Unleashing the hidden potential of the anaerobic fungi (Neocallimastigomycota)
Bioinformatics and Theoretical Biology
Final Report Abstract
Anaerobic fungi (Neocallimastigomycota) are part of the gut microbiome of many herbivores, where they are responsible for a large proportion of the mechanical and enzymatic fiber digestion. They therefore offer great potential for a more efficient utilization of lignocellulosic residues (worldwide production of about 200 million tons per year). Although interest in the biotechnological use of this understudied group has increased considerably in recent years, there are still many unanswered questions about their life cycle and hardly any standardized methods for studying them. Therefore, a consortium of European anaerobic fungal experts had set up the project "HiPoAF - Unleashing the Hidden Potential of Anaerobic Fungi (Neocallimastigomycota)" to solve fundamental problems in anaerobic fungal research. Standardized protocols for culture media production and cryopreservation were developed and a redundant culture collection of anaerobic fungal isolates was established at all participating institutes. The diversity and distribution of anaerobic fungi were further investigated using comprehensive data analysis, Real-Time quantitative PCR, next-generation sequencing, and metagenomics. Subsequent targeted isolation of anaerobic fungi from rodents led to the discovery of a novel genus from the mara (Dolichotis patagonum) and a new Piromyces species from the capybara (Hydrochoerus hydrochaeris). Significant progress has been made in the molecular detection of anaerobic fungi. A primer system for quantification and metabarcoding from environmental samples, a novel method for characterization by nanopore sequencing of the entire ribosomal operon including a bioinformatic routine, and a detection system for activity monitoring based on quantification of transcripts of a cellulase belonging to glycosyl hydrolase family 6 have been developed specifically for anaerobic fungi. As a first step towards biotechnological application, a reactor system for semi-continuous cultivation of anaerobic fungi was developed and the above mentioned molecular biological methods were tested in the form of process monitoring. In addition to numerous scientific results and publications, the HiPoAF team has gained international recognition for its expertise through proactive public relations and dedicated collaboration in the "Anaerobic Fungi Network". The latter has led to several national and international collaborations resulting in, for example, the world's largest collection of anaerobic fungal DNA, which is stored at the LfL. After the successful collaboration in the HiPoAF project, which closed some fundamental knowledge gaps in anaerobic fungal research, the consortium was able to go one step further and acquire a complementary research project (FUNGAS), which aims to use anaerobic fungal enzymes for the pretreatment of lignocellulosic residues for biogas production.
Publications
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Employing anaerobic fungi in biogas production: challenges & opportunities. Bioresource Technology, 300, 122687.
Vinzelj, Julia; Joshi, Akshay; Insam, Heribert & Podmirseg, Sabine Marie
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All for one and one for all –improved screening for anaerobic gut fungi in environmental samples. Talk at the Anaerobic Fungi Network webinar series, 05.11.2021, online
Young, D. & Lebuhn, M.
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Primers for environmental screening of anaerobic gut fungi (AGF). Talk for the Anaerobic Fungi Network ITS1 → LSU Initiative, 06.04.2021, online
Young, D. & Lebuhn, M.
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Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota). International Journal of Systematic and Evolutionary Microbiology, 72(7).
Elshahed, Mostafa S.; Hanafy, Radwa A.; Cheng, Yanfen; Dagar, Sumit S.; Edwards, Joan E.; Flad, Veronika; Fliegerová, Kateřina Olša; Griffith, Gareth W.; Kittelmann, Sandra; Lebuhn, Michael; O.'Malley, Michelle A.; Podmirseg, Sabine Marie; Solomon, Kevin V.; Vinzelj, Julia; Young, Diana & Youssef, Noha H.
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Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats. Microorganisms, 10(10), 1972.
Joshi, Akshay; Young, Diana; Huang, Liren; Mosberger, Lona; Munk, Bernhard; Vinzelj, Julia; Flad, Veronika; Sczyrba, Alexander; Griffith, Gareth W.; Podmirseg, Sabine Marie; Warthmann, Rolf; Lebuhn, Michael & Insam, Heribert
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March 10th 2021, May 10th 2022 and June 7th 2022. Presentation of the HiPoAF project and tasks to the Microbial Systems Group, Microbiological Laboratory, TUM-Garching. online.
