Journal Club 2019





Friday, Dec. 13th, 2019 - Francesca Ronchi

Nature, 574 (7777), 254-258 Oct 2019.
Light-entrained and Brain-Tuned Circadian Circuits Regulate ILC3s and Gut Homeostasis
Cristina Godinho-Silva, Rita G Domingues, Miguel Rendas, Bruno Raposo, Hélder Ribeiro, Joaquim Alves da Silva, Ana Vieira, Rui M Costa, Nuno L Barbosa-Morais, Tânia Carvalho, Henrique Veiga-Fernandes.

PMID: PubMed Link

Nat Med, 25 (10), 1500-1504 Oct 2019. DOI: 10.1038/s41591-019-0600-6
Vaginal Microbiome Transplantation in Women With Intractable Bacterial Vaginosis
Ahinoam Lev-Sagie, Debra Goldman-Wohl, Yotam Cohen, Mally Dori-Bachash, Avner Leshem, Uria Mor, Jacob Strahilevitz, Allon E Moses, Hagit Shapiro, Simcha Yagel, Eran Elinav.

PubMed Link


Friday, Nov. 25th, 2019 - Hai Li

Nature, 575 (7781), 224-228 Nov 2019. DOI: 10.1038/s41586-019-1708-z
Human Gut Bacteria Contain Acquired Interbacterial Defence Systems
Benjamin D Ross, Adrian J Verster, Matthew C Radey, Danica T Schmidtke, Christopher E Pope, Lucas R Hoffman, Adeline M Hajjar, S Brook Peterson, Elhanan Borenstein, Joseph D Mougous.

PMID: PubMed Link

Nature, 575 (7783), 505-511 Nov 2019. DOI: 10.1038/s41586-019-1742-x
Bacteriophage Targeting of Gut Bacterium Attenuates Alcoholic Liver Disease
Yi Duan, Cristina Llorente, Sonja Lang, Katharina Brandl, Huikuan Chu, Lu Jiang, Richard C White, Thomas H Clarke, Kevin Nguyen, Manolito Torralba, Yan Shao, Jinyuan Liu, Adriana Hernandez-Morales, Lauren Lessor, Imran R Rahman, Yukiko Miyamoto, Melissa Ly, Bei Gao, Weizhong Sun, Roman Kiesel, Felix Hutmacher, Suhan Lee, Meritxell Ventura-Cots, Francisco Bosques-Padilla, Elizabeth C Verna, Juan G Abraldes, Robert S Brown Jr, Victor Vargas, Jose Altamirano, Juan Caballería, Debbie L Shawcross, Samuel B Ho, Alexandre Louvet, Michael R Lucey, Philippe Mathurin, Guadalupe Garcia-Tsao, Ramon Bataller, Xin M Tu, Lars Eckmann, Wilfred A van der Donk, Ry Young, Trevor D Lawley, Peter Stärkel, David Pride, Derrick E Fouts, Bernd Schnabl

PubMed Link


Monday, Oct. 21th, 2019 - Cristina Kalbermatter

Science, 366 (6464) 2019 Oct 25. DOI: 10.1126/science.aax6624
MAIT Cells Are Imprinted by the Microbiota in Early Life and Promote Tissue Repair
Michael G Constantinides, Verena M Link, Samira Tamoutounour, Andrea C Wong, P Juliana Perez-Chaparro, Seong-Ji Han, Y Erin Chen, Kelin Li, Sepideh Farhat, Antonin Weckel, Siddharth R Krishnamurthy, Ivan Vujkovic-Cvijin, Jonathan L Linehan, Nicolas Bouladoux, E Dean Merrill, Sobhan Roy, Daniel J Cua, Erin J Adams, Avinash Bhandoola, Tiffany C Scharschmidt, Jeffrey Aubé, Michael A Fischbach, Yasmine Belkaid.
PMID:
PubMed Link

Science, 365 (6460), 1428-1434 2019 Sep 27. DOI: 10.1126/science.aaw3134
The Intestinal Microbiota Programs Diurnal Rhythms in Host Metabolism Through Histone Deacetylase 3
Zheng Kuang, Yuhao Wang, Yun Li, Cunqi Ye, Kelly A Ruhn, Cassie L Behrendt, Eric N Olson, Lora V Hooper.

