Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • 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 Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • 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 Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Applied and Environmental Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Environmental Microbiology

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

Stefanie Kautz, Benjamin E. R. Rubin, Jacob A. Russell, Corrie S. Moreau
Stefanie Kautz
aField Museum of Natural History, Department of Zoology, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benjamin E. R. Rubin
aField Museum of Natural History, Department of Zoology, Chicago, Illinois, USA
bUniversity of Chicago, Committee on Evolutionary Biology, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jacob A. Russell
cDrexel University, Department of Biology, Philadelphia, Pennsylvania, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Corrie S. Moreau
aField Museum of Natural History, Department of Zoology, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AEM.03107-12
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • Fig 1
    • Open in new tab
    • Download powerpoint
    Fig 1

    Phylogenetic tree of bacteria associated with Cephalotes varians turtle ants and their GenBank relatives. Shown is a maximum likelihood phylogeny of the most prevalent OTUs as generated by 454 sequencing and by cloning. For each method, we clustered reads (454 sequencing) or sequences (cloning) at 97% similarity and selected the top clusters that accounted for 90% of reads or sequences, respectively. The branch color and inner circle refer to the source from which the bacteria were isolated, the middle circle refers to the bacterial order, and the outer circle refers to the method used to acquire the respective sequence. Colony CSM1323 was excluded from these analyses due to an infection with Entomoplasmatales bacteria. Please note the misplacement of Campylobacterales, which should group with other Proteobacteria.

  • Fig 2
    • Open in new tab
    • Download powerpoint
    Fig 2

    Comparison of bacterial communities in Cephalotes varians ants detected through 454 pyrosequencing (upper rows) and cloning (lower rows). Samples were prepared from dissected ant body parts or entire workers of Cephalotes varians. Sample names are given above pies and sample sizes below pies. The relative abundance of reads at the taxonomic level of bacterial orders is displayed. Orders that accounted for less than 1% in a sample are summarized in a category termed “other.” “Unclass. gamma” refers to an unclassified gammaproteobacterium that clustered with the Pseudomonadales bacteria.

  • Fig 3
    • Open in new tab
    • Download powerpoint
    Fig 3

    PCoA analysis of bacterial communities from samples that were subjected to 454 sequencing and cloning. Positions of the bacterial communities for each species along the two first principal coordinate axes are illustrated, along with the percentage of variation explained by each axis. Results based on 454 sequencing are displayed with no lines, while the same symbols with black outlines illustrate results obtained through cloning and Sanger sequencing. Note the distinct clustering of samples prepared from colony CSM1323 (gray symbols), which was infected by bacteria of the order Entomoplasmatales (Spiroplasma sp.), and also the clustering of the samples prepared from the hindguts of colony CSM1280 (1280 hind-2 and 1280 hind-3), as well as of the midguts of colony CSM1280 (1280 mid-2 and 1280 mid-3). “Hind” refers to the hindgut, “mid” refers to the midgut, and “wk” refers to samples prepared from whole worker extractions. Results are based on weighted UniFrac distances.

Tables

  • Figures
  • Additional Files
  • Table 1

    The most common OTUs (at 97% identity level) associated with Cephalotes varians ants as discovered by 454 sequencinga

