ABSTRACT
Turicibacter is a common mammalian gut commensal; however, very few genomes have been sequenced, and little is understood regarding its importance for host health. Here, we add a complete Turicibacter sp. genome isolated from a spore-forming community in mice.
KEYWORDS: gut microbiota, bacteria, metabolism, spore forming bacteria, genomics
ANNOUNCEMENT
Turicibacter is a genus of Bacilli within phylum Bacillota (1). This Gram-positive spore-forming bacterium lives in the intestines of humans and other animals (2 – 4). Recent studies point to important roles for Turicibacter in intestinal health (5). Turicibacter has two established species: Turicibacter sanguinis, isolated from the blood of a febrile patient (3), and Turicibacter bilis, isolated from chicken eggs and pig ileum (4). Other species of Turicibacter likely exist and have been vastly understudied.
We present a draft Turicibacter genome, strain KK003, isolated from mice from a spore-forming (SF) community. To isolate SF bacteria, feces from C57BL/6 mice (IACUC Protocol 00001562) were incubated anaerobically with 0.1% cysteine and 3% chloroform at 37°C for 1 h to kill vegetative bacteria. Chloroform was removed by bubbling CO2 through the sample for 30 s. To propagate SF, the sample was gavaged into a breeder pair of germ-free C57BL/6 mice. To isolate Turicibacter, feces from SF animals were chloroform treated again, serial diluted, and plated on Schaedler agar (Thermo Scientific) at 37°C anaerobically. Individual colonies were picked after 48 h, streaked to isolation, and DNA was extracted from overnight cultures in Schaedler broth using a Purelink Microbiome DNA purification kit according the manufacturer (Invitrogen) for all sequencing. One of the colonies picked was identified as Turicibacter by Sanger 16S rRNA gene sequencing using primers 16S_F:AGAGTTTGATCMTGGC and 16S_R:TACCTTGTTACGACTT and the Silva classifier (6).
The KK003 genome was sequenced using Illumina NovaSeq (paired-end 150) and Oxford Nanopore Technologies (ONT) minION reads. Illumina libraries were prepared with NEBNext Ultra II FS DNA kit (NEB, E7805S), and the resulting 8M reads were adapter and quality-trimmed with cutadapt (v2.10) (7) in the trim_galore (v0.6.6) wrapper using default parameters. ONT libraries were prepared without DNA shearing or size selection using rapid barcoding kit R9.4.1 chemistry (ONT, SQK-RBK004). The resulting 41.8K long reads (120.7M total bases) were basecalled, demultiplexed, adapter, barcode-trimmed with guppy (v6.0.1_gpu), quality-filtered with NanoFilt v2.8 (8) for a minimum average read-quality of 10 and minimum length of 200. The genome was assembled using SPAdes v3.15.5 within Unicycler v0.5.0 “normal mode” (9, 10), annotated with PGAP v6.6 (11). The KK003 assembly contains 2,503,176 bp, 37% GC content, and 2,447 predicted genes, which are 66.23% complete and 100th percentile by Genbank standards using CheckM v1.2.2 (12). The single contig was circularized and rotated within Unicycler by identification of linked ends and a DnaA gene that was put on the forward strand.
The taxonomic classification KK003 is genus Turicibacter, species unclassified (GTDB-Tk - v1.7.0). KK003 is not a member of T. sanguinis or T. bilis because it only shares 80% sequence identity with either species (using FastANI v0.1.3) (13). The nearest genome is Turicibacter sp. TS3 (GCF_009935875.1), which shares 99% sequence identity, indicating that Turicibacter should be their own species. The KK003 genome contains bsh, which codes for choloylglycine hydrolase, the enzyme for bile salt metabolism (5). KK003 contains a bile salt transporter, sulfur metabolism genes, sporulation genes, and elements of a Type II secretion system (Table 1).
TABLE 1.
