Lyticase Facilitates Mycobiome Resolution Without Disrupting Microbiome Fidelity in Primates.

Journal Article (Journal Article)

Background

Microbiome research has expanded to consider contributions of microbial kingdoms beyond bacteria, including fungi (i.e., the mycobiome). However, optimal specimen handling protocols are varied, including uncertainty of how enzymes utilized to facilitate fungal DNA recovery may interfere with bacterial microbiome sequencing from the same samples.

Methods

With Institutional Animal Care and Use Committee approval, fecal samples were obtained from 20 rhesus macaques (10 males, 10 females; Macaca mulatta). DNA was extracted using commercially available kits, with or without lyticase enzyme treatment. 16S ribosomal RNA (bacterial) and Internal Transcribed Spacer (ITS; fungal) sequencing was performed on the Illumina MiSeq platform. Bioinformatics analysis was performed using Qiime and Calypso.

Results

Inclusion of lyticase in the sample preparation pipeline significantly increased usable fungal ITS reads, community alpha diversity, and enhanced detection of numerous fungal genera that were otherwise poorly or not detected in primate fecal samples. Bacterial 16S ribosomal RNA amplicons obtained from library preparation were statistically unchanged by the presence of lyticase.

Conclusions

We demonstrate inclusion of the enzyme lyticase for fungal cell wall digestion markedly enhances mycobiota detection while maintaining fidelity of microbiome identification and community features in non-human primates. In restricted sample volumes, as are common in limited human samples, use of single sample DNA isolation will facilitate increased rigor and controlled approaches in future work.

Full Text

Duke Authors

Cited Authors

  • Pierre, JF; Phillips, GJ; Chandra, LC; Rendina, DN; Thomas-Gosain, NF; Lubach, GR; Lyte, M; Coe, CL; Gosain, A

Published Date

  • November 2021

Published In

Volume / Issue

  • 267 /

Start / End Page

  • 336 - 341

PubMed ID

  • 34186310

Pubmed Central ID

  • PMC8678161

Electronic International Standard Serial Number (EISSN)

  • 1095-8673

International Standard Serial Number (ISSN)

  • 0022-4804

Digital Object Identifier (DOI)

  • 10.1016/j.jss.2021.06.023

Language

  • eng