Open access
Announcement
7 May 2020

Draft Genome Sequence of Blautia luti DSM 14534T, Isolated from Human Stool

ABSTRACT

Here, we report the draft sequence of Blautia luti strain DSM 14534T, originally isolated from human feces. This draft contains 74 contigs, comprising 3,718,760 bp with a G+C content of 42.87%. The annotated draft contains 3,338 coding sequences (CDSs) and 110 RNA genes.

ANNOUNCEMENT

Blautia, a genus of anaerobic, nonsporulating, coccobacillus-shaped bacteria from the Firmicutes phylum, is a group of Gram-positive bacteria inhabiting the gastrointestinal tract in different animals, including humans (1). Members of this genus are common inhabitants of the healthy human intestinal microbiota (2) and are one of the most abundant groups in adults (3, 4). One member of this genus, Blautia luti (formerly known as Ruminococcus luti), was originally isolated from human feces and characterized as an anaerobic carbohydrate fermenter (5).
The type strain of B. luti (DSM 14534) was sequenced from lyophilized pure DNA, directly purchased from the DSMZ repository (catalog number 14534; Germany), using an Illumina MiSeq platform in two independent runs. For each run, a Nextera DNA Flex library prep kit was used to prepare the MiSeq library, and MiSeq paired-end reads were generated using a MiSeq reagent kit v3 (600 cycles; Illumina). Reads from both runs were filtered and trimmed by using Trimmomatic (6), with a minimum quality value (QV) score of <30, a minimum nucleotide length of <100, and removal of Illumina adapters, resulting in 2,200,391 reads (coverage, 173.37×). The filtered reads from both runs were used simultaneously to generate a unique assembly (7) using the SPAdes software v3.13.0 (8) with default parameters, including the additional “-careful” parameter. This resulted in an assembly of 74 contigs, comprising 3,718,760 bp with a G+C content of 42.87%. The N50 contig size was 205,916 bp, and the longest contig size was 614,844 bp.
The B. luti genome completeness and contamination were evaluated using CheckM v1.1.2 (9) with default parameters, showing that the completeness was 99.37% and the contamination was 2.53%. The taxonomic features of the B. luti genome confirmed its placement in the Blautia genus by use of the “classify_wf” command of GTDB-tk software v0.3.3 with default parameters (10). Subsequently, the assembled genome was annotated with Prokka v1.13 (11) using the “–rfam,” “–gram pos,” and “–genus, –species, –strain” parameters, which resulted in 3,338 coding sequences (CDSs) and 110 RNA genes. Of the CDSs, 1,089 (32.62%) have a cluster of orthologous groups (COG) assigned, and 1,661 (49.76%) correspond to hypothetical proteins. SignalP 5.0b (12) predicted a signal peptide for 326 CDSs (9.77%). Of the RNA genes, 58 were tRNAs, 7 were rRNAs, and 1 was a transfer-messenger RNA (tmRNA) gene. In a dbCAN2 HMM database search with default parameters and the v8 database (13), a total of 91 B. luti CDSs (2.7% of the total) were predicted to be glycoside hydrolases (GHs) or glycoside transferases (GTs). This number is within the range of the number of GHs observed in most gut-associated microbes (14).

Data availability.

The assembled genome sequence of B. luti strain DSM 14534T was deposited in GenBank under accession number WMBC00000000. Illumina MiSeq raw reads for the two runs for this sequencing project (BioProject number PRJNA590133) can be accessed under accession numbers SRR10482250 and SRR11245637.

ACKNOWLEDGMENTS

This work was developed as part of R.L.O.’s doctoral research, supported by uBiome, Inc., and by a CONICYT National Doctoral Studies Grant (Chile, 2014 to 2017, grant number 21140549). J.P.C. is supported by Universidad Mayor, Chile. J.A.U. is supported by the Millennium Science Initiative of the Ministry of Economy, Development and Tourism, Government of Chile. J.P.-D. acknowledges the support of INACH RT-25-16.

REFERENCES

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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 9Number 197 May 2020
eLocator: 10.1128/mra.00088-20
Editor: David Rasko, University of Maryland School of Medicine

History

Received: 3 February 2020
Accepted: 5 April 2020
Published online: 7 May 2020

Contributors

Authors

Rodrigo L. Ortiz
Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
Felipe Melis-Arcos
Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
Paulo C. Covarrubias
Independent Researcher, Santiago, Chile
Juan A. Ugalde
Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
Zachary S. Apte
Independent Researcher, San Francisco, California, USA
José Pérez-Donoso
BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
Juan P. Cárdenas
Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Huechuraba, Chile
Escuela de Biotecnología, Faculty of Sciences, Universidad Mayor, Campus Huechuraba, Huechuraba, Chile
Daniel E. Almonacid
Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile

Editor

David Rasko
Editor
University of Maryland School of Medicine

Notes

Address correspondence to Juan P. Cárdenas, [email protected], or Daniel E. Almonacid, [email protected].

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