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

Informazioni relative al progetto

RuMicroPlas

ID dell’accordo di sovvenzione: 640384

DOI

10.3030/640384

Progetto chiuso

Data della firma CE 27 Agosto 2015

Data di avvio 1 Gennaio 2016

Data di completamento 31 Dicembre 2021

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 499 000,00

Contributo UE

€ 1 499 000,00

Coordinato da

BEN-GURION UNIVERSITY OF THE NEGEV
Israel

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (32)

Unravelling plasmidome distribution and interaction with its hosting microbiome

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

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

Autori: Nir Friedman; Elie Jami; Itzhak Mizrahi
Pubblicato in: Environmental Microbiology, Numero 1, 2017, ISSN 0000-0000
Editore: SFAM
DOI: 10.1111/1462-2920.13846

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

Autori: Shenhav, Liat; Furman, Ori; Briscoe, Leah; Thompson, Mike; Silverman, Justin D.; Mizrahi, Itzhak; Halperin, Eran
Pubblicato in: PLoS Computational Biology, Numero 20, 2019, ISSN 0000-0000
Editore: Plos
DOI: 10.1371/journal.pcbi.1006960

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

Autori: 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
Pubblicato in: Sciences Advances, Numero 9, 2019, ISSN 2375-2548
Editore: 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).

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

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

Autori: Lizi Bensoussan; Sarah Moraïs; Bareket Dassa; Nir Friedman; Bernard Henrissat; Vincent Lombard; Edward A. Bayer; Itzhak Mizrahi
Pubblicato in: Environmental Microbiology, Numero 2, 2017, ISSN 0000-0000
Editore: Wiley
DOI: 10.1111/1462-2920.13561

Segregational drift and the interplay between plasmid copy number and evolvability

Autori: Judith Ilhan; Anneke Kupczok; Christian Woehle; Tanita Wein; Nils F Huelter; Philip Rosenstiel; Giddy Landan; Itzhak Mizrahi; Tal Dagan
Pubblicato in: Molecular Biology and Evolution, Numero 21, 2018, ISSN 1537-1719
Editore: Oxford Academic
DOI: 10.1093/molbev/msy225

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

Autori: Wein, Tanita; Hülter, Nils F.; Mizrahi, Itzhak; Dagan, Tal
Pubblicato in: Nature Communications, Numero 1, 2019, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-10600-7

SCAPP: an algorithm for improved plasmid assembly in metagenomes

Autori: Pellow, D., Zorea, A., Probst, M. et al.
Pubblicato in: Microbiome, 2021, ISSN 2049-2618
Editore: 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

Autori: Yonit Ben-David; Sarah Moraïs; Sarah Moraïs; Edward A. Bayer; Itzhak Mizrahi
Pubblicato in: Microbial Biotechnology, Numero 1, 2020, ISSN 1751-7915
Editore: Wiley
DOI: 10.1111/1751-7915.13584

The rumen microbiome: balancing food security and environmental impacts

Autori: Itzhak Mizrahi 1 , R John Wallace 2 , Sarah Moraïs 3
Pubblicato in: Nature reviews microbiology, 2021, ISSN 1740-1526
Editore: Nature Publishing Group
DOI: 10.1038/s41579-021-00543-6

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

Autori: 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
Pubblicato in: Nature Biotechnology, 2021, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-021-01130-z

PlasClass improves plasmid sequence classification

Autori: David Pellow; Itzik Mizrahi; Ron Shamir
Pubblicato in: PLoS Computational Biology, Vol 16, Iss 4, p e1007781 (2020), Numero 4, 2020, ISSN 1553-7358
Editore: 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

Autori: 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
Pubblicato in: mBio, Numero 8/4, 2017, ISSN 2150-7511
Editore: American Society for Microbiology
DOI: 10.1128/mBio.00703-17

Insights Into Culturomics of the Rumen Microbiome

Autori: Tamar Zehavi, Maraike Probst, Itzhak Mizrahi
Pubblicato in: Frontiers in Microbiology, Numero 9, 2018, ISSN 1664-302X
Editore: 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

Autori: I. Mizrahi, E. Jami
Pubblicato in: animal, 2018, Pagina/e 1-13, ISSN 1751-7311
Editore: Cambridge University Press
DOI: 10.1017/S1751731118001957

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

Autori: Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir
Pubblicato in: Bioinformatics, 2016, Pagina/e btw651, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btw651

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

Autori: Sheerli Kruger Ben Shabat, Goor Sasson, Adi Doron-Faigenboim, Thomer Durman, Shamay Yaacoby, Margret E Berg Miller, Bryan A White, Naama Shterzer, Itzhak Mizrahi
Pubblicato in: The ISME Journal, Numero 10/12, 2016, Pagina/e 2958-2972, ISSN 1751-7362
Editore: 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

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

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

Autori: Yoav Shaani, Tamar Zehavi, Stav Eyal, Joshuah Miron, Itzhak Mizrahi
Pubblicato in: The ISME Journal, Numero 12/10, 2018, Pagina/e 2446-2457, ISSN 1751-7362
Editore: Nature Publishing Group
DOI: 10.1038/s41396-018-0203-0

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

Autori: 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
Pubblicato in: Frontiers in Microbiology, Numero 9, 2018, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2018.02161

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

Autori: Nir Friedman, Elie Jami, Itzhak Mizrahi
Pubblicato in: Environmental Microbiology, Numero 19/8, 2017, Pagina/e 3365-3373, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13846

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

Autori: Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Pubblicato in: Environmental Microbiology, Numero 19/1, 2017, Pagina/e 174-184, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.13551

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

Autori: Fotini Kokou, Goor Sasson, Tali Nitzan, Adi Doron-Faigenboim, Sheenan Harpaz, Avner Cnaani, Itzhak Mizrahi
Pubblicato in: eLife, Numero 7, 2018, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/eLife.36398

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

Autori: Sarah Moraïs, Itzhak Mizrahi
Pubblicato in: Trends in Microbiology, 2019, ISSN 0966-842X
Editore: Elsevier BV
DOI: 10.1016/j.tim.2018.12.011

Man-made microbial resistances in built environments

Autori: Mahnert, Alexander; Moissl-Eichinger, Christine; Zojer, Markus; Bogumil, David; Mizrahi, Itzhak; Rattei, Thomas; Martinez, José Luis; Berg, Gabriele
Pubblicato in: Nature Communications, Numero 15, 2019, ISSN 2041-1723
Editore: 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.

Autori: Itzhak Mizrahi; Elie Jami
Pubblicato in: animal, Numero 7, 2018, ISSN 1751-7311
Editore: 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.

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

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

Autori: Moraïs, Sarah; Mizrahi, Itzhak
Pubblicato in: FEMS Microbiology Reviews, Numero 3, 2019, ISSN 0168-6445
Editore: Blackwell
DOI: 10.1093/femsre/fuz007

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

Autori: 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,
Pubblicato in: Nature Biotechnology, Numero 16, 2021, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1101/2020.01.13.905091

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

Autori: Leonora S. Bittleston; Leonora S. Bittleston; Matti Gralka; Gabriel E. Leventhal; Itzhak Mizrahi; Otto X. Cordero
Pubblicato in: Nature Communications, Numero 6, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-15169-0

Disentangling the individual forces that shape the rumen microbiome

Autori: Itzhak Mizrahi; Elie Jami
Pubblicato in: EMBO, Numero 5, 2021, ISSN 1469-221X
Editore: Nature Publishing Group
DOI: 10.15252/embr.202052269