PubMed Link


Friday, Oct. 11th, 2019 - Ian Young

Cell, 178 (1), 202-215.e14 2019 Jun 27
Fc Glycan-Mediated Regulation of Placental Antibody Transfer
Madeleine F Jennewein, Ilona Goldfarb, Sepideh Dolatshahi, Cormac Cosgrove, Francesca J Noelette, Marina Krykbaeva, Jishnu Das, Aniruddh Sarkar, Matthew J Gorman, Stephanie Fischinger, Carolyn M Boudreau, Joelle Brown, Jennifer H Cooperrider, Jasneet Aneja, Todd J Suscovich, Barney S Graham, Georg M Lauer, Tessa Goetghebuer, Arnaud Marchant, Douglas Lauffenburger, Arthur Y Kim, Laura E Riley, Galit Alter.

PubMed Link

Proc Natl Acad Sci U S A, 116 (26), 12672-12677 2019 Jun 25. DOI: 10.1073/pnas.1904099116
Ruminococcus gnavus, a Member of the Human Gut Microbiome Associated With Crohn's Disease, Produces an Inflammatory Polysaccharide
Matthew T Henke, Douglas J Kenny, Chelsi D Cassilly, Hera Vlamakis, Ramnik J Xavier, Jon Clardy.

PubMed Link


Friday, Sep. 30th, 2019 - Steven Misztal

Nat Commun, 10 (1), 3031 2019 Jul 10
Decreased Maternal Serum Acetate and Impaired Fetal Thymic and Regulatory T Cell Development in Preeclampsia
Mingjing Hu, David Eviston, Peter Hsu, Eliana Mariño, Ann Chidgey, Brigitte Santner-Nanan, Kahlia Wong, James L Richards, Yu Anne Yap, Fiona Collier, Ann Quinton, Steven Joung, Michael Peek, Ron Benzie, Laurence Macia, David Wilson, Ann-Louise Ponsonby, Mimi L K Tang, Martin O'Hely, Norelle L Daly, Charles R Mackay, Jane E Dahlstrom , BIS Investigator Group, Peter Vuillermin, Ralph Nanan.

PubMed Link

Nat Microbiol, 4 (11), 1851-1861 Nov 2019. DOI: 10.1038/s41564-019-0498-2
Elevated Faecal 12,13-diHOME Concentration in Neonates at High Risk for Asthma Is Produced by Gut Bacteria and Impedes Immune Tolerance
Sophia R Levan, Kelsey A Stamnes, Din L Lin, Ariane R Panzer, Elle Fukui, Kathryn McCauley, Kei E Fujimura, Michelle McKean, Dennis R Ownby, Edward M Zoratti, Homer A Boushey, Michael D Cabana, Christine C Johnson, Susan V Lynch.

PubMed Link


Friday, Sep. 9th, 2019 - Anna Wenning

Nature, 572 (7769), 329-334 Aug 2019. DOI: 10.1038/s41586-019-1451-5
Human Placenta Has No Microbiome but Can Contain Potential Pathogens
Marcus C de Goffau 1 2, Susanne Lager 3 4 5, Ulla Sovio 3 4, Francesca Gaccioli 3 4, Emma Cook 3, Sharon J Peacock 1 6 7, Julian Parkhill 8 9, D Stephen Charnock-Jones 3 4, Gordon C S Smith 10 11
Affiliations expand
PMID: 31367035 PMCID: PMC6697540 

PubMed Link


Friday, August. 16th, 2019 - Hai Li

Science, 365 (6451) 2019 Jul 26. DOI: 10.1126/science.aat9351
T Cell-Mediated Regulation of the Microbiota Protects Against Obesity
Charisse Petersen, Rickesha Bell, Kendra A Klag, Soh-Hyun Lee, Raymond Soto, Arevik Ghazaryan, Kaitlin Buhrke, H Atakan Ekiz, Kyla S Ost, Sihem Boudina, Ryan M O'Connell, James E Cox, Claudio J Villanueva, W Zac Stephens, June L Round 

PubMed Link

Science, 365 (6452) 2019 Aug 2. DOI: 10.1126/science.aaw4361
Laboratory Mice Born to Wild Mice Have Natural Microbiota and Model Human Immune Responses
Stephan P Rosshart, Jasmin Herz, Brian G Vassallo, Ashli Hunter, Morgan K Wall, Jonathan H Badger, John A McCulloch, Dimitrios G Anastasakis, Aishe A Sarshad, Irina Leonardi, Nicholas Collins, Joshua A Blatter, Seong-Ji Han, Samira Tamoutounour, Svetlana Potapova, Mark B Foster St Claire, Wuxing Yuan, Shurjo K Sen, Matthew S Dreier, Benedikt Hild, Markus Hafner, David Wang, Iliyan D Iliev, Yasmine Belkaid, Giorgio Trinchieri, Barbara Rehermann.

PubMed Link


Friday, July. 5th, 2019 - Jakob Zimmermann

Nature, 547 (7661), 89-93 2017 Jul 6. DOI: 10.1038/nature22383
Quantifiable Predictive Features Define Epitope-Specific T Cell Receptor Repertoires
Pradyot Dash, Andrew J Fiore-Gartland, Tomer Hertz, George C Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E Bridie Clemens, Thi H O Nguyen, Katherine Kedzierska, Nicole L La Gruta, Philip Bradley, Paul G Thomas.

PubMed Link

Immunity, 51 (1), 77-89.e6 2019 Jul 16. DOI: 10.1016/j.immuni.2019.05.004
The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells
Sara Omenetti, Claudio Bussi, Amina Metidji, Andrea Iseppon, Sunjae Lee, Mauro Tolaini, Ying Li, Gavin Kelly, Probir Chakravarty, Saeed Shoaie, Maximiliano G Gutierrez, Brigitta Stockinger.

PubMed Link


Friday, June. 28th, 2019 - Steven Misztal

Cell, 177 (5), 1217-1231.e18 2019 May 16. DOI: 10.1016/j.cell.2019.03.036
A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology
Haiwei Chen, Phu-Khat Nwe, Yi Yang, Connor E Rosen, Agata A Bielecka, Manik Kuchroo, Gary W Cline, Andrew C Kruse, Aaron M Ring, Jason M Crawford, Noah W Palm.

PubMed Link

Cell Host Microbe, 25 (5), 681-694.e8 2019 May 8. DOI: 10.1016/j.chom.2019.03.004
Mucispirillum Schaedleri Antagonizes Salmonella Virulence to Protect Mice Against Colitis
Simone Herp, Sandrine Brugiroux, Debora Garzetti, Diana Ring, Lara M Jochum, Markus Beutler, Claudia Eberl, Saib Hussain, Steffi Walter, Roman G Gerlach, Hans J Ruscheweyh, Daniel Huson, Mikael E Sellin, Emma Slack, Buck Hanson, Alexander Loy, John F Baines, Philipp Rausch, Marijana Basic, André Bleich, David Berry, Bärbel Stecher.

PubMed Link


Friday, May. 24th, 2019 - Yuan Dong

Cell Host Microbe, 25 (5), 756-765.e5 2019 May 8. DOI: 10.1016/j.chom.2019.03.003
Colitis-Induced Th17 Cells Increase the Risk for Severe Subsequent Clostridium Difficile Infection
Mahmoud M Saleh, Alyse L Frisbee, Jhansi L Leslie, Erica L Buonomo, Carrie A Cowardin, Jennie Z Ma, Morgan E Simpson, Kenneth W Scully, Mayuresh M Abhyankar, William A Petri Jr.

PubMed Link

Immunity, 50 (1), 212-224.e4 2019 Jan 15. DOI: 10.1016/j.immuni.2018.12.015
Microbiotas From Humans With Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt + Regulatory T Cells and Exacerbate Colitis in Mice
Graham J Britton, Eduardo J Contijoch, Ilaria Mogno, Olivia H Vennaro, Sean R Llewellyn, Ruby Ng, Zhihua Li, Arthur Mortha, Miriam Merad, Anuk Das, Dirk Gevers, Dermot P B McGovern, Namita Singh, Jonathan Braun, Jonathan P Jacobs, Jose C Clemente 1, Ari Grinspan, Bruce E Sands, Jean-Frederic Colombel, Marla C Dubinsky, Jeremiah J Faith.

PubMed Link


Friday, May. 10th, 2019 - Francesca Ronchi

Nature, 569 (7754), 126-130 May 2019. DOI: 10.1038/s41586-019-1125-3
Compartmentalized Gut Lymph Node Drainage Dictates Adaptive Immune Responses
Daria Esterházy, Maria C C Canesso, Luka Mesin, Paul A Muller, Tiago B R de Castro, Ainsley Lockhart, Mahmoud ElJalby, Ana M C Faria, Daniel Mucida.

PubMed Link

Nature, 569 (7754), 121-125 May 2019. DOI: 10.1038/s41586-019-1154-y
Single-cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell
Arshad Ayyaz, Sandeep Kumar, Bruno Sangiorgi, Bibaswan Ghoshal, Jessica Gosio, Shaida Ouladan, Mardi Fink, Seda Barutcu, Daniel Trcka, Jess Shen, Kin Chan, Jeffrey L Wrana, Alex Gregorieff.

