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A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework

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Abstract

Obligate anaerobic fungi of the phylum Neocallimastigomycota play a key role in digesting fibrous feeds in the gut of herbivores, but little is known about their global diversity. In this study, the collective diversity of gut anaerobic fungi was examined using all curated internal transcribed spacer 1 (ITS1) sequences of anaerobic gut fungi available in GenBank. The 262,770 quality-checked fungal ITS1 sequences downloaded from GenBank were assigned to 274 operational taxonomic units (OTUs) at the approximate species level. Of these approximate species-equivalent (Sp-eq) OTUs, 119 were represented by at least five ITS1 sequences, with 38 containing known species and 81 containing no known species. Based on a rarefaction analysis, the currently available ITS1 sequences represent nearly all the major species of gut anaerobic fungi, but much more sequencing effort is needed to assess the actual richness of minor OTUs. One dataset of ITS1 reference sequences (referred to as AF-RefSeq) and one comprehensive taxonomic framework are also presented, and they are shown to be suitable for taxonomic classification of most of the ITS1 sequences in GenBank. The results of the present study may help guide future studies involving taxonomic and phylogenetic analysis of ITS1 sequences of anaerobic fungi and targeted isolation and characterization of new anaerobic fungi.

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Acknowledgements

This work was supported in part by an OARDC Grant (2010-007). S. Paul’s tenure at The Ohio State University was supported by a Cutting Edge Research Enhancement and Scientific Training Award Overseas Fellowship from Department of Biotechnology, Government of India. There is no potential source of conflict of interest regarding this article.

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Authors and Affiliations

  1. Department of Animal Sciences, The Ohio State University, 2029 Fyffe Court, Columbus, OH, 43210, USA

    Shyam Sundar Paul & Zhongtang Yu

  2. ICAR-Central Institute for Research on Buffaloes, Sirsa Road, Hisar, Haryana, 125001, India

    Shyam Sundar Paul

  3. State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China

    Dengpan Bu, Jianchu Xu & Zhongtang Yu

  4. CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry, World Agroforestry Centre, East and Central Asia, Beijing, 100193, China

    Dengpan Bu

  5. Hunan Co-Innovation Center of Animal Production Safety, CICAPS, Changsha, 410128, China

    Dengpan Bu

  6. Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China

    Jianchu Xu

  7. Center of Excellence in Fungal Diversity, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Kevin D. Hyde

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  1. Shyam Sundar Paul
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  2. Dengpan Bu
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Contributions

S.S.P. and Z.Y. conceived the study and prepared the plan of analysis. S.S.P. collected and analyzed the data. S.S.P. and Z.Y. wrote the paper. D.B., J.X. and K.H. emended the paper.

Corresponding author

Correspondence to Zhongtang Yu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1: AF-RefSeq - reference sequence dataset for ITS1 sequences of anaerobic fungi (FASTA 241 kb)

Supplementary material 2: The phylogenetic tree constructed using the AF-RefSeq dataset (PDF 2961 kb)

13225_2018_396_MOESM3_ESM.zip

Supplementary material 3: The AF-PP.RefPkg - A reference package for phylogenetic placement-based taxonomic classification of ITS1 sequences of anaerobic fungi for use with PPLACER. The reference package contains the following eight files: afsgo.fasta, afsgo.phyml.nwk, afsgo_phy_phyml_stats.txt, afsgo_seq_info.csv, afsgo_taxa.csv, CONTENTS.json, Phylo_modelQ5KBdB.json, and treeDf2s_R.tre (ZIP 21 kb)

Supplementary material 4: Rarefaction curves (PPTX 515 kb)

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Paul, S.S., Bu, D., Xu, J. et al. A phylogenetic census of global diversity of gut anaerobic fungi and a new taxonomic framework. Fungal Diversity 89, 253–266 (2018). https://doi.org/10.1007/s13225-018-0396-6

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