Young, D.
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Medium without CRF for Neocallimastigomycota v1.
Vinzelj, Julia; Young, Diana; Joshi, Akshay; Strobl, Sophia; Begovic, Ljubica; Peer, Nico; Nagler, Magdalena; Warthmann, Rolf; Flad, Veronika; Baier, Urs; Lebuhn, Michael & M.Podmirseg, Sabine
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No time to die: Comparative study on preservation protocols for anaerobic fungi. Frontiers in Microbiology, 13.
Vinzelj, Julia; Joshi, Akshay; Young, Diana; Begovic, Ljubica; Peer, Nico; Mosberger, Lona; Luedi, Katharina Cécile Schmid; Insam, Heribert; Flad, Veronika; Nagler, Magdalena & Podmirseg, Sabine Marie
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Screening environmental samples for anaerobic gut fungi – Development of a specific primer pair for their conjoined detection, quantification, and classification. Abstract & talk at the International Anaerobic Fungi Congress - IAFC 2022, 14.09.2022, online
Young, D., Lebuhn, M. & Flad, V.
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Screening environmental samples for anaerobic gut fungi –Development of a specific primer pair for their conjoined detection, quantification, and classification. Abstract & talk at the International Anaerobic Fungi Congress - IAFC 2022, 14.09.2022, online
Young, D., Joshi, A., Huang, L., Munk, B., Wurzbacher, C., Youssef, N., Elshahed, M., Moon, C., Ochsenreither, K., Griffith, G., Callaghan, T., Alex Sczyrba, A., Lebuhn, M. & Flad V.
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Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms, 10(9), 1749.
Young, Diana; Joshi, Akshay; Huang, Liren; Munk, Bernhard; Wurzbacher, Christian; Youssef, Noha H.; Elshahed, Mostafa S.; Moon, Christina D.; Ochsenreither, Katrin; Griffith, Gareth W.; Callaghan, Tony M.; Sczyrba, Alexander; Lebuhn, Michael & Flad, Veronika
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Third-generation sequencing to the rescue: Analysing the whole ribosomal operon to classify Neocallimastigales. Abstract & talk at the International Anaerobic Fungi Congress - IAFC 2022, 14.09.2022, online
Stüer-Patowsky, K., Young, D., Lebuhn, M. & Flad, V.
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Editorial for Special Issue “Unleashing the Hidden Potential of Anaerobic Fungi”. Microorganisms, 11(3), 652.
Lebuhn, Michael; Podmirseg, Sabine Marie & Baier, Urs
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Novel anaerobic fungi isolated from rodents of the family Caviidae. Abstract & poster presentation at the ISAM 2023 - 12th International Symposium on Anaerobic Microbiology, 23.05.-26.05.2023, Innsbruck, Austria
Lukas, N., Veitengruber, J., Gohl, C., Lücht, M., Steinmetz, H., Lebuhn, M. & Flad, V.
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Patterns and determinants of the global herbivorous mycobiome. Nature Communications, 14(1).
Meili, Casey H.; Jones, Adrienne L.; Arreola, Alex X.; Habel, Jeffrey; Pratt, Carrie J.; Hanafy, Radwa A.; Wang, Yan; Yassin, Aymen S.; TagElDein, Moustafa A.; Moon, Christina D.; Janssen, Peter H.; Shrestha, Mitesh; Rajbhandari, Prajwal; Nagler, Magdalena; Vinzelj, Julia M.; Podmirseg, Sabine M.; Stajich, Jason E.; Goetsch, Arthur L.; Hayes, Jerry ... & Elshahed, Mostafa S.
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Quantification of GH6 cellobiohydrolase transcripts as a proxy for anaerobic fungal activity? Abstract & poster presentation at the ISAM 2023 - 12th International Symposium on Anaerobic Microbiology, 23.05.-26.05.2023, Innsbruck, Austria
Falterbaum, C., Veitengruber, J., Lukas, N., Young, D., Lebuhn, M., Wurzbacher, C. & Flad, V.
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Defined medium for Neocallimastigomycota v1.
Strobl, Sophia; Vinzelj, Julia; Peer, Nico; Young, Diana; Joshi, Akshay; Warthmann, Rolf; Flad, Veronika; Baier, Urs; Lebuhn, Michael; Nