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 .
Accession numbers and genome characteristics of sDMDMm2 species
| Organism | Total size (bp) | G+C content (%) | No. of genes | DSM no. | Accession no. |
|---|---|---|---|---|---|
| Lachnoclostridium sp. YL32 | 7,225,343 | 48.1 | 7,759 | DSM 26114 | CP015399 |
| Ruminiclostridium sp. KB18 | 3,802,817 | 54.6 | 3,981 | DSM 26090 | CP015400 |
| Bacteroides sp. I48 | 4,839,918 | 42.6 | 4,262 | DSM 26085 | CP015401 |
| Parabacteroides sp. YL27 | 3,306,456 | 50.1 | 2,790 | DSM 28989 | CP015402 |
| Burkholderiales bacterium YL45 | 2,923,068 | 44.1 | 2,778 | DSM 26109 | CP015403 |
| Erysipelotrichaceae bacterium I46 | 4,468,295 | 43.2 | 4,659 | DSM 26113 | CP015404 |
| Blautia sp. YL58 | 5,128,792 | 45.7 | 5,232 | DSM 26115 | CP015405 |
| Flavonifractor plautii YL31 | 3,818,500 | 60.9 | 3,929 | DSM 26117 | CP015406 |
| Bifidobacterium animalis subsp. animalis YL2 | 1,800,480 | 60.1 | 1,555 | DSM 26074 | CP015407 |
| Lactobacillus reuteri I49 | 2,044,770 | 38.8 | 1,988 | DSM 32035 | CP015408 |
| Akkermansia muciniphila YL44 | 2,745,273 | 55.7 | 2,746 | DSM 26127 | CP015409 |
| Enterococcus faecalis KB1 | 3,026,016 | 37.2 | 2,938 | DSM 32036 | CP015410 |
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.
Footnotes
Citation Uchimura Y, Wyss M, Brugiroux S, Limenitakis JP, Stecher B, McCoy KD, Macpherson AJ. 2016. Complete genome sequences of 12 species of stable defined moderately diverse mouse microbiota 2. Genome Announc 4(5):e00951-16. doi:10.1128/genomeA.00951-16.
REFERENCES
- 1.Macpherson AJ, McCoy KD. 2015. Standardised animal models of host microbial mutualism. Mucosal Immunol 8:476–486. doi: 10.1038/mi.2014.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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. doi: 10.1084/jem.122.1.59. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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. doi: 10.1126/science.1162986. [DOI] [PubMed] [Google Scholar]
- 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. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 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. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]