Gut microbiota strain richness is species specific and affects engraftment

被引：13

作者：

Chen-Liaw, Alice ^{[1
]}

Aggarwala, Varun ^{[1
,2
]}

Mogno, Ilaria ^{[1
,2
]}

Haifer, Craig ^{[3
,4
]}

Li, Zhihua ^{[1
,2
]}

Eggers, Joseph ^{[2
]}

Helmus, Drew ^{[5
]}

Hart, Amy ^{[6
]}

Wehkamp, Jan ^{[6
]}

Lamouse-Smith, Esi S. N. ^{[6
]}

Kerby, Robert L. ^{[7
]}

Rey, Federico E. ^{[7
]}

Colombel, Jean Frederic ^{[5
]}

Kamm, Michael A. ^{[8
]}

Olle, Bernat ^{[9
]}

Norman, Jason M. ^{[9
]}

Menon, Rajita ^{[9
]}

Watson, Andrea R. ^{[9
]}

Crossett, Emily ^{[9
]}

Terveer, Elisabeth M. ^{[10
,11
]}

Keller, Josbert J. ^{[10
,12
,13
]}

Borody, Thomas J. ^{[14
]}

Grinspan, Ari ^{[5
]}

Paramsothy, Sudarshan ^{[3
,15
]}

Kaakoush, Nadeem O. ^{[16
]}

Dubinsky, Marla C. ^{[5
]}

Faith, Jeremiah J. ^{[1
,2
]}

机构：

[1] Icahn Sch Med Mt Sinai, Precis Immunol Inst, New York, NY 10029 USA

[2] Icahn Sch Med Mt Sinai, Icahn Genom Inst, New York, NY 10029 USA

[3] Univ Sydney, Concord Clin Sch, Sydney, NSW, Australia

[4] Univ New South Wales, Sch Clin Med, Sydney, NSW, Australia

[5] Icahn Sch Med Mt Sinai, Dr Henry D Janowitz Div Gastroenterol, New York, NY 10029 USA

[6] Janssen R&D, Spring House, PA USA

[7] Univ Wisconsin Madison, Dept Bacteriol, Madison, WI USA

[8] St Vincents Hosp, Dept Gastroenterol & Med, Melbourne, Vic, Australia

[9] Vedanta Biosci, Cambridge, MA USA

[10] Leiden Univ, Med Ctr, Netherlands Donor Feces Bank, Leiden, Netherlands

[11] Leiden Univ, Med Ctr, Dept Med Microbiol, Leiden, Netherlands

[12] Haaglanden Med Ctr, Dept Gastroenterol, The Hague, Netherlands

[13] Leiden Univ, Med Ctr, Dept Gastroenterol & Hepatol, Leiden, Netherlands

[14] Ctr Digest Dis, Sydney, NSW, Australia

[15] Macquarie Univ Hosp, Dept Gastroenterol & Hepatol, Sydney, NSW, Australia

[16] Univ New South Wales, Sch Med Sci, Sydney, NSW, Australia

来源：

NATURE | 2025年 / 637卷 / 8045期

基金：

美国国家卫生研究院;

关键词：

CLOSTRIDIUM-DIFFICILE; POPULATION-STRUCTURE; DIVERSITY; REVEALS; TRANSPLANTATION; TRANSMISSION; LANDSCAPE; EVOLUTION; COLITIS;

D O I：

10.1038/s41586-024-08242-x

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Despite the fundamental role of bacterial strain variation in gut microbiota function(1-6), the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.

引用

页码：422 / +

页数：25

共 84 条

[1] Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes [J].

Aggarwala, Varun ;

Mogno, Ilaria ;

Li, Zhihua ;

Yang, Chao ;

Britton, Graham J. ;

Chen-Liaw, Alice ;

Mitcham, Josephine ;

Bongers, Gerold ;

Gevers, Dirk ;

Clemente, Jose C. ;

Colombel, Jean-Frederic ;

Grinspan, Ari ;

Faith, Jeremiah .