Key Turicibacter sp. K003 genomic elements
| Genes | Type | Protein name and function |
|---|---|---|
| bsh | Bile salt metabolism | Choloylglycine hydrolase 1 |
| bsh | Bile salt metabolism | Choloylglycine hydrolase 2 |
| unnamed | Bile salt metabolism | Conjugated bile salt MFS transporter |
| unnamed | Metabolism | Putative mucin/carbohydrate-binding domain-containing protein |
| unnamed | Metabolism | Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme |
| unnamed | Metabolism | DegT/DnrJ/EryC1/StrS family aminotransferase |
| unnamed | Sulfur metabolism | Desulfoferrodoxin family protein |
| sufB | Sulfur metabolism | sufB Fe-S cluster assembly protein |
| sufC | Sulfur metabolism | sufC Fe-S cluster assembly ATPase |
| sufD | Sulfur metabolism | sufD Fe-S cluster assembly protein |
| unnamed | Sulfur metabolism | TauE/SafE family protein sulfite exporter |
| unnamed | Sulfur metabolism | Radical SAM/SPASM domain-containing protein |
| cotE | Sporulation | CotE outer spore coat protein |
| gerQ | Sporulation | GerQ spore coat protein |
| spo0A | Sporulation | Spo0A sporulation transcription factor |
| ffh | Secretion system | Signal recognition particle protein |
| ftsY | Secretion system | FtsY signal recognition particle-docking protein |
| IspA | Secretion system | Signal peptidase II |
| lepB | Secretion system | Signal peptidase I |
| unnamed | Secretion system | Type II secretion system F family protein |
| unnamed | Secretion system | GspE/PulE family protein |
| yajC | Secretion system | YajC preprotein translocase subunit |
| yihY | Virulence | YihY/virulence factor BrkB family protein |
| unnamed | Toxin–antitoxin | Type II system antitoxin SocA domain-containing protein |
| unnamed | Toxin–antitoxin | Type II system PemK/MazF family toxin |
ACKNOWLEDGMENTS
We thank the Round lab for help with mouse work, bacteria isolation, and editing this manuscript.
Contributor Information
June L. Round, Email: june.round@path.utah.edu.
Vanja Klepac-Ceraj, Wellesley College, Wellesley, Massachusetts, USA .
DATA AVAILABILITY
The genome is under GCF_037014675.1; reads are SRR28014011, SRR28014012.
REFERENCES
- 1. Oren A, Garrity GM. 2021. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 71. doi: 10.1099/ijsem.0.005056 [DOI] [PubMed] [Google Scholar]
- 2. Auchtung TA, Holder ME, Gesell JR, Ajami NJ, Duarte RTD, Itoh K, Caspi RR, Petrosino JF, Horai R, Zárate-Bladés CR. 2016. Complete genome sequence of Turicibacter sp strain H121, isolated from the feces of a contaminated germ-free mouse. Genome Announc 4:e00114-16. doi: 10.1128/genomeA.00114-16 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Bosshard PP, Zbinden R, Altwegg M. 2002. Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int J Syst Evol Microbiol 52:1263–1266. doi: 10.1099/00207713-52-4-1263 [DOI] [PubMed] [Google Scholar]
- 4. Maki JJ, Looft T. 2022. Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum. Int J Syst Evol Microbiol 72:005153. doi: 10.1099/ijsem.0.005153 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Lynch JB, Gonzalez EL, Choy K, Faull KF, Jewell T, Arellano A, Liang J, Yu KB, Paramo J, Hsiao EY. 2023. Gut microbiota Turicibacter strains differentially modify bile acids and host lipids. Nat Commun 14:3669. doi: 10.1038/s41467-023-39403-7 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. doi: 10.1093/nar/gks1219 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10. doi: 10.14806/ej.17.1.200 [DOI] [Google Scholar]
- 8. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669. doi: 10.1093/bioinformatics/bty149 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. 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]
- 10. Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. doi: 10.1371/journal.pcbi.1005595 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. 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]
- 12. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36:1925–1927. doi: 10.1093/bioinformatics/btz848 [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 genome is under GCF_037014675.1; reads are SRR28014011, SRR28014012.