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Neurauter M, Vinzelj JM, Strobl SFA, Kappacher C, Schlappack T, Badzoka J, Rainer M, Huck CW, Podmirseg SM. Exploring near-infrared spectroscopy and hyperspectral imaging as novel characterization methods for anaerobic gut fungi. FEMS MICROBES 2024; 5:xtae025. [PMID: 39301047 PMCID: PMC11412074 DOI: 10.1093/femsmc/xtae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/18/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024] Open
Abstract
Neocallimastigomycota are a phylum of anaerobic gut fungi (AGF) that inhabit the gastrointestinal tract of herbivores and play a pivotal role in plant matter degradation. Their identification and characterization with marker gene regions has long been hampered due to the high inter- and intraspecies length variability in the commonly used fungal marker gene region internal transcribed spacer (ITS). While recent research has improved methodology (i.e. switch to LSU D2 as marker region), molecular methods will always introduce bias through nucleic acid extraction or PCR amplification. Here, near-infrared spectroscopy (NIRS) and hyperspectral imaging (HSI) are introduced as two nucleic acid sequence-independent tools for the characterization and identification of AGF strains. We present a proof-of-concept for both, achieving an independent prediction accuracy of above 95% for models based on discriminant analysis trained with samples of three different genera. We further demonstrated the robustness of the NIRS model by testing it on cultures of different growth times. Overall, NIRS provides a simple, reliable, and nondestructive approach for AGF classification, independent of molecular approaches. The HSI method provides further advantages by requiring less biomass and adding spatial information, a valuable feature if this method is extended to mixed cultures or environmental samples in the future.
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Affiliation(s)
- Markus Neurauter
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Julia M Vinzelj
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Sophia F A Strobl
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
| | - Christoph Kappacher
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Tobias Schlappack
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Jovan Badzoka
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Sabine M Podmirseg
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria
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Meili CH, TagElDein MA, Jones AL, Moon CD, Andrews C, Kirk MR, Janssen PH, J. Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores. Appl Environ Microbiol 2024; 90:e0149223. [PMID: 38299813 PMCID: PMC10880628 DOI: 10.1128/aem.01492-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.
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Affiliation(s)
- Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Moustafa A. TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Christina D. Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Catherine Andrews
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Michelle R. Kirk
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | - Savannah Grace
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | | | - Andrew P. Foote
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Yosra I. Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Aymen S. Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Jones AL, Pratt CJ, Meili CH, Soo RM, Hugenholtz P, Elshahed MS, Youssef NH. Anaerobic gut fungal communities in marsupial hosts. mBio 2024; 15:e0337023. [PMID: 38259066 PMCID: PMC10865811 DOI: 10.1128/mbio.03370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.
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Affiliation(s)
- Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rochelle M. Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Hanafy RA, Wang Y, Stajich JE, Pratt CJ, Youssef NH, Elshahed MS. Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827202 DOI: 10.1099/ijsem.0.005735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as 'genera incertae sedis' in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Joshi A, Young D, Huang L, Mosberger L, Munk B, Vinzelj J, Flad V, Sczyrba A, Griffith GW, Podmirseg SM, Warthmann R, Lebuhn M, Insam H. Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms 2022; 10:1972. [PMID: 36296248 PMCID: PMC9612151 DOI: 10.3390/microorganisms10101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 12/02/2022] Open
Abstract
Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.
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Affiliation(s)
- Akshay Joshi
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Diana Young
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Lona Mosberger
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Bernhard Munk
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Julia Vinzelj
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Veronika Flad
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Gareth W. Griffith
- Department of Life Sciences, Cledwyn Building, Aberystwyth University, Aberystwyth SY23 3DD, UK
| | - Sabine Marie Podmirseg
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
| | - Rolf Warthmann
- Biocatalysis, Environment and Process Technology Unit, Life Science and Facility Management, Zurich University of Applied Sciences (ZHAW), 8820 Wadenswil, Switzerland
| | - Michael Lebuhn
- Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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