NATURE MICROBIOLOGY, 2021, 6 (10) :1309-+

[2] Intestinal Dysbiosis and Depletion of Butyrogenic Bacteria in Clostridium difficile Infection and Nosocomial Diarrhea [J].

Antharam, Vijay C. ;

Li, Eric C. ;

Ishmael, Arif ;

Sharma, Anuj ;

Mai, Volker ;

Rand, Kenneth H. ;

Wang, Gary P. .

JOURNAL OF CLINICAL MICROBIOLOGY, 2013, 51 (09) :2884-2892

[3] Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota [J].

Arthur, Janelle C. ;

Perez-Chanona, Ernesto ;

Muehlbauer, Marcus ;

Tomkovich, Sarah ;

Uronis, Joshua M. ;

Fan, Ting-Jia ;

Campbell, Barry J. ;

Abujamel, Turki ;

Dogan, Belgin ;

Rogers, Arlin B. ;

Rhodes, Jonathan M. ;

Stintzi, Alain ;

Simpson, Kenneth W. ;

Hansen, Jonathan J. ;

Keku, Temitope O. ;

Fodor, Anthony A. ;

Jobin, Christian .

SCIENCE, 2012, 338 (6103) :120-123

[4] Human Microbiome: Composition and Role in Inflammatory Skin Diseases [J].

Balato, Anna ;

Cacciapuoti, Sara ;

Di Caprio, Roberta ;

Marasca, Claudio ;

Masara, Anna ;

Raimondo, Annunziata ;

Fabbrocini, Gabriella .

ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS, 2019, 67 (01) :1-18

[5] Commensal microbes provide first line defense against Listeria monocytogenes infection [J].

Becattini, Simone ;

Littmann, Eric R. ;

Carter, Rebecca A. ;

Kim, Sohn G. ;

Morjaria, Sejal M. ;

Ling, Lilan ;

Gyaltshen, Yangtsho ;

Fontana, Emily ;

Taur, Ying ;

Leiner, Ingrid M. ;

Pamer, Eric G. .

JOURNAL OF EXPERIMENTAL MEDICINE, 2017, 214 (07) :1973-1989

[6] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[7]

Blaser Martin, 2014, Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues

[8] Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas [J].

Britton, Graham J. ;

Contijoch, Eduardo J. ;

Spindler, Matthew P. ;

Aggarwala, Varun ;

Dogan, Belgin ;

Bongers, Gerold ;

San Mateo, Lani ;

Baltus, Andrew ;

Das, Anuk ;

Gevers, Dirk ;

Borody, Thomas J. ;

Kaakoush, Nadeem O. ;

Kamm, Michael A. ;

Mitchell, Hazel ;

Paramsothy, Sudarshan ;

Clemente, Jose C. ;

Colombel, Jean-Frederic ;

Simpson, Kenneth W. ;

Dubinsky, Marla C. ;

Grinspan, Ari ;

Faith, Jeremiah J. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2020, 117 (35) :21536-21545

[9] Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice [J].

Britton, Graham J. ;

Contijoch, Eduardo J. ;

Mogno, Ilaria ;

Vennaro, Olivia H. ;

Llewellyn, Sean R. ;

Ng, Ruby ;

Li, Zhihua ;

Mortha, Arthur ;

Merad, Miriam ;

Das, Anuk ;

Gevers, Dirk ;

McGovern, Dermot P. B. ;

Singh, Namita ;

Braun, Jonathan ;

Jacobs, Jonathan P. ;

Clemente, Jose C. ;

Grinspan, Ari ;

Sands, Bruce E. ;

Colombel, Jean-Frederic ;

Dubinsky, Marla C. ;

Faith, Jeremiah J. .

IMMUNITY, 2019, 50 (01) :212-+

[10] Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation [J].

Browne, Hilary P. ;

Forster, Samuel C. ;

Anonye, Blessing O. ;

Kumar, Nitin ;

Neville, B. Anne ;

Stares, Mark D. ;

Goulding, David ;

Lawley, Trevor D. .

NATURE, 2016, 533 (7604) :543-+

← 1 2 3 4 5 6 7 8 9 →