Berg Miller, Bryan A White, Naama Shterzer, Itzhak Mizrahi
Published in: The ISME Journal, Issue 10/12, 2016, Page(s) 2958-2972, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/ismej.2016.62

Assembly of Synthetic Functional Cellulosomal Structures onto the Cell Surface of Lactobacillus plantarum , a Potent Member of the Gut Microbiome

Author(s): Johanna Stern, Sarah Moraïs, Yonit Ben-David, Rachel Salama, Melina Shamshoum, Raphael Lamed, Yuval Shoham, Edward A. Bayer, Itzhak Mizrahi
Published in: Applied and Environmental Microbiology, Issue 84/8, 2018, ISSN 0099-2240
Publisher: American Society for Microbiology
DOI: 10.1128/AEM.00282-18

Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects

Author(s): Yoav Shaani, Tamar Zehavi, Stav Eyal, Joshuah Miron, Itzhak Mizrahi
Published in: The ISME Journal, Issue 12/10, 2018, Page(s) 2446-2457, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-018-0203-0

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

Author(s): Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, Milka Popova, Rafael Muñoz-Tamayo, Evelyne Forano, Sinead M. Waters, Matthias Hess, Ilma Tapio, Hauke Smidt, Sophie J. Krizsan, David R. Yáñez-Ruiz, Alejandro Belanche, Leluo Guan, Robert J. Gruninger, Tim A. McAllister, C. Jamie Newbold, Rainer Roehe, Richard J. Dewhurst, Tim J. Snelling, Mick Watson, Gar
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2018.02161

Compositional and functional dynamics of the bovine rumen methanogenic community across different developmental stages

Author(s): Nir Friedman, Elie Jami, Itzhak Mizrahi
Published in: Environmental Microbiology, Issue 19/8, 2017, Page(s) 3365-3373, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13846

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community

Author(s): Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Published in: Environmental Microbiology, Issue 19/1, 2017, Page(s) 174-184, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13551

Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature

Author(s): Fotini Kokou, Goor Sasson, Tali Nitzan, Adi Doron-Faigenboim, Sheenan Harpaz, Avner Cnaani, Itzhak Mizrahi
Published in: eLife, Issue 7, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.36398

The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States

Author(s): Sarah Moraïs, Itzhak Mizrahi
Published in: Trends in Microbiology, 2019, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2018.12.011

Man-made microbial resistances in built environments

Author(s): Mahnert, Alexander; Moissl-Eichinger, Christine; Zojer, Markus; Bogumil, David; Mizrahi, Itzhak; Rattei, Thomas; Martinez, José Luis; Berg, Gabriele
Published in: Nature Communications, Issue 15, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08864-0

Review: The compositional variation of the rumen microbiome and its effect on host performance and methane emission.

Author(s): Itzhak Mizrahi; Elie Jami
Published in: animal, Issue 7, 2018, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1017/s1751731118001957

Assembly of Synthetic Functional Cellulosomal Structures onto the Cell Surface of Lactobacillus plantarum, a Potent Member of the Gut Microbiome.

Author(s): Stern, Johanna; Moraïs, Sarah; Ben-David, Yonit; Salama, Rachel; Shamshoum, Melina; Lamed, Raphael; Shoham, Yuval; Bayer, Edward A.; Mizrahi, Itzhak
Published in: AEM, Issue 8, 2018, ISSN 0000-0000
Publisher: American Society for microbiology
DOI: 10.1128/aem.00282-18

Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem.

Author(s): Moraïs, Sarah; Mizrahi, Itzhak
Published in: FEMS Microbiology Reviews, Issue 3, 2019, ISSN 0168-6445
Publisher: Blackwell
DOI: 10.1093/femsre/fuz007

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS

Author(s): Aksenov, Alexander A.; Laponogov, Ivan; Zhang, Zheng; Doran, Sophie LF; Belluomo, Ilaria; Veselkov, Dennis; Bittremieux, Wout; Nothias, Louis Felix; Nothias-Esposito, Mélissa; Maloney, Katherine N.; Misra, Biswapriya B.; Melnik, Alexey V.; Jones II, Kenneth L.; Dorrestein, Kathleen; Panitchpakdi, Morgan; Ernst, Madeleine; van der Hooft, Justin J.J.; Gonzalez, Mabel; Carazzone, Chiara; Amézquita,
Published in: Nature Biotechnology, Issue 16, 2021, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1101/2020.01.13.905091

Context-dependent dynamics lead to the assembly of functionally distinct microbial communities.

Author(s): Leonora S. Bittleston; Leonora S. Bittleston; Matti Gralka; Gabriel E. Leventhal; Itzhak Mizrahi; Otto X. Cordero
Published in: Nature Communications, Issue 6, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15169-0

Disentangling the individual forces that shape the rumen microbiome

Author(s): Itzhak Mizrahi; Elie Jami
Published in: EMBO, Issue 5, 2021, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.15252/embr.202052269