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

Informacje na temat projektu

RuMicroPlas

Identyfikator umowy o grant: 640384

DOI

10.3030/640384

Projekt został zamknięty

Data podpisania przez KE 27 Sierpnia 2015

Data rozpoczęcia 1 Stycznia 2016

Data zakończenia 31 Grudnia 2021

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 1 499 000,00

Wkład UE

€ 1 499 000,00

Koordynowany przez

BEN-GURION UNIVERSITY OF THE NEGEV
Israel

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (32)

Unravelling plasmidome distribution and interaction with its hosting microbiome

Autorzy: Brown Kav, Aya; Rozov, Roye; Bogumil, David; Sørensen, Søren Johannes; Hansen, Lars Hestbjerg; Benhar, Itai; Halperin, Eran; Shamir, Ron; Mizrahi, Itzhak
Opublikowane w: Environmental Microbiology, Numer 14, 2020, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14813

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

Autorzy: Nir Friedman; Elie Jami; Itzhak Mizrahi
Opublikowane w: Environmental Microbiology, Numer 1, 2017, ISSN 0000-0000
Wydawca: SFAM
DOI: 10.1111/1462-2920.13846

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

Autorzy: Shenhav, Liat; Furman, Ori; Briscoe, Leah; Thompson, Mike; Silverman, Justin D.; Mizrahi, Itzhak; Halperin, Eran
Opublikowane w: PLoS Computational Biology, Numer 20, 2019, ISSN 0000-0000
Wydawca: Plos
DOI: 10.1371/journal.pcbi.1006960

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

Autorzy: 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
Opublikowane w: Sciences Advances, Numer 9, 2019, ISSN 2375-2548
Wydawca: 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).

Autorzy: Kokou, Fotini; Con, Pazit; Barki, Assaf; Nitzan, Tali; Slosman, Tatiana; Mizrahi, Itzhak; Cnaani, Avner
Opublikowane w: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, Numer 8, 2019, ISSN 1095-6433
Wydawca: Elsevier BV
DOI: 10.1016/j.cbpa.2019.01.018

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

Autorzy: Lizi Bensoussan; Sarah Moraïs; Bareket Dassa; Nir Friedman; Bernard Henrissat; Vincent Lombard; Edward A. Bayer; Itzhak Mizrahi
Opublikowane w: Environmental Microbiology, Numer 2, 2017, ISSN 0000-0000
Wydawca: Wiley
DOI: 10.1111/1462-2920.13561

Segregational drift and the interplay between plasmid copy number and evolvability

Autorzy: Judith Ilhan; Anneke Kupczok; Christian Woehle; Tanita Wein; Nils F Huelter; Philip Rosenstiel; Giddy Landan; Itzhak Mizrahi; Tal Dagan
Opublikowane w: Molecular Biology and Evolution, Numer 21, 2018, ISSN 1537-1719
Wydawca: Oxford Academic
DOI: 10.1093/molbev/msy225

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

Autorzy: Wein, Tanita; Hülter, Nils F.; Mizrahi, Itzhak; Dagan, Tal
Opublikowane w: Nature Communications, Numer 1, 2019, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-019-10600-7

SCAPP: an algorithm for improved plasmid assembly in metagenomes

Autorzy: Pellow, D., Zorea, A., Probst, M. et al.
Opublikowane w: Microbiome, 2021, ISSN 2049-2618
Wydawca: 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

Autorzy: Yonit Ben-David; Sarah Moraïs; Sarah Moraïs; Edward A. Bayer; Itzhak Mizrahi
Opublikowane w: Microbial Biotechnology, Numer 1, 2020, ISSN 1751-7915
Wydawca: Wiley
DOI: 10.1111/1751-7915.13584

The rumen microbiome: balancing food security and environmental impacts

Autorzy: Itzhak Mizrahi 1 , R John Wallace 2 , Sarah Moraïs 3
Opublikowane w: Nature reviews microbiology, 2021, ISSN 1740-1526
Wydawca: Nature Publishing Group
DOI: 10.1038/s41579-021-00543-6

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

Autorzy: 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
Opublikowane w: Nature Biotechnology, 2021, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-021-01130-z

PlasClass improves plasmid sequence classification

Autorzy: David Pellow; Itzik Mizrahi; Ron Shamir
Opublikowane w: PLoS Computational Biology, Vol 16, Iss 4, p e1007781 (2020), Numer 4, 2020, ISSN 1553-7358
Wydawca: 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

Autorzy: 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
Opublikowane w: mBio, Numer 8/4, 2017, ISSN 2150-7511
Wydawca: American Society for Microbiology
DOI: 10.1128/mBio.00703-17

