RESEARCH ARTICLE

Genome analysis of Bacteroides sp.CACC 737 isolated from feline for its potential application

Jung-Ae Kim1,2http://orcid.org/0000-0002-0694-477X, Min Young Jung1http://orcid.org/0000-0001-9599-2345, Dae-Hyuk Kim1,3http://orcid.org/0000-0002-9948-5313, Yangseon Kim1,*http://orcid.org/0000-0002-8285-3407
Author Information & Copyright
1Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea
2Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, Korea
3Department of Molecular Biology, Jeonbuk National University, Jeonju 54896, Korea
*Corresponding author: Yangseon Kim, Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea., Tel: +82-63-536-6712, E-mail: yangseon@cialm.or.kr

© Copyright 2020 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Aug 04, 2020; Revised: Sep 21, 2020; Accepted: Oct 15, 2020

Published Online: Nov 30, 2020

Abstract

Bacteroides sp. CACC 737 was isolated from a feline, and its potential probiotic properties were characterized using functional genome analysis. Whole-genome sequencing was performed using the PacBio RSII and Illumina HiSeq platforms. The complete genome of strain CACC 737 contained 4.6 Mb, with a guanine (G) + cytosine (C) content of 45.8%, six cryptic plasmids, and extracellular polysaccharide gene as unique features. The strain was beneficial to animal health when consumed as feed, for example, for ameliorating immunological dysfunctions and metabolic disorders. The genome information adds to the comprehensive understanding of Bacteroides sp. and suggests potential animal-related industrial applications for this strain.

Keywords: Bacteroides sp.; Feline; Whole genome sequencing

ANNOUNCEMENT

Bacteroides species are gram-negative, anaerobic, non-spore-forming, bile-resistant bacteria that reside in the gut. They constitute approximately 25% to 30% of the intestinal gut microbiota of humans and other animals [1]. These bacteria have been proposed as next-generation probiotics by virtue of the action on the intestinal immune system [2]. In companion animals, Bacteroides associated with immune proteins, such as Tumor necrosis factor (TNF)-α and decreased the relative abundance with chronic enteropathy [3,4].

We isolated Bacteroides sp. CACC 737 (KACC 22065) from the feces of a male 9-year-old Persian chinchilla in Korea. The sample was incubated in anaerobic atmosphere (5% carbon dioxide, 5% hydrogen, and 90% nitrogen) at 37°C for 48 h on De, Rogosa and Sharpe (MRS) media. The isolate was considered to be a novel species of Bacteroides based on its 16S rRNA sequence that displayed the highest similarity to the type strain B. uniformis ATCC8492T (97.5%), which was below the suggested novel species recognition threshold of 98.6% [5]. Genomic DNA was extracted from CACC 737 cell pellets using a DNeasy UltraClean microbial kit (QIAGEN, Hilden, Germany), consistent with the manufacturer’s instructions. The isolated DNA was sequenced using single molecular real-time Portal (v2.3) with the PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA; Macrogen, Seoul, Korea). The annotation of the genome sequences was carried out using the combined results of the automatic National Center for Biotechnology Information Prokaryotic Genomes Annotation Pipeline and the Rapid Annotations Subsystems Technology prokaryotic genome annotation server (http://rast.nmpdr.org) [6]. The clustered regularly interspaced short palindromic repeats (CRISPR) were assessed using CRISPR web server (http://crispr.i2bc.paris-saclay.fr) [7,8].

Bacteroides species harbor cryptic plasmids at a high frequency (50%) [9]. The complete genome of Bacteroides sp. CACC 737 genome revealed six cryptic plasmids ranging from 20 to 40 kb with an average GC content of 40.9% as well as a single circular chromosome of 4,470,359 bp with a GC content of 46.0% (Table 1 and Fig. 1A). The genome also contained 13 rRNAs and 69 transfer RNAs. A total of 3,938 protein-coding sequences (CDSs) were identified. Plasmids include hypothetical proteins and include genes involved in carbohydrate metabolism. Furthermore, 3,938 CDSs were specifically to clusters of 20 Clusters of Orthologous Groups of proteins (COGs)-based functional categories (Fig. 1B). Many genes were classified into functional categories for carbohydrate transport and metabolism (n = 270), cell wall/membrane/envelope biogenesis (n = 263), recombination and repair (n = 231), inorganic ion transport and metabolism (n = 227), amino acid transport and metabolism (n = 176), translation, ribosomal structure, and biogenesis (n = 151).

