Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation

Radwa A. Hanafy, Britny Johnson, Noha H. Youssef, Mostafa S. Elshahed
doi: https://doi.org/10.1101/2020.03.24.005967
Radwa A. Hanafy
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Britny Johnson
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Noha H. Youssef
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mostafa S. Elshahed
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: Mostafa@okstate.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of ingested plant material. Accurate assessment of AGF diversity has been hampered by inherent deficiencies of the internal transcribed spacer1 (ITS1) region as a phylogenetic marker. Here, we report on the development and implementation of the D1/D2 region of the large ribosomal subunit (D1/D2 LSU) as a novel marker for assessing AGF diversity in culture-independent surveys. Sequencing a 1.4-1.5 Kbp amplicon encompassing the ITS1-5.8S rRNA-ITS2-D1/D2 LSU region in the ribosomal RNA locus from fungal strains and environmental samples generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior ITS1-based diversity surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing technology was conducted on fecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified in the 17.7 K sequences obtained, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to twelve different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, and the culturability of a wide range of AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted March 25, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation
Radwa A. Hanafy, Britny Johnson, Noha H. Youssef, Mostafa S. Elshahed
bioRxiv 2020.03.24.005967; doi: https://doi.org/10.1101/2020.03.24.005967
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation
Radwa A. Hanafy, Britny Johnson, Noha H. Youssef, Mostafa S. Elshahed
bioRxiv 2020.03.24.005967; doi: https://doi.org/10.1101/2020.03.24.005967

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4691)
  • Biochemistry (10382)
  • Bioengineering (7698)
  • Bioinformatics (26381)
  • Biophysics (13553)
  • Cancer Biology (10735)
  • Cell Biology (15465)
  • Clinical Trials (138)
  • Developmental Biology (8509)
  • Ecology (12844)
  • Epidemiology (2067)
  • Evolutionary Biology (16891)
  • Genetics (11417)
  • Genomics (15499)
  • Immunology (10643)
  • Microbiology (25269)
  • Molecular Biology (10243)
  • Neuroscience (54611)
  • Paleontology (402)
  • Pathology (1671)
  • Pharmacology and Toxicology (2900)
  • Physiology (4356)
  • Plant Biology (9265)
  • Scientific Communication and Education (1588)
  • Synthetic Biology (2562)
  • Systems Biology (6789)
  • Zoology (1472)