Insights Into Culturomics of the Rumen Microbiome

Autorzy: Tamar Zehavi, Maraike Probst, Itzhak Mizrahi
Opublikowane w: Frontiers in Microbiology, Numer 9, 2018, ISSN 1664-302X
Wydawca: 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

Autorzy: I. Mizrahi, E. Jami
Opublikowane w: animal, 2018, Strona(/y) 1-13, ISSN 1751-7311
Wydawca: Cambridge University Press
DOI: 10.1017/S1751731118001957

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

Autorzy: Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
Opublikowane w: Bioinformatics, 2016, Strona(/y) btw651, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btw651

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

Autorzy: Sheerli Kruger Ben Shabat, Goor Sasson, Adi Doron-Faigenboim, Thomer Durman, Shamay Yaacoby, Margret E Berg Miller, Bryan A White, Naama Shterzer, Itzhak Mizrahi
Opublikowane w: The ISME Journal, Numer 10/12, 2016, Strona(/y) 2958-2972, ISSN 1751-7362
Wydawca: 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

Autorzy: Johanna Stern, Sarah Moraïs, Yonit Ben-David, Rachel Salama, Melina Shamshoum, Raphael Lamed, Yuval Shoham, Edward A. Bayer, Itzhak Mizrahi
Opublikowane w: Applied and Environmental Microbiology, Numer 84/8, 2018, ISSN 0099-2240
Wydawca: American Society for Microbiology
DOI: 10.1128/AEM.00282-18

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

Autorzy: Yoav Shaani, Tamar Zehavi, Stav Eyal, Joshuah Miron, Itzhak Mizrahi
Opublikowane w: The ISME Journal, Numer 12/10, 2018, Strona(/y) 2446-2457, ISSN 1751-7362
Wydawca: Nature Publishing Group
DOI: 10.1038/s41396-018-0203-0

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

Autorzy: 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
Opublikowane w: Frontiers in Microbiology, Numer 9, 2018, ISSN 1664-302X
Wydawca: Frontiers Media
DOI: 10.3389/fmicb.2018.02161

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

Autorzy: Nir Friedman, Elie Jami, Itzhak Mizrahi
Opublikowane w: Environmental Microbiology, Numer 19/8, 2017, Strona(/y) 3365-3373, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13846

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

Autorzy: Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Opublikowane w: Environmental Microbiology, Numer 19/1, 2017, Strona(/y) 174-184, ISSN 1462-2912
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13551

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

Autorzy: Fotini Kokou, Goor Sasson, Tali Nitzan, Adi Doron-Faigenboim, Sheenan Harpaz, Avner Cnaani, Itzhak Mizrahi
Opublikowane w: eLife, Numer 7, 2018, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/eLife.36398

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

Autorzy: Sarah Moraïs, Itzhak Mizrahi
Opublikowane w: Trends in Microbiology, 2019, ISSN 0966-842X
Wydawca: Elsevier BV
DOI: 10.1016/j.tim.2018.12.011

Man-made microbial resistances in built environments

Autorzy: Mahnert, Alexander; Moissl-Eichinger, Christine; Zojer, Markus; Bogumil, David; Mizrahi, Itzhak; Rattei, Thomas; Martinez, José Luis; Berg, Gabriele
Opublikowane w: Nature Communications, Numer 15, 2019, ISSN 2041-1723
Wydawca: 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.

Autorzy: Itzhak Mizrahi; Elie Jami
Opublikowane w: animal, Numer 7, 2018, ISSN 1751-7311
Wydawca: 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.

Autorzy: Stern, Johanna; Moraïs, Sarah; Ben-David, Yonit; Salama, Rachel; Shamshoum, Melina; Lamed, Raphael; Shoham, Yuval; Bayer, Edward A.; Mizrahi, Itzhak
Opublikowane w: AEM, Numer 8, 2018, ISSN 0000-0000
Wydawca: American Society for microbiology
DOI: 10.1128/aem.00282-18

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

Autorzy: Moraïs, Sarah; Mizrahi, Itzhak
Opublikowane w: FEMS Microbiology Reviews, Numer 3, 2019, ISSN 0168-6445
Wydawca: Blackwell
DOI: 10.1093/femsre/fuz007

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

Autorzy: 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,
Opublikowane w: Nature Biotechnology, Numer 16, 2021, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1101/2020.01.13.905091

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

Autorzy: Leonora S. Bittleston; Leonora S. Bittleston; Matti Gralka; Gabriel E. Leventhal; Itzhak Mizrahi; Otto X. Cordero
Opublikowane w: Nature Communications, Numer 6, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-15169-0

Disentangling the individual forces that shape the rumen microbiome

Autorzy: Itzhak Mizrahi; Elie Jami
Opublikowane w: EMBO, Numer 5, 2021, ISSN 1469-221X
Wydawca: Nature Publishing Group
DOI: 10.15252/embr.202052269