Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Omics Data Sets

Metagenomic Exploration of Atelerix albiventris Gut Microbiome

Makhabbat Amanbayeva, Elmira Anarkulova, Andrey Bogoyavlenskiy, Madina Alexyuk, Anar Imangazy, Vladimir Berezin
Simon Roux, Editor
Makhabbat Amanbayeva
aAbai Kazakh National Pedagogical University, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elmira Anarkulova
aAbai Kazakh National Pedagogical University, Almaty, Kazakhstan
bResearch and Production Center for Microbiology and Virology, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrey Bogoyavlenskiy
bResearch and Production Center for Microbiology and Virology, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrey Bogoyavlenskiy
Madina Alexyuk
bResearch and Production Center for Microbiology and Virology, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anar Imangazy
aAbai Kazakh National Pedagogical University, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vladimir Berezin
bResearch and Production Center for Microbiology and Virology, Almaty, Kazakhstan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Roux
DOE Joint Genome Institute
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.01342-20
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Here, we report the metagenomic analysis of the gut of Atelerix albiventris, an animal typically kept as a pet in Kazakhstan. In this case, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.

ANNOUNCEMENT

Nowadays, pets are becoming more and more important (1, 2). At the same time, not only familiar cats and dogs but also exotic hedgehogs, lizards, snails, and spiders are being acquired as pets. The introduction of exotic domestic pets in the house creates the need for a more thorough study of the pets’ ability to transmit infectious diseases to humans; therefore, the investigation of their microbiomes is an important task in assessing the epidemiological well-being of the population.

Here, the viral and microbial community from the feces of a healthy white-bellied pygmy hedgehog, Atelerix albiventris (an ordinary representative of pet shops and minizoos in Almaty, Kazakhstan [43°13′38.6″N, 76°51′52.2″E]), is presented.

Two grams of feces was homogenized in 18 ml of phosphate-buffered saline using the IKA Ultra-Turrax disposable workstation with a disperser tube, filtered using a 0.45-μm membrane to remove most bacteria, and concentrated by ultracentrifugation using a Beckman Coulter Avanti J30I ultracentrifuge at 29,000 rpm for 2 h at 4°C.

Viral RNA was extracted using a QIAamp viral RNA minikit (Qiagen). The sample extracts were pretreated with RNase-free DNase (Promega). Double-stranded cDNA was obtained with a SuperScript double-stranded cDNA synthesis kit (Invitrogen) according to the manufacturer’s instructions. Total DNA was isolated using a PureLink genomic DNA extraction kit (Thermo Fisher Scientific, USA) and stored at −80°C. Genomic DNA and synthesized double-stranded cDNA were pooled. DNA libraries were prepared from 1 ng of the pooled isolated nucleic acids using the Nextera XT DNA sample preparation kit (Illumina, USA). High-throughput sequencing was performed by using an Illumina MiSeq system (paired-end sequencing [2 × 300 bp] with a MiSeq kit v3).

The resulting sequences (852,082 reads) were tested for quality using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and Trimmomatic v0.36 (3) from the Genome Detective tool (4). After the removal of low-quality reads (Q scores of <30) and adapter trimming, 766,874 reads were analyzed by the Kaiju program (5). All tools were run with default parameters unless otherwise specified.

Taxonomic classification of metagenomic data for the Atelerix albiventris feces showed that 1% of the sequences corresponded to archaea, 11% to lower eukaryotes, 27% to viruses, 57% to bacteria, and 4% to unclassified organisms (Fig. 1). Although most of the sequences belonged to either normal microflora or microorganisms from food, unfortunately, 1 to 2% of the reads were assigned to microflora potentially capable of causing a number of diseases in humans, including sequences of representatives of Candida, Salmonella, Mycobacterium, Acinetobacter, Klebsiella, Chlamydia, Yersinia, Bartonella, Herpesviridae, Bunyaviridae, rabies virus, and the tick-borne encephalitis virus group.

FIG 1
  • Open in new tab
  • Download powerpoint
FIG 1

Taxonomic diversity of the microbial and viral communities of Atelerix albiventris. Taxonomic assignment of the metagenomic reads was based on the NCBI BLAST nonredundant plus eukaryotes database using Kaiju.

Data availability.Raw sequence reads are available under BioProject accession number PRJNA656141 and SRA accession number SRR12422733.

ACKNOWLEDGMENTS

This work was supported by a Grant-in-Aid for Scientific Research from Abai Kazakh National Pedagogical University and by the Ministry of Education and Science of the Republic of Kazakhstan (grant BR05236330).

We declare no conflicts of interest. This article does not contain any studies with human or animal subjects performed by any of the authors.

FOOTNOTES

    • Received 24 November 2020.
    • Accepted 8 December 2020.
    • Published 7 January 2021.
  • Copyright © 2021 Amanbayeva et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Riley PY,
    2. Chomel BB
    . 2005. Hedgehog zoonoses. Emerg Infect Dis 11:1–5. doi:10.3201/eid1101.040752.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Okada K,
    2. Kondo H,
    3. Sumi A,
    4. Kagawa Y
    . 2018. A retrospective study of disease incidence in African pygmy hedgehogs (Atelerix albiventris). J Vet Med Sci 80:1504–1510. doi:10.1292/jvms.18-0238.
    OpenUrlCrossRef
  3. 3.↵
    1. Bolger AM,
    2. Lohse M,
    3. Usadel B
    . 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    1. Vilsker M,
    2. Moosa Y,
    3. Nooij S,
    4. Fonseca V,
    5. Ghysens Y,
    6. Dumon K,
    7. Pauwels R,
    8. Alcantara LC,
    9. Vanden Eynden E,
    10. Vandamme A-M,
    11. Deforche K,
    12. de Oliveira T
    . 2019. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 35:871–873. doi:10.1093/bioinformatics/bty695.
    OpenUrlCrossRef
  5. 5.↵
    1. Menzel P,
    2. Ng KL,
    3. Krogh A
    . 2016. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun 7:11257. doi:10.1038/ncomms11257.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Metagenomic Exploration of Atelerix albiventris Gut Microbiome
Makhabbat Amanbayeva, Elmira Anarkulova, Andrey Bogoyavlenskiy, Madina Alexyuk, Anar Imangazy, Vladimir Berezin
Microbiology Resource Announcements Jan 2021, 10 (1) e01342-20; DOI: 10.1128/MRA.01342-20

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Metagenomic Exploration of Atelerix albiventris Gut Microbiome
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Metagenomic Exploration of Atelerix albiventris Gut Microbiome
Makhabbat Amanbayeva, Elmira Anarkulova, Andrey Bogoyavlenskiy, Madina Alexyuk, Anar Imangazy, Vladimir Berezin
Microbiology Resource Announcements Jan 2021, 10 (1) e01342-20; DOI: 10.1128/MRA.01342-20
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X