Microbiome Bioinformatics

Dr. Itai Sharon

Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT

Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., Horn, M., Cohen, Y., Moor, A.E., Zeevi, D., Korem, T., Kotler, E., Harmelin, A., Itzkovitz, S., Maharshak, N., Shibolet, O., Pevsner-Fischer, M., Shapiro, H., Sharon, I., Halpern, Z., Segal, S. and Elinav, E.
2018

Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features

Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., Cohen, Y., Linevsky, R., Rothschild, D., Moor, A.E., Ben-Moshe, S., Harmelin, A., Itzkovitz, S., Maharshak, N., Shibolet, O., Shapiro, H., Pevsner-Fischer, M., Sharon, I., Halpern, Z., Segal, E. and Elinav, E.
2018

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems.

Burstein, D., Sun, C.L., Brown, C.T., Sharon, I., Anantharaman, K., Probst, A.J., Thomas, B.C., Banfield, J.F.
Nat Commun, 2016
2016

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.

Wrighton, K.C., Castelle, C.J., Varaljay, V.A., Satagopan, S., Brown, C.T., Wilkins, M.J., Thomas, B.C., Sharon, I., Williams, K.H., Tabita, F.R., Banfield, J.F.
ISME J. 2016
2016

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.

Hug, L.A., Thomas, B.C., Sharon, I., Brown, C.T., Sharma, R., Hettich, R.L., Wilkins, M.J., Williams, K.H., Singh, A., Banfield, J.F.
Environ Microbiol. 2016 Volume 18 Issue 1 Pages 159-173
2016

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Anantharaman, K., Brown, C.T., Hug, L.A., Sharon, I., Castelle, C.J., Probst, A.J., Thomas, B.C., Singh, A., Wilkins, M.J., Karaoz, U., Brodie, E.L., Williams, K.H., Hubbard, S.S., Banfield, J.F.
Nat Commun 2016 Issue 13219 (2016)
2016

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

Raveh-Sadka, T., Firek, B., Sharon, I., Baker, R., Brown, C.T., Thomas, B.C., Morowitz, M.J., Banfield, J.F.
ISME J. 2016
2016

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations.

Probst, A.J., Castelle, C.J., Singh, A., Brown, C.T., Anantharaman, K., Sharon, I., Hug, L.A., Burstein, D., Emerson, J.B., Thomas, B.C., Banfield, J.F.
Eviron Microbiol. 2016
2016

CRISPR immunity drives rapid phage genome evolution.

Paez-Espino, D., Sharon, I., Morovic, W., Stahl, B., Thomas, B.C., Barrangou, R., Banfield, J.F.
mBio 2015 Volume 6 Issue 2 Pages e00262-15
2015

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Hug, L.A., Thomas, B.C., Sharon, I., Brown, C.T., Sharma, R., Hettich, R.L., Wilkins, M.J., Williams, K.H., Singh, A., Banfield, J.F.
Environ Microbiol 2015
2015

Gut bacteria are rarely shared by cohospitalized premature infants, regardless of necrotizing enterocolitis development

Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., Banfield, J.F.
eLife 2015 Volume 4 Pages e05477
2015

Unusual biology across a group comprising more than 15% of domain Bacteria

Brown, C.T., Hug, L.A., Thomas, B.C., Sharon, I., Castelle, C.J., Singh, A., Wilkins, M.J., Wrighton, K.C., Williams, K.H. and Banfield, J.F.
Nature 2015
2015

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Sharon, I., Kertesz, M., Hug, L.A., Pushkarev, D., Blauwkamp, T.A., Castelle, C.J., Amirebrahimi, M., Thomas, B.C., Burstein, D., Tringe, S.G., Williams, K.H., Banfield, J.F.
Genome Res 2015 Volume 25 Pages 534-543
2015

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Brooks, B., Firek, B.A., Miller, C.S., Sharon, I., Thomas, B.C., Baker, R., Morowitz, M.J., Banfield, J.F.
Microbiome 2014 Volume 2 Issue 1
2014

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Wrighton, K.C., Castelle, C.J., Wilkins, M.J., Hug, L.A., Sharon, I., Thomas, B.C., Handley, K.M., Mullin, S.W., Nicora, C.D., Singh, A., Lipton, M.S., Long, P.E., Williams, K.H., Banfield, J.F.
ISME J 2014 Volume 8 Issue 7 Pages 1452-1463
2014

Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla

Kantor, R.S., Wrighton, K.C., Handley, K.M., Sharon, I., Hug, L.A., Castelle, C.J., Thomas, B.C., Banfield, J.F
mBio 2013 Volume 4 Issue 5 Pages e00708-13
2013

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

Di Rienzi, S.C.*, Sharon, I.*, Wrighton, K.C., Koren, O., Hug, L.A., Thomas, B.C., Goodrich, J.K., Bell, J.T., Spector, T.D., Banfield, J.F., Ley, R.E.
eLife 2013 Volume 2 Pages e01102
2013

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

Hug, L.A., Castelle, C.J., Wrighton, K.C., Thomas, B.C., Sharon, I., Frischkorn, K.R., Williams, K.H., Tringe, S.G., Banfield, J.F
Microbiome 2013 Volume 1 Issue 22
2013

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

Sharon, I., Morowitz, M.J., Thomas, B.C., Costello, E.K., Relman, D.A., Banfield, J.F
Genome Res 2013 Volume 23 Issue 1 Pages 111-120
2013

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

Brown, C.T., Sharon, I., Thomas, B.C., Castelle, C.J., Morowitz, M.J., Banfield, J.F.
Microbiome 2013 Volume 1 Issue 30
2013

Perspective: Genomes from metagenomics

Sharon, I., Banfield, J.F.
Science 2013 Volume 342 Issue 6162 Pages 1057-1058
2013

Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

Handley, K.M., VerBerkmoes, N.C., Steefel, C.I., Williams, K.H., Sharon, I., Miller, C.S., Frischkorn, K.R., Chourey, K., Thomas, B.C., Shah, M.B., Long, P.E., Hettich, R.L., Banfield, J.F
ISME J 2012 Volume 7 Issue 4 Pages 800-816
2012

Fermentation, Hydrogen and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Wrighton, K.C., Thomas, B.C., Sharon, I., Miller, C.S., Castelle, C.J., VerBerkmoes, N.C., Wilkins, M.J., Hettich, R.J., Lipton, M.S., Williams, K.H., Long, P.E., Banfield, J.F
Science 2012 Volume 337 Issue 6102 Pages 1661-1665
2012

Comparative metagenomics of microbial traits within oceanic viral communities

Sharon, I., Battchikova, N., Aro, E.-M., Giglione, C., Meinnel, T., Glaser, F., Pinter, R.Y., Breitbart, M., Rohwer, F., Béjà, O
ISME J 2011 Volume 5 Issue 7 Pages 1178-1190
2011

Genomic island variability facilitates Prochlorococcus-virus coexistence

Avrani, S., Wurtzel, O., Sharon, I., Sorek, R., Lindell, D
Nature 2011 Volume 474 Pages 604-608
2011