Open access
Announcement
15 September 2016

Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2

ABSTRACT

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

GENOME ANNOUNCEMENT

Isobiotic animal models with a defined stable composition are being developed to study host-microbial mutualism under reproducible conditions (1). The commonly used altered Schaedler flora (ASF) of eight species was devised to minimize immunopathology from blooms of nosocomial immigrant microbes (2, 3). Unfortunately, since ASF-colonized mice neither fully recapitulate immune adaptations nor disease models seen in diversely colonized mice, the microbiota is insufficient to model most aspects of host microbial mutualism (1).
Here, we report the genomic sequences of 12 bacterial organisms in a stable defined moderately diverse microbiota in the specific-pathogen-free mouse 2 (sDMDMm2) (4) covering five major phyla of prokaryotes (Table 1). This sDMDMm2 (also termed Oligo-MM12) gnotobiotic mouse model has been maintained successfully for over five generations in the clean mouse facility of the University of Bern and LMU Munich. These bacterial strains are publically available from the German Type Culture Collection (DSMZ) (Table 1).
TABLE 1
TABLE 1 Accession numbers and genome characteristics of sDMDMm2 species
OrganismTotal size (bp)G+C content (%)No. of genesDSM no.Accession no.
Lachnoclostridium sp. YL327,225,34348.17,759DSM 26114CP015399
Ruminiclostridium sp. KB183,802,81754.63,981DSM 26090CP015400
Bacteroides sp. I484,839,91842.64,262DSM 26085CP015401
Parabacteroides sp. YL273,306,45650.12,790DSM 28989CP015402
Burkholderiales bacterium YL452,923,06844.12,778DSM 26109CP015403
Erysipelotrichaceae bacterium I464,468,29543.24,659DSM 26113CP015404
Blautia sp. YL585,128,79245.75,232DSM 26115CP015405
Flavonifractor plautii YL313,818,50060.93,929DSM 26117CP015406
Bifidobacterium animalis subsp. animalis YL21,800,48060.11,555DSM 26074CP015407
Lactobacillus reuteri I492,044,77038.81,988DSM 32035CP015408
Akkermansia muciniphila YL442,745,27355.72,746DSM 26127CP015409
Enterococcus faecalis KB13,026,01637.22,938DSM 32036CP015410
Full-genome sequencing of these sDMDMm2 species was carried out from a single colony of each bacterial species grown in brain heart infusion (BHI) medium (Oxoid) supplemented with four chemicals (0.025% cysteine, 0.025% Na2S, 0.001% hemin, and 0.00005% menadione) in an anaerobic chamber (10% CO2, 10% H2, 80% N2), except for Akkermansia muciniphila YL44 (further supplementation of 0.025% mucin to the BHI medium) and Lactobacillus reuteri I49 (grown in MRS medium; Oxoid). Genomic DNA was purified by standard phenol-chloroform extraction. Whole-genome sequencing was carried out using PacBio RS II sequencing platform with a 10-kb insert library and XL/C2 chemistry (5). Hierarchical Genome Assembly Process (HGAP) performed high-quality de novo assembly using a single PacBio library preparation. HGAP consisted of preassembly, de novo assembly with Celera Assembler, HGAP2 assembly, and circularization (6). The assembled sequences were annotated using the RAST server (7).

Accession number(s).

All 12 assembled sequences have been deposited in DDBJ/ENA/GenBank under the accession numbers as provided in Table 1.

ACKNOWLEDGMENTS

We acknowledge Mélanie Dupasquier and Emmanuel Beaudoing at the Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Switzerland for PacBio sequencing.

REFERENCES

1.
Macpherson AJ, McCoy KD. 2015. Standardised animal models of host microbial mutualism. Mucosal Immunol 8:476–486.
2.
Schaedler RW, Dubos R, Costello R. 1965. The development of the bacterial flora in the gastrointestinal tract of mice. J Exp Med 122:59–66.
3.
Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP, Schauer DB, Fox JG. 1999. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol 65:3287–3292.
4.
Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, Brugiroux S, Keller I, Macpherson JA, Rupp S, Stolp B, Stein JV, Stecher B, Sauer U, McCoy KD, Macpherson AJ. 2015. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun 6:8292.
5.
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133–138.
6.
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569.
7.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 4Number 527 October 2016
eLocator: 10.1128/genomea.00951-16

History

Received: 14 July 2016
Accepted: 26 July 2016
Published online: 15 September 2016

Contributors

Authors

Yasuhiro Uchimura
Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
Madeleine Wyss
Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
Sandrine Brugiroux
Max-von-Pettenkofer Institute and German Centre for Infection Research (DZIF), Munich, Germany
Julien P. Limenitakis
Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
Bärbel Stecher
Max-von-Pettenkofer Institute and German Centre for Infection Research (DZIF), Munich, Germany
Kathy D. McCoy
Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
Andrew J. Macpherson
Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland

Notes

Address correspondence to Andrew J. Macpherson, [email protected].
Y.U. and M.W. contributed equally to this article.

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy