Koren Lab

Scientific papers:


Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P & N Segata. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.
Cell Host Microbe. 2018 Jul 11;24(1):133-145

Neuman H, Forsythe P, Uzan A, Avni O* & O. Koren* Antibiotics in early life: dysbiosis and the damage done.
FEMS Microbiology Reviews. Epub ahead of print

Reed S, Knez M, Uzan A, Stangoulis JCR, Glahn RP, Koren O, Tako E. Alterations in the Gut ( Gallus gallus) Microbiota Following the Consumption of Zinc Biofortified Wheat ( Triticum aestivum)-Based Diet.
Journal of Agricultural and Food Chemistry. Epub ahead of print

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, del Rio TG, Tringe SG, Buckler ES, Dangl JL, & RE Ley. Large-scale replicated field study of maize rhizosphere identifies heritable microbes.
PNAS. Epub ahead of print

Binyamin D, Nitzan O, Azrad M, Hamo Z, Koren O* & A Peretz*. In vitro Activity of Tedizolid, Dalbavancin, and Ceftobiprole Against Clostridium difficile.
Frontiers in Microbiology, 9:1256

Tabouy L, Getselter D, Ziv O, Karpuj M, Tabouy T, Lukic I, Maayouf R, Werbner N, Ben-Amram H, Nuriel-Ohayon Meital, Koren O & E Evan. Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders. 
Brain, Behavior and Immunity. Epub ahead of print. 

Nunberg M*, Werbner N*, Neuman H, Bersudsky M, Braiman A, Ben-Shoshan M, Ben Izhak M, Louzoun Y, Apte RN, Voronov E & O Koren. IL-1α deficient mice have an altered gut microbiota leading to protection from DSS-induced colitis.
mSystems, 3:e00213-17. Editor's choice and Cover image

Avni O* & O Koren*. Molecular (Me)micry.
Cell Host Microbe, 23(5):576-578.


Gerassy-Vainberg S, Blatt A, Danin-Poleg Y, Gershovich K, Sabo E, Nevelsky A, Daniel S, Dahan A, Ziv O, Dheer R, Abreu MT, Koren O, Kashi Y & Y. Chowers. Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction.

Gut, 67(1):97-107.

Dahan S, Segal Y, Watad A, Azrielant S, Shemer A, Maymon D, Stroev YI, Sobolevskaya PA, Korneva EA, Blank M, Gilburd B, Shovman O, Amital H, Ehrenfeld M, Tanay A, Kivity S, Pras E, Chapman J, Damoiseaux J, Cervera R, Putterman C, Shapiro I, Mouthon L, Periconne R, Bizzaro N, Koren O, Riemekasten G, Chereshnev VA, Mazurov VI, Goloviznin M, Gurevich V, Churilov LP & Shoenfeld Y. Novelties in the field of autoimmunity - 1st Saint Petersburg congress of autoimmunity, the bridge between east and west.
Autoimmunity Reviews, Epub ahead of print.

Reed S, Neuman H, Glahn RP, Koren O & E Tako. Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet.
PLoS One, 12(8): e0182431.

Ben-Amram H, Bashi T, Werbner N, Neuman H, Fridkin M, Blank M, Shoenfeld Y & O Koren. Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice. 
Frontiers in Microbiology, 8:1222.

Pitlik S & O Koren. How holobionts get sick: towards a unifying scheme of disease.
Microbiome, 5:64.

Neuman H & O Koren. The gut microbiota: a possible factor influencing systemic lupus erythematosus.
Current Opinion in Rheumatology, 29(4): 374-377.

Leclercq S, Mian FM, Stanisz AM, Bindels LB, Cambier E, Ben-Amram H, Koren O, Forsythe P & J. Bienenstock. Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior.
Nature Communications, 8:15062.

Neuman H & O Koren. The pregnancy microbiome.
Nestle Nutrition Institute Workshop Series, 88:1-9.


Nuriel-Ohayon M, Neuman H & O Koren. Microbial changes during pregnancy, birth and infancy.
Frontiers in Microbiology, 7:1031.

Shamriz O, Mizrahi H, Werbner M, Shoenfeld Y, Avni O* & O Koren*. The microbiota at the crossroads of autoimmunity.
Autoimmunity Reviews, 15(9):859-869.

Kuperman A & O Koren. Antibiotics during Pregnancy: How bad is it?
BMC Medicine, 14(1): 91.

Reed S, Neuman H, Moscovich S, Glahn RP, Koren O & E Tako. Chronic zinc deficiency alters chick gut microbiota composition and function.
Nutrients, 7(12): 9768-84.

Neuman H,  Debelius, JW, Knight, R and O Koren. Microbial endocrinology: the interplay between microbiota and the endocrine system.
FEMS Microbiology Reviews, 39(4): 509-521.

Kuperman A & O Koren. Editorial: The era of fecal microbiota transplantation.
The Israel Medical Association Journal, 17:2-3

Chassing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE & AT Gewirtz. Dietary emulsifiers alter gut microbiota-intestinal interactions promoting colitis and metabolic syndrome.
Nature, 5(519): 92-96.

Tracy A, Koren O, Douglas N, Weil E & D Harvell. Persistent shifts in Caribbean coral microbiota are linked to the 2010 warm thermal anomaly.
Environmental Microbiology Reports, 7(3): 471-9.

Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG & RE Ley. Human genetics shape the gut microbiome.
Cell, 150(4): 789-799.
Recommended by Faculty of 1000.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R & RE Ley. Conducting a microbiome study.
Cell, 158(2): 250-262.

