Here, we report the annotated draft genome sequences of 13 Eggerthellaceae strains isolated from fecal samples from two healthy human volunteers in Karlsruhe, Germany, i.e., Adlercreutzia equolifaciens ResAG-91, Eggerthella lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59.
ABSTRACT
Here, we report the annotated draft genome sequences of 13 Eggerthellaceae strains isolated from fecal samples from two healthy human volunteers in Karlsruhe, Germany, i.e., Adlercreutzia equolifaciens ResAG-91, Eggerthella lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59.
ANNOUNCEMENT
Bacterial strains belonging to the family Eggerthellaceae are members of the human gut microbiome (1). Many strains that are able to metabolize secondary plant compounds, such as digoxin (2), daidzein (3), ellagic acid (4), and pyrrolizidine alkaloids (5), have been investigated. The type strain of Adlercreutzia equolifaciens subsp. equolifaciens is capable of metabolizing daidzein and resveratrol to equol and dihydroresveratrol, respectively (3, 6). Strains of the genus Gordonibacter show the ability to transform ellagic acid into various urolithin derivatives (4). Strains of Eggerthella lenta have been reported to metabolize resveratrol and digoxin to dihydroresveratrol and dihydrodigoxin, respectively (2, 7). Bisanz et al. (8) analyzed 24 different strains of E. lenta and published a variable pan-genome, which underlines the diverse biochemical potential of E. lenta strains (8).
In this study, we announce the annotated draft genome sequences of 13 Eggerthellaceae strains isolated from fecal samples from two healthy (i.e., not suffering from chronic or acute disease) adult human volunteers in Karlsruhe, Germany, namely, Adlercreutzia equolifaciens ResAG-91, Eggerthella lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59.
MRI-F and ResAG strains were isolated at 37°C under strictly anaerobic conditions (N2-CO2-H2 [80:10:10]) in an A45 anaerobic workstation (Don Whitley Scientific). For ResAG strains, isolation was performed as described previously (9). In brief, 7.5 g of a fecal sample was diluted with N2-CO2 (80:20)-flushed brain heart infusion (BHI) medium (Merck) supplemented with 0.5% yeast extract, 0.05% l-cysteine monohydrochloride (Roth), 1 mg ml−1 resazurin sodium salt, 2.5 mg liter−1 heme solution, and 2 μg ml−1 vitamin K1 solution (Sigma-Aldrich). After incubation for 10 min at 37°C at 120 rpm, the sample was centrifuged for 10 min at 300 × g. The supernatant was used as a fecal suspension. A Hungate tube containing 9 ml BHI medium supplemented with ampicillin (1 μg ml−1), colistin (5 μg ml−1), chloramphenicol (5 μg ml−1), cholic acid (18 μg ml−1), and trans-resveratrol (80 μM) was inoculated with 1 ml fresh fecal suspension. For isolation of MRI-F strains, the preparation of the fecal suspension was the same as described above except BHI medium without supplements was used for preparation of the fecal suspension. Pure cultures were obtained from colonies from different agar plates (Table 1).
TABLE 1.
Isolation medium, accession numbers, assembly metrics, and annotated features of the isolated and sequenced strains
| Bacterial species and strain | Isolation mediuma | Estimated insert size (bp) | Total no. of generated reads | No. of trimmed reads | Trimmed reads mapped against respective contigs (%) | Genome size (bp) | No. of contigs (avg coverage [×]) | N50 (bp) | Total no. of genes | G+C content (%) | GenBank accession no. for: |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| WGS sequence | SRA | 16S rRNA | |||||||||||
| Adlercreutzia equolifaciens ResAG-91 | BHI | 273.686 | 985,811 | 977,851 | 99.25 | 2,798,076 | 74 (94.93) | 107,842 | 2,394 | 63.31 | WPOO00000000 | SRX7372034 | MH553318 |
| Eggerthella lenta MRI-F 36 | DSMZ medium 339 | 246.491 | 1,435,469 | 1,423,441 | 99.51 | 3,299,594 | 52 (105.81) | 129,153 | 2,869 | 64.18 | WPOJ00000000 | SRX7372042 | MH741250 |
| Eggerthella lenta MRI-F 37 | DSMZ medium 339 | 261.130 | 1,154,148 | 1,142,818 | 99.30 | 3,296,275 | 54 (89.90) | 98,732 | 2,870 | 64.17 | WPOI00000000 | SRX7372043 | MH741251 |
| Eggerthella lenta MRI-F 40 | DSMZ medium 209 | 266.125 | 1,404,393 | 1,394,064 | 99.57 | 3,300,040 | 51 (111.94) | 141,895 | 2,871 | 64.17 | WPOH00000000 | SRX7372044 | MH741252 |
