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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162460
mra00205-24
10.1128/mra.00205-24
mra.00205-24
Genome Sequences
clinical-microbiologyClinical MicrobiologyDraft genome sequence of two Fusobacterium varium strains isolated from patients in Kazakhstan with colorectal cancer
Kurentay Botakoz 1
Gusmaulemova Alua 1
Utupov Talgat 1
Auganova Dana 1
Tarlykov Pavel 1
Daniyarov Asset 2 3
Khamzina Saule 4
Mamlin Meiram 4
Kozhakhmetov Arman 5
Shalekenov Sanzhar 4
https://orcid.org/0000-0001-8723-3752
Kulmambetova Gulmira 1 Conceptualization Data curation Formal analysis Project administration Supervision Writing – original draft Writing – review and editing kulmambetova@biocenter.kz

1 National Center for Biotechnology , Astana, Kazakhstan
2 National Laboratory Astana, Nazarbayev University , Astana, Kazakhstan
3 L.N. Gumilyov Eurasian National University , Astana, Kazakhstan
4 National Research Oncology Center , Astana, Kazakhstan
5 Nazarbayev University School of Medicine , Astana, Kazakhstan
Editor Rasko David University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Gulmira Kulmambetova, kulmambetova@biocenter.kz
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00205-2404 3 2024
26 7 2024
Copyright © 2024 Kurentay et al.
2024
Kurentay et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Fusobacterium varium is a Gram-negative, invasive, obligate anaerobe in the gastrointestinal tract microbiota, associated with various clinical conditions, including colorectal cancer (CRC). Here, we announce the draft genome sequence of two F. varium strains Fv36kaz and Fv63kaz from patients with CRC in Kazakhstan.

KEYWORDS

Fusobacterium varium
genome sequence
colorectal cancer
Ministry of Education and Science of the Republic of Kazakhstan (Ministry of Education and Science, Republic of Kazakhstan) AP14869820 Kulmambetova Gulmira cover-dateSeptember 2024
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pmcANNOUNCEMENT

Fusobacterium varium, an opportunistic pathogen, is mostly reported in ulcerative colitis and should be considered a potential cause of colorectal cancer (CRC) (1–4).

Biopsy samples were collected from the CRC tissue of patients from the National Research Oncology Center. The homogenized solution from the biopsy, which was stored in 20% sucrose, was cultivated on Columbia agar (5% defibrinated sheep blood, 1 µg/mL menadione, 5 µg/mL hemin, 3 µg/mL josamycin, 4 µg/mL vancomycin, and 1 µg/mL neomycin) and incubated for 72 h under anaerobic conditions in an AnaeroGen system (Thermo) at 37°C. The isolated single colonies were identified as F. varium by V1–V4 region fragment of 16S rRNA gene sequencing with more than 99% similarity for strains and the Bruker Biotyper microbial identification system. About 20 µL reactions mix contained template DNA, 0.2 U Taq Polymerase, 2 mM each dNTP, 10× PCR buffer, 25 mM MgCl2, and 10 pmol primers (8 f 5′-AGAGTTTGATCCTGGCTCAG-3′, 806R 5′-GGACTACCAGGGTATCTAAT-3′). The PCR annealing temperature was set to 55°C for 30 cycles. Sequencing was performed using a 3730 Genetic Analyzer (Thermo). The comparative method was constructed using the NCBI BLAST nucleotide, comparing the sequencing of both strains to the reference Fv (ATCC 27725). For DNA isolation, the colonies were grown at 37°C in Columbia agar (5% defibrinated sheep blood, 1 µg/mL menadione, 5 µg/mL hemin, 3 µg/mL josamycin, 4 µg/mL vancomycin, and 1 µg/mL neomycin) for 72 h under anaerobic condition. DNA was extracted using a QIAamp DNA mini kit (Qiagen). An Illumina MiSeq platform was used to carry out whole-genome sequencing, and a MiSeq reagent v3 600 cycles cartridge was used. DNA libraries were prepared using an Illumina DNA Prep kit. The total number of reads for Fv36kaz was 3,082,394, and the total number of reads for Fv63kaz was 2,402,302. Quality control and trimming of forward and reverse reads for both strains Fv36kaz and Fv63kaz were performed using Trim Galore version 0.6.5dev (5). The genome was assembled using Unicycler v0.4.8 (6). Contigs were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.6 (7). Default parameters were used for all software. The genome of F. varium strain Fv36kaz with 72-fold coverage had a length of 3,388,962 bp, 145 contigs, an N50 value was 74,423 bp, and a G + C content of 29.01%. The genome of F. varium strain Fv63kaz with 185-fold coverage had a length of 3,393,562 bp, 107 contigs, an N50 value was 91,866 bp, and a G + C content of 29.11%. Additionally, annotation by the Bacterial and Viral Bioinformatics Resource Center Annotation Service of the Fv36kaz had 3,262 coding DNA sequences (CDSs), and Fv63kaz had 3,221 CDSs (8).

ACKNOWLEDGMENTS

This work was funded by grant AP14869820 “Thе role of Fusоbасtеrium nuсlеаtum in соlоrесtаl саrсinоgеnеsis,” from the Ministry of Science and Higher Education of the Republic of Kazakhstan.

DATA AVAILABILITY

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBAJGW000000000 (Fv36kaz) and JBAKJD000000000 (Fv63kaz). The raw data from BioProject numbers PRJNA1078108 (Fv36kaz) and PRJNA1079513 (Fv63kaz) were submitted to the NCBI Sequence Read Archive under experiment accession numbers SRR28022417 (Fv36kaz) and SRR28059462 (Fv63kaz). The 16S rRNA sequences from two F. varium were deposited in GenBank as separate submissions under accession numbers PP789727-PP789728 (Fv36kaz) and PP800236-PP800237 (Fv63kaz).
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