Bel S, Elkis Y, Elifantz H, Koren O, Ben-Hamo R, Lerer-Goldshtein T, Rahimi R, Ben Horin S, Nyska A, Shpungin S & U Nir. Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF-/- mice.
PNAS, 111(13): 4964-9.

Chassing B, Koren O, Carvalho FA, Ley RE & AT Gewirtz. AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition.
Gut, 63(7): 1069-80.

Di Rienzi SC*, Sharon I*, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield J* & RE Ley*. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.
eLIFE, 2:e01102. *These authors contributed equally.
Recommended by Faculty of 1000.

Peiffer JA*, Spor A*, Jin Z, Koren O, Tringe SG, Dangl JL, Buckler ES & RE Ley. Diversity and heritability of the maize rhizosphere microbiome under field conditions.
PNAS, 110(16): 6548-53. *These authors contributed equally.

Koren O*, Pena AG*, Knights D*, Waldron L, Segata N, Knight R, Huttenhower C & RE Ley. A guide to enterotypes across the human body: Meta-analysis of microbial community structures in human microbiome datasets.
PLoS Computational Biology, 9(1), e1002863. *These authors contributed equally.

Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed H, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S and RE Ley. Host remodeling of the gut microbiome and metabolic changes during pregnancy.
Cell, 150(3), 470-480.
Recommended by Faculty of 1000.

Carvalho FA, Koren O, Johansson M, Nalbantogl I, Aitken JD, SuY, Chassing B, Walters WA, Pena AG, Clemente JC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE & AT Gewirtz. Transient inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice.
Cell, Host and Microbe, 12(2), 139-152.

The Human Microbiome Consortium. Structure, function and diversity of the healthy human microbiome.  
Nature, 486, 207-214.
Recommended by Faculty of 1000.

The Human Microbiome Consortium. A framework for human microbiome research.
Nature, 486, 215-221.
Recommended by Faculty of 1000.

Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M & AT Gewirtz. Interleukin-1b (IL-1b) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis.
Gut, 61, 373-384.

Ravussin Y*, Koren O*, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE & R Leibel. Response of gut microbiotas to diet composition and weight loss in lean and obese mice.
Obesity, 20(4), 738-47. *These authors contributed equally.

Larsson E, Tremaroli V, Shiuan Lee Y, Koren O, Nookaew I, Fricker A, Nielsen J, Ley RE & F Backhed. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88.
Gut, 61:1124-31.
Recommended by Faculty of 1000.

Ran-Ressler R, Khailova L, Arganbright KM, Adkins-Rieck CK, Jouni ZE, Koren O, Ley RE, Brenna JT & Dvorak B. Branched chain fatty acids alter gastrointestinal microbial ecology and reduce the incidence of necrotizing enterocolitis in a neonatal rat model.
PLoS One, 6(12), e29032.

Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley RE, Wakeland EK & LV Hooper. The antibacterial lectin RegIIIg promotes the spatial segregation of microbiota and host in the intestine.
Science, 334, 255-58.
Recommended by Faculty of 1000.

Werner JJ *, Koren O*, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R & RE Ley. Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys.
The ISME Journal, 6(1), 94-103. *These authors contributed equally.

Yilmaz, P, the MIMARKS consortium*. Minimum Information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nature Biotechnology, 29, 415-20. *These authors contributed equally.

Spor A*, Koren O* & RE Ley. Unraveling the effects of the environment and host genotype on the gut microbiome.
Nature Reviews Microbiology, 9, 279-90. *These authors contributed equally.

Koren O*, Spor A*, Felin J*, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE & F Bäckhed. Human oral, gut and plaque microbiota in patients with atherosclerosis.
PNAS, 15:108 Suppl 1:4592-8. *These authors contributed equally.
Recommended by Faculty of 1000.

Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ & ST. Kelley Supervised classification of microbiota mitigates mislabeling errors.
The ISME Journal, 5, 570-573.

Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI & R Knight. Direct sequencing of the human microbiome readily reveals community differences.
Genome Biology, 5, 210-219.

Koren O & E Rosenberg. Bacteria associated with the bleached and cave coral Oculina patagonica.
Microbial Ecology, 55, 523-529.

Rosenberg E, Koren O, Reshef L, Efrony R & I Zilber-Rosenberg. The role of microorganisms in coral health, disease and evolution.
Nature Reviews Microbiology, 5, 355-362.
Recommended by Faculty of 1000.

Reshef L, Koren O, Loya Y, Zilber-Rosenberg I & E Rosenberg. The coral probiotic hypothesis.  
Environmental Microbiology, 8, 2068-2073.

Koren O & E Rosenberg. (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter.
Applied and Environmental Microbiology, 72, 5254- 5259.
Recommended by Faculty of 1000.

Knezevich V, Koren O, Ron EZ & E Rosenberg. (2006) Petroleum bioremediation in seawater using guano as the fertilizer.
Bioremediation Journal, 10, 83-91.

Koren O, Knezevich V, Ron EZ & E Rosenberg. (2003) Petroleum pollution bioremediation using water-insoluble uric acid as the nitrogen source.
Applied and Environmental Microbiology, 69, 6337-6339.

Book chapters:

Neuman H & O Koren. (2015) The Gut Microbiome. In Encyclopedia of Cell Biology. Elsevier.
Koren O & RE Ley. (2015) The Human Intestinal Microbiota and Microbiome. In: Yamada’s Textbook of Gastroenterology, 6th Edition. Shanahan F (ed.). Wiley-Blackwell, West Sussex, UK.

Rosenberg E & O Koren. (2006) Vibrios in Coral Health and Disease, p 231-238. In F.L. Thompson, B. Austin, and J. Swings (ed.), The Biology of Vibrios. ASM Press.