| Eggerthella lenta ResAG-49 | BHI | 272.720 | 1,418,094 | 1,407,300 | 99.55 | 3,401,533 | 75 (112.32) | 104,054 | 2,974 | 64.02 | WPON00000000 | SRX7372035 | MN326807 |
| Eggerthella lenta ResAG-88 | BHI | 250.974 | 1,142,425 | 1,132,812 | 99.49 | 3,472,506 | 81 (81.46) | 120,561 | 3,005 | 64.02 | WPOM00000000 | SRX7372039 | MH553319 |
| Eggerthella lenta ResAG-121 | BHI | 244.812 | 939,424 | 934,970 | 99.29 | 3,485,223 | 147 (65.21) | 68,051 | 3,049 | 64.01 | WPOL00000000 | SRX7372040 | MN326808 |
| Eggerthella lenta ResAG-145 | BHI | 246.178 | 1,070,253 | 1,061,803 | 99.36 | 3,501,112 | 154 (74.18) | 70,468 | 3,081 | 64.01 | WPOK00000000 | SRX7372041 | MH553320 |
| Gordonibacter urolithinfaciens ResAG-5 | BHI | 273.836 | 1,200,885 | 1,191,875 | 99.20 | 3,654,461 | 148 (88.60) | 63,214 | 3,271 | 65.84 | WPOG00000000 | SRX7372045 | MN326811 |
| Gordonibacter urolithinfaciens ResAG-26 | BHI | 292.846 | 1,308,806 | 1,305,933 | 99.59 | 3,609,950 | 92 (105.51) | 92,475 | 3,205 | 65.91 | WPOF00000000 | SRX7372046 | MN326812 |
| Gordonibacter urolithinfaciens ResAG-43 | BHI | 307.341 | 1,022,809 | 1,020,471 | 99.59 | 3,663,595 | 82 (85.26) | 86,434 | 3,253 | 65.88 | WPOE00000000 | SRX7372036 | MH553321 |
| Gordonibacter urolithinfaciens ResAG-50 | BHI | 282.045 | 960,936 | 957,184 | 99.31 | 3,610,667 | 117 (74.25) | 64,270 | 3,212 | 65.92 | WPOD00000000 | SRX7372037 | MN326813 |
| Gordonibacter urolithinfaciens ResAG-59 | BHI | 284.838 | 1,256,789 | 1,253,103 | 99.62 | 3,664,069 | 77 (97.04) | 98,836 | 3,250 | 65.88 | WPOC00000000 | SRX7372038 | MN326814 |
DSMZ medium 339, Wilkins-Chalgren anaerobe broth; DSMZ medium 209 (Eubacterium lentum medium), chopped meat medium supplemented with 0.5% arginine.
Strains were cultured and genomic DNA was isolated as described previously (9–12). Briefly, strains were cultivated for 2 days at 37°C, under anaerobic conditions, in N2-CO2 (80:20)-flushed BHI broth. DNA was extracted using a blood and tissue kit (Qiagen). DNA was quantified with the double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit on a Qubit version 2.0 fluorometer (Thermo Fischer Scientific) and was adjusted to a concentration of 10 ng μl−1 or 0.2 ng μl−1 for 16S rRNA gene sequencing or whole-genome shotgun (WGS) sequencing, respectively.
Initial molecular identification of the isolated strains by 16S rRNA gene sequencing was performed as described previously (9). The 16S rRNA gene sequences were subjected to a BLASTn search (13) and have been deposited in DDBJ/ENA/GenBank (Table 1). Species identification was performed using BioNumerics software (version 7.6; Applied Maths) with a 98.7% 16S rRNA gene sequence identity threshold, in comparison with related type strains (14).
The genome sequencing library was constructed as described previously (12) using a Nextera XT DNA library preparation kit and a Nextera XT index kit (Illumina). WGS sequencing was performed with an Illumina MiSeq benchtop sequencer using a 500-cycle version 2 kit (read length, 2 × 250 bp). For each strain, the total number of generated reads is listed in Table 1. Data processing was performed as described previously (10–12). Default parameters were used for all software unless otherwise specified. Sequence reads were quality trimmed using Trimmomatic version 0.39 (15) and assembled using SPAdes version 3.13.1 in the careful mode (16, 17). The estimated insert size for each published sequence obtained in this study is listed in Table 1. Adequate trimming was verified by mapping the adapter sequences to the assembled contigs using Bowtie 2 version 2.3.3.1 (18). To eliminate sequence contamination, the contigs were aligned to the genome of coliphage phi-X174 (GenBank accession number NC_001422) using a BLASTn search (13). All contigs of <500 bp were manually excluded, and renaming of contigs was done by Awk (19). To calculate the genome coverage for each strain, trimmed reads were mapped against the remaining contigs by Bowtie 2 (Table 1). Draft genome sequences were annotated using the automated NCBI Prokaryotic Genome Annotation Pipeline (20). The assembly metrics and annotated features of all the strains are given in Table 1.
Data availability.