Table 1. Genome overview of Bacteroides sp. CACC 737
Attribute Chromosome Plasmids
1 2 3 4 5 6
Size (kb) 4,470 29 22 40 23 29 20
GC% 45.96 40.69 41.13 44.75 39.87 40.88 38.36
Protein 3761 31 25 39 35 31 16
rRNA 13 - - - - - -
tRNA 65 1 - 3 - - -
Acession No. CP 059408 CP 059406 CP 059407 CP 059409 CP 059410 CP 059411 CP 059412

GC, guanine-cytosine; rRNA, ribosomal RNA; tRNA, transfer RNA.

Download Excel Table
jast-62-6-952-g1
Fig. 1. Genome features of Bacteroides sp. CACC 737. (A) Circular genome maps of Bacteroides sp. CACC 737 chromosome and plasmids. Circles from the outside to the center denote rRNA and tRNA gene, reverse strand CDS, forward strand CDS, GC skew, and GC content. (B) Genome number of COG functional categories; rRNA, ribosomal RNA; tRNA, transfer RNA; COG, clusters of orthologous group; CDS, coding sequence; GC, guanine-cytosine.
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Two confirmed CRISPR regions (1 and 2) and one questionable CRISPR 9 region were detected. The pattern was identified as the CRISPR-CAS II type. The characterization of type II elements may reveal molecular genome editing tools for the development of next-generation probiotics [10]. The complete genome sequence of Bacteroides sp. CACC 737 will provide fundamental knowledge of the probiotic effects in host healthcare.

The complete genome of strain CACC 737 has been deposited to the National Center for Biotechnology Information GenBank database under accession numbers CP059408 (chromosome) and CP059406, CP059407, CP059409 - CP059412 (plasmids).

Competing interests

No potential conflict of interest relevant to this article was reported.

Funding sources

This research was supported the Strategic Initiative for Microbiomes in Agriculture and Food grant No. 918002-4, Ministry of Agriculture, Food and Rural Affairs, Korea and the Next-Generation BioGreen 21 Program (Project No. PJ01322304), Rural Development Administration, Korea.

Acknowledgements

Not applicable.

Availability of data and material

Upon reasonable request, the datasets of this study can be available from the corresponding author.

Authors’ contributions

Conceptualization: Kim Y.

Data curation: Kim JA.

Formal analysis: Jung MY.

Methodology: Kim JA.

Software: Jung MY.

Validation: Kim JA, Kim DH.

Investigation: Kim Y.

Writing - original draft: Kim JA, Kim Y.

Writing - review & editing: Kim Y.

Ethics approval and consent to participate

This article does not require IRB/IACUC approval because there are no human and animal participants.

REFERENCES

1.

Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev. 2007; 20:593-621

2.

Dahiya DK, Renuka , Dangi AK, Shandilya UK, Puniya AK, Shukla P. New-generation probiotics: perspectives and applications.In In: Faintuch J, Fainguch S, editors.editors Microbiome and metabolome in diagnosis, therapy, and other strategic applications. Cambridge, MA: Academic Press. 2019; p p. 417-24

3.

Xu H, Huang W, Hou Q, Kwok LY, Laga W, Wang Y, et al. Oral administration of compound probiotics improved canine feed intake, weight gain, immunity and intestinal microbiota. Front Immunol. 2019; :10-666

4.

Marsilio S, Pilla R, Sarawichitr B, Chow B, Hill SL, Ackermann MR, et al. Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma. Sci Rep. 2019; :9-19208

5.

Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014; 64:346-51

6.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008; :9-75

7.

Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007; 35Suppl 2:W52-7

8.

Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016; 44:W16-21

9.

Nguyen M, Vedantam G. Mobile genetic elements in the genus Bacteroides, and their mechanism(s) of dissemination. Mobile Genet Elem. 2011; 1:187-96

10.

Hidalgo-Cantabrana C, Crawley AB, Sanchez B, Barrangou R. Characterization and exploitation of CRISPR loci in Bifidobacterium longum. Front Microbiol. 2017; :8-1851

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