PubMed Link


Monday, April. 26th, 2019 - Anna Wenning

Nat Commun,10 (1), 1745 2019 Apr 15. DOI: 10.1038/s41467-019-09744-3
Early Life Stress Disrupts Intestinal Homeostasis via NGF-TrkA Signaling
Hoi Leong Xavier Wong, Hong-Yan Qin, Siu Wai Tsang, Xiao Zuo, Sijia Che, Chi Fung Willis Chow, Xi Li, Hai-Tao Xiao, Ling Zhao, Tao Huang, Cheng Yuan Lin, Hiu Yee Kwan, Tao Yang, Frank M Longo, Aiping Lyu, Zhao-Xiang Bian
Affiliations expand

PubMed Link

Cell, 176 (5), 982-997.e16 2019 Feb 21. DOI: 10.1016/j.cell.2018.12.031
Homeostatic Control of Sebaceous Glands by Innate Lymphoid Cells Regulates Commensal Bacteria Equilibrium
Tetsuro Kobayashi, Benjamin Voisin, Do Young Kim, Elizabeth A Kennedy, Jay-Hyun Jo, Han-Yu Shih, Amanda Truong, Thomas Doebel, Keiko Sakamoto, Chang-Yi Cui, David Schlessinger, Kazuyo Moro, Susumu Nakae, Keisuke Horiuchi, Jinfang Zhu, Warren J Leonard, Heidi H Kong, Keisuke Nagao.

PubMed Link


Monday, March. 29th, 2019 - Bahtiyar Yilmaz

Cell Host Microbe. 2019 Jan 9;25(1):128-139.e5. doi: 10.1016/j.chom.2018.12.003.
Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition.
Litvak Y, Mon KKZ, Nguyen H, Chanthavixay G, Liou M, Velazquez EM, Kutter L, Alcantara MA, Byndloss MX, Tiffany CR, Walker GT, Faber F1, Zhu Y, Bronner DN, Byndloss AJ, Tsolis RM, Zhou H, Bäumler AJ.

PubMed Link

Immunity. 2019 Jan 15;50(1):212-224.e4. doi: 10.1016/j.immuni.2018.12.015.
Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.
Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ.

PubMed Link


Monday, March. 18th, 2019 - Cristina Kalbermatter

Science. 2018 Jan 12;359(6372):177-186. doi: 10.1126/science.aah6499.
The epigenetic control of stemness in CD8+ T cell fate commitment.
Pace L, Goudot C, Zueva E, Gueguen P, Burgdorf N, Waterfall JJ, Quivy JP, Almouzni G, Amigorena S.

PubMed Link

Science. 2019 Mar 8;363(6431). pii: eaat4042. doi: 10.1126/science.aat4042.
Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis.
Ladinsky MS, Araujo LP, Zhang X, Veltri J, Galan-Diez M, Soualhi S, Lee C, Irie K, Pinker EY, Narushima S, Bandyopadhyay S, Nagayama M, Elhenawy W, Coombes BK, Ferraris RP, Honda K, Iliev ID, Gao N, Bjorkman PJ, Ivanov II.

PubMed Link


Monday, March. 15th, 2019 - Jakob Zimmermann

J Exp Med. 2019 Apr 1;216(4):728-742. doi: 10.1084/jem.20180871. Epub 2019 Feb 27.
Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria.
Melo-Gonzalez F, Kammoun H, Evren E, Dutton EE, Papadopoulou M, Bradford BM, Tanes C, Fardus-Reid F, Swann JR, Bittinger K, Mabbott NA, Vallance BA, Willinger T, Withers DR, Hepworth MR.

PubMed Link

Nature. 2019 Feb;566(7743):249-253. doi: 10.1038/s41586-019-0899-7. Epub 2019 Jan 30.
Interleukin-22 protects intestinal stem cells against genotoxic stress.
Gronke K, Hernández PP, Zimmermann J, Klose CSN, Kofoed-Branzk M, Guendel F, Witkowski M, Tizian C, Amann L, Schumacher F, Glatt H, Triantafyllopoulou A, Diefenbach A.

PubMed Link


Monday, March. 4th, 2019 - Hai Li

Nature. 2019 Jan;565(7741):600-605. doi: 10.1038/s41586-019-0878-z. Epub 2019 Jan 23.
A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K.

PubMed Link

Science. 2019 Feb 15;363(6428):748-753. doi: 10.1126/science.aau8475.
BCR-dependent lineage plasticity in mature B cells.
Graf R, Seagal J, Otipoby KL, Lam KP, Ayoub S, Zhang B, Sander S, Chu VT, Rajewsky K.