The WGS project, including raw reads for Adlercreutzia equolifaciens ResAG-91, E. lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59, has been deposited in DDBJ/ENA/GenBank under BioProject accession number PRJNA591748. The versions described in this publication are the first versions and are listed in Table 1.
ACKNOWLEDGMENTS
We thank Lilia Rudolf and Luisa Martinez for excellent technical assistance in the anaerobe laboratory.
We declare no conflicts of interest.
REFERENCES
- 1.Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD. 2019. A new genomic blueprint of the human gut microbiota. Nature 568:499–504. doi: 10.1038/s41586-019-0965-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Koppel N, Bisanz JE, Pandelia ME, Turnbaugh PJ, Balskus EP. 2018. Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. Elife 7:e33953. doi: 10.7554/eLife.33953. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Maruo T, Sakamoto M, Ito C, Toda T, Benno Y. 2008. Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol 58:1221–1227. doi: 10.1099/ijs.0.65404-0. [DOI] [PubMed] [Google Scholar]
- 4.Selma MV, Beltrán D, García-Villalba R, Espín JC, Tomás-Barberán FA. 2014. Description of urolithin production capacity from ellagic acid of two human intestinal Gordonibacter species. Food Funct 5:1779–1784. doi: 10.1039/c4fo00092g. [DOI] [PubMed] [Google Scholar]
- 5.Lanigan GW. 1976. Peptococcus heliotrinreducans, sp. nov., a cytochrome-producing anaerobe which metabolizes pyrrolizidine alkaloids. J Gen Microbiol 94:1–10. doi: 10.1099/00221287-94-1-1. [DOI] [PubMed] [Google Scholar]
- 6.Bode LM, Bunzel D, Huch M, Cho GS, Ruhland D, Bunzel M, Bub A, Franz CM, Kulling SE. 2013. In vivo and in vitro metabolism of trans-resveratrol by human gut microbiota. Am J Clin Nutr 97:295–309. doi: 10.3945/ajcn.112.049379. [DOI] [PubMed] [Google Scholar]
- 7.Jung CM, Heinze TM, Schnackenberg LK, Mullis LB, Elkins SA, Elkins CA, Steele RS, Sutherland JB. 2009. Interaction of dietary resveratrol with animal-associated bacteria. FEMS Microbiol Lett 297:266–273. doi: 10.1111/j.1574-6968.2009.01691.x. [DOI] [PubMed] [Google Scholar]
- 8.Bisanz JE, Soto-Perez P, Lam KN, Bess EN, Haiser HJ, Allen-Vercoe E, Rekdal VM, Balskus EP, Turnbaugh PJ. 2018. Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria. bioRxiv 304840. doi: 10.1101/304840. [DOI]
- 9.Danylec N, Göbl A, Stoll DA, Hetzer B, Kulling SE, Huch M. 2018. Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces. Int J Syst Evol Microbiol 68:1533–1540. doi: 10.1099/ijsem.0.002705. [DOI] [PubMed] [Google Scholar]
- 10.Stoll DA, Danylec N, Dötsch A, Becker B, Huch M. 2018. Draft genome sequence of Salmonella enterica subsp. enterica serovar Enteritidis MS 501, a potential human pathogen isolated from red lettuce (Lactuca sativa var. capitata) in Karlsruhe, Germany. Microbiol Resour Announc 7:e00938-18. doi: 10.1128/MRA.00938-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Danylec N, Stoll DA, Dötsch A, Huch M. 2019. Draft genome sequences of type strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola, Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens. Microbiol Resour Announc 8:e01532-18. doi: 10.1128/MRA.01532-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Danylec N, Stoll DA, Huch M. 2019. Draft genome sequences of type strains of Adlercreutzia muris and Ellagibacter urolithinifaciens, belonging to the family Eggerthellaceae. Microbiol Resour Announc 8:e01306-19. doi: 10.1128/MRA.01306-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- 14.Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K-H, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. 2014. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645. doi: 10.1038/nrmicro3330. [DOI] [PubMed] [Google Scholar]
- 15.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. doi: 10.1089/cmb.2013.0084. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi: 10.1038/nmeth.1923. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Aho AV, Kernighan BW, Weinberger PJ. 1979. Awk—a pattern scanning and processing language. Softw Pract Exp 9:267–279. doi: 10.1002/spe.4380090403. [DOI] [Google Scholar]
- 20.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The WGS project, including raw reads for Adlercreutzia equolifaciens ResAG-91, E. lenta MRI-F 36, MRI-F 37, MRI-F 40, ResAG-49, ResAG-88, ResAG-121, and ResAG-145, and Gordonibacter urolithinfaciens ResAG-5, ResAG-26, ResAG-43, ResAG-50, and ResAG-59, has been deposited in DDBJ/ENA/GenBank under BioProject accession number PRJNA591748. The versions described in this publication are the first versions and are listed in Table 1.