    Cluster no.Cluster sizeCumulative %Bacterial orderThree closest GenBank matchesGenBank accession no.% identityCloningCultivation
    01139229.0RhizobialesUncultured RhizobialesFJ47755196.0YesNo
    Uncultured RhizobialesFJ47764793.4
    Uncultured RhizobialesFJ47765491.3
    0296349.0OpitutalesUncultured OpitutusFJ47761996.3YesNo
    Uncultured OpitutusFJ47756696.1
    Uncultured OpitutusFJ47762095.9
    0368863.4PseudomonadalesUncultured bacteriumFM99604896.7NoNo
    Uncultured bacteriumFM99686996.7
    Uncultured bacteriumFM99608896.7
    0435070.7CampylobacteralesAcrobacter sp.GU30076895.1YesNo
    Acrobacter sp.FN65033395.1
    Acrobacter sp.FN65033295.1
    0519774.8Unclassified gammaproteobacteriumGammaproteobacteriumFJ47767799.0YesNo
    Uncultured gammaproteobacteriumFJ47762699.0
    Uncultured gammaproteobacteriumFJ47760698.8
    0619678.9RhizobialesUncultured RhizobialesFJ47765296.8YesNo
    Uncultured RhizobialesFJ47759396.8
    Uncultured RhizobialesFJ47765196.4
    079680.9BurkholderialesAlcaligenaceae bacteriumFJ47767598.7YesNo
    Uncultured AlcaligenaceaeFJ47756098.0
    Uncultured betaproteobacteriumAF50783893.8
    087782.5XanthomonadalesUncultured XanthomonadaceaeFJ47762296.9YesNo
    Uncultured XanthomonadaceaeFJ47759896.7
    Uncultured XanthomonadaceaeFJ47762196.7
    096983.9RhizobialesUncultured RhizobialesFJ47759395.7YesNo
    Uncultured RhizobialesFJ47765495.7
    Uncultured RhizobialesFJ47765395.5
    106985.3XanthomonadalesUncultured XanthomonadaceaeFJ47761898.3YesNo
    Uncultured XanthomonadaceaeFJ47759492.0
    Uncultured XanthomonadaceaeFJ47755491.8
    115386.4SphingobacterialesUncultured bacteriumFJ47760797.1NoNo
    Uncultured BacteroidetesFJ47764988.3
    Uncultured bacteriumGQ26363983.8
    124787.4BurkholderialesUncultured ComamonadaceaeFJ47761099.0NoNo
    Uncultured bacteriumHQ72824390.3
    Uncultured bacteriumAF39091790.3
    133788.2FlavobacterialesFlavobacterium terraeEF11732990.3YesNo
    Flavobacterium columnareAB01548090.3
    Flavobacterium columnareAZ84290090.3
    143688.9BurkholderialesUncultured AlcaligenaceaeFJ47761294.5YesNo
    Uncultured AlcaligenaceaeFJ47759293.9
    Uncultured AlcaligenaceaeFJ47759093.7
    153389.6XanthomonadalesUncultured XanthomonadaceaeFJ47762296.2YesNo
    Uncultured XanthomonadaceaeFJ47760396.1
    Uncultured XanthomonadaceaeFJ47759896.1
    163290.3OpitutalesUncultured OpitutusFJ47760898.3YesNo
    Uncultured OpitutusFJ47761998.0
    Uncultured OpitutusFJ47762097.5
    • ↵a A total of 400 reads were randomly selected for each of 13 C. varians samples. Colony CSM1323 was excluded, as it was infected with Enteroplasmatales bacteria, which strongly biased the data toward this group of bacteria alone. This table provides the cluster size, cumulative percentage, the three top BLAST hits, GenBank accession numbers, percent identity, and the detection of the same OTUs through cloning or cultivation. Sixteen OTUs accounted for about 90% of bacterial diversity. BLAST searches were performed against the NCBI GenBank database on 12 October 2011.

Additional Files

  • Figures
  • Tables
  • Supplemental material

    Files in this Data Supplement:

    • Supplemental file 1 -

      Ant bacterial species richness rarefaction curves (Fig. S1).

      PDF, 377K

    • Supplemental file 2 -

      Overview of culture-independent approaches of bacterial diversity (Fig. S2).

      PDF, 8.6K

    • Supplemental file 3 -

      Comparison of bacterial communities associated with different body parts of Cephalotes varians ants detected through 454 pyrosequencing (Fig. S3).

      PDF, 272K

    • Supplemental file 4 -

      Sample characteristics and alpha diversity measures for all samples subjected to 454 pyrosequencing and to Sanger sequencing of clone libraries (Table S1).

      PDF, 360K

    • Supplemental file 5 -

      Information on the sequences utilized in this study (Table S2).

      PDF, 574K

    • Supplemental file 6 -

      RDP library comparison results for 454 and clone libraries (Table S3).

      PDF, 193K

PreviousNext
Back to top
Download PDF
Citation Tools
Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity
Stefanie Kautz, Benjamin E. R. Rubin, Jacob A. Russell, Corrie S. Moreau
Applied and Environmental Microbiology Dec 2012, 79 (2) 525-534; DOI: 10.1128/AEM.03107-12

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 Applied and Environmental Microbiology 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.
Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity
(Your Name) has forwarded a page to you from Applied and Environmental Microbiology
(Your Name) thought you would be interested in this article in Applied and Environmental Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity
Stefanie Kautz, Benjamin E. R. Rubin, Jacob A. Russell, Corrie S. Moreau
Applied and Environmental Microbiology Dec 2012, 79 (2) 525-534; DOI: 10.1128/AEM.03107-12
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • MATERIALS AND METHODS
    • RESULTS
    • DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About AEM
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AppEnvMicro

@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

 

Print ISSN: 0099-2240; Online ISSN: 1098-5336