PubMed Link


Friday, March. 1st, 2019 - Francesca Ronchi

Nature. 2019 Feb;566(7742):110-114. doi: 10.1038/s41586-019-0884-1. Epub 2019 Jan 23.
GPR31-dependent dendrite protrusion of intestinal CX3CR1+ cells by bacterial metabolites.
Morita N, Umemoto E, Fujita S, Hayashi A, Kikuta J, Kimura I, Haneda T, Imai T, Inoue A, Mimuro H, Maeda Y, Kayama H, Okumura R, Aoki J, Okada N, Kida T, Ishii M, Nabeshima R, Takeda K.

PubMed Link

Nature. 2019 Feb;566(7742):115-119. doi: 10.1038/s41586-018-0849-9. Epub 2019 Jan 30.
Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease.
He S, Kahles F, Rattik S, Nairz M, McAlpine CS, Anzai A, Selgrade D, Fenn AM, Chan CT, Mindur JE, Valet C, Poller WC, Halle L, Rotllan N, Iwamoto Y, Wojtkiewicz GR, Weissleder R, Libby P, Fernández-Hernando C, Drucker DJ, Nahrendorf M, Swirski FK.

PubMed Link


Monday, Feb. 8th, 2019 - Tim Rollenske

Cell. 2019 Apr 4;177(2):492-493. doi: 10.1016/j.cell.2019.03.037. No abstract available.
Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, Burrows K, Robinson HG, Allanach JR, Yam J, Luck H, Campbell DJ, Allman D, Brooks DG, Tomura M, Baumann R, Zamvil SS, Bar-Or A, Horwitz MS, Winer DA, Mortha A, Mackay F, Prat A, Osborne LC, Robbins C, Baranzini SE, Gommerman JL.

PubMed Link

Nat Med. 2019 Feb;25(2):249-254. doi: 10.1038/s41591-018-0326-x. Epub 2019 Jan 28.
Identification of preexisting adaptive immunity to Cas9 proteins in humans.
Charlesworth CT, Deshpande PS, Dever DP, Camarena J, Lemgart VT, Cromer MK, Vakulskas CA, Collingwood MA, Zhang L, Bode NM, Behlke MA, Dejene B, Cieniewicz B, Romano R, Lesch BJ, Gomez-Ospina N, Mantri S, Pavel-Dinu M, Weinberg KI, Porteus MH.

PubMed Link


Monday, Jan. 21st, 2019 - Disha Tandon

Appl Microbiol Biotechnol. 2018 Dec;102(23):10219-10230. doi: 10.1007/s00253-018-9378-6. Epub 2018 Oct 9.
Alterations in the diversity and composition of mice gut microbiota by lytic or temperate gut phage treatment.
Bao HD, Pang MD, Olaniran A, Zhang XH, Zhang H, Zhou Y, Sun LC, Schmidt S, Wang R.

PubMed Link

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20236-41. doi: 10.1073/pnas.1319470110. Epub 2013 Nov 20.
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.
Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI.

PubMed Link


Monday, Jan. 18th, 2019 - Julien Limenitakis

Microbiome. 2019 Jan 3;7(1):1. doi: 10.1186/s40168-018-0604-3.
Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases.
Armstrong H, Alipour M, Valcheva R, Bording-Jorgensen M, Jovel J, Zaidi D, Shah P, Lou Y, Ebeling C, Mason AL, Lafleur D, Jerasi J, Wong GK, Madsen K, Carroll MW, Huynh HQ, Dieleman LA, Wine E.

PubMed Link

BioRxiv
High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
Mandeep Singh, Ghamdan Al-Eryani, ProfileShaun Carswell, James M. Ferguson, James Blackburn, ProfileKirston Barton, Daniel Roden, Fabio Luciani, Tri Phan, Simon Junankar, Katherine Jackson, Christopher C. Goodnow, Martin A. Smith, Alexander Swarbrick



Monday, Jan. 7th, 2019 - Anna Wenning

Nat Commun. 2018 Dec 7;9(1):5238. doi: 10.1038/s41467-018-07716-7.
PDL2+ CD11b+ dermal dendritic cells capture topical antigen through hair follicles to prime LAP+ Tregs.
Tordesillas L, Lozano-Ojalvo D, Dunkin D, Mondoulet L, Agudo J, Merad M, Sampson H, Berin MC.

PubMed Link

Nat Commun. 2018 Dec 21;9(1):5424. doi: 10.1038/s41467-018-07803-9.
The gut microbiome is required for full protection against acute arsenic toxicity in mouse models.
Coryell M, McAlpine M, Pinkham NV, McDermott TR, Walk ST.

PubMed Link

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