The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Ilias Lagkouvardos; Rüdiger Pukall; Birte Abt; Bärbel U. Foesel; Jan P. Meier-Kolthoff; Neeraj Kumar; Anne Gøther Bresciani; Inés Martínez; Sarah Just; Caroline Ziegler; Sandrine Brugiroux; Debora Garzetti; Mareike Wenning; Thi P. N. Bui; Jun Wang; Floor Hugenholtz; Caroline M. Plugge; Daniel A. Peterson; Mathias W. Hornef; John F. Baines; Hauke Smidt; Jens Walter; Karsten Kristiansen; Henrik Bjørn Nielsen; Dirk Haller; Jörg Overmann; Bärbel Stecher; Thomas Clavel

doi:10.1038/nmicrobiol.2016.131

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff, Neeraj Kumar, Anne Gøther Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz, Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. BainesHauke Smidt, Jens Walter, Karsten Kristiansen, Henrik Bjørn Nielsen, Dirk Haller, Jörg Overmann, Bärbel Stecher, Thomas Clavel

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Abstract

Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

Original language	English
Article number	16131
Journal	Nature Microbiology
Volume	1
Issue number	10
Number of pages	15
ISSN	2058-5276
DOIs	https://doi.org/10.1038/nmicrobiol.2016.131
Publication status	Published - 2016

Bibliographical note

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Keywords

Bacteria
Biodiversity
Microbial ecology
Microbiology
Microbiome

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10.1038/nmicrobiol.2016.131

The Mouse Intestinal Bacterial Collection miBC provides host specific insight into cultured diversity and functional potential of the gut microbiotaFinal published version, 1.41 MB

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Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B. U., Meier-Kolthoff, J. P., Kumar, N., Bresciani, A. G., Martínez, I., Just, S., Ziegler, C., Brugiroux, S., Garzetti, D., Wenning, M., Bui, T. P. N., Wang, J., Hugenholtz, F., Plugge, C. M., Peterson, D. A., Hornef, M. W., ... Clavel, T. (2016). The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology, 1(10), [16131]. https://doi.org/10.1038/nmicrobiol.2016.131

Lagkouvardos, Ilias ; Pukall, Rüdiger ; Abt, Birte ; Foesel, Bärbel U. ; Meier-Kolthoff, Jan P. ; Kumar, Neeraj ; Bresciani, Anne Gøther ; Martínez, Inés ; Just, Sarah ; Ziegler, Caroline ; Brugiroux, Sandrine ; Garzetti, Debora ; Wenning, Mareike ; Bui, Thi P. N. ; Wang, Jun ; Hugenholtz, Floor ; Plugge, Caroline M. ; Peterson, Daniel A. ; Hornef, Mathias W. ; Baines, John F. ; Smidt, Hauke ; Walter, Jens ; Kristiansen, Karsten ; Nielsen, Henrik Bjørn ; Haller, Dirk ; Overmann, Jörg ; Stecher, Bärbel ; Clavel, Thomas. / The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. In: Nature Microbiology. 2016 ; Vol. 1, No. 10.

@article{0daf16002bd34e96baf55255de1cf989,

title = "The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota",

abstract = "Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.",

keywords = "Bacteria, Biodiversity, Microbial ecology, Microbiology, Microbiome",

author = "Ilias Lagkouvardos and R{\"u}diger Pukall and Birte Abt and Foesel, {B{\"a}rbel U.} and Meier-Kolthoff, {Jan P.} and Neeraj Kumar and Bresciani, {Anne G{\o}ther} and In{\'e}s Mart{\'i}nez and Sarah Just and Caroline Ziegler and Sandrine Brugiroux and Debora Garzetti and Mareike Wenning and Bui, {Thi P. N.} and Jun Wang and Floor Hugenholtz and Plugge, {Caroline M.} and Peterson, {Daniel A.} and Hornef, {Mathias W.} and Baines, {John F.} and Hauke Smidt and Jens Walter and Karsten Kristiansen and Nielsen, {Henrik Bj{\o}rn} and Dirk Haller and J{\"o}rg Overmann and B{\"a}rbel Stecher and Thomas Clavel",

note = "This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/",

year = "2016",

doi = "10.1038/nmicrobiol.2016.131",

language = "English",

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Lagkouvardos, I, Pukall, R, Abt, B, Foesel, BU, Meier-Kolthoff, JP, Kumar, N, Bresciani, AG, Martínez, I, Just, S, Ziegler, C, Brugiroux, S, Garzetti, D, Wenning, M, Bui, TPN, Wang, J, Hugenholtz, F, Plugge, CM, Peterson, DA, Hornef, MW, Baines, JF, Smidt, H, Walter, J, Kristiansen, K, Nielsen, HB, Haller, D, Overmann, J, Stecher, B & Clavel, T 2016, 'The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota', Nature Microbiology, vol. 1, no. 10, 16131. https://doi.org/10.1038/nmicrobiol.2016.131

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. / Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U.; Meier-Kolthoff, Jan P.; Kumar, Neeraj; Bresciani, Anne Gøther; Martínez, Inés; Just, Sarah; Ziegler, Caroline; Brugiroux, Sandrine; Garzetti, Debora; Wenning, Mareike; Bui, Thi P. N.; Wang, Jun; Hugenholtz, Floor; Plugge, Caroline M.; Peterson, Daniel A.; Hornef, Mathias W.; Baines, John F.; Smidt, Hauke; Walter, Jens; Kristiansen, Karsten; Nielsen, Henrik Bjørn; Haller, Dirk; Overmann, Jörg; Stecher, Bärbel; Clavel, Thomas.

In: Nature Microbiology, Vol. 1, No. 10, 16131, 2016.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

AU - Lagkouvardos, Ilias

AU - Pukall, Rüdiger

AU - Abt, Birte

AU - Foesel, Bärbel U.

AU - Meier-Kolthoff, Jan P.

AU - Kumar, Neeraj

AU - Bresciani, Anne Gøther

AU - Martínez, Inés

AU - Just, Sarah

AU - Ziegler, Caroline

AU - Brugiroux, Sandrine

AU - Garzetti, Debora

AU - Wenning, Mareike

AU - Bui, Thi P. N.

AU - Wang, Jun

AU - Hugenholtz, Floor

AU - Plugge, Caroline M.

AU - Peterson, Daniel A.

AU - Hornef, Mathias W.

AU - Baines, John F.

AU - Smidt, Hauke

AU - Walter, Jens

AU - Kristiansen, Karsten

AU - Nielsen, Henrik Bjørn

AU - Haller, Dirk

AU - Overmann, Jörg

AU - Stecher, Bärbel

AU - Clavel, Thomas

N1 - This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

PY - 2016

Y1 - 2016

N2 - Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

AB - Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

KW - Bacteria

KW - Biodiversity

KW - Microbial ecology

KW - Microbiology

KW - Microbiome

U2 - 10.1038/nmicrobiol.2016.131

DO - 10.1038/nmicrobiol.2016.131

M3 - Journal article

C2 - 27670113

VL - 1

JO - Nature Microbiology

JF - Nature Microbiology

SN - 2058-5276

IS - 10

M1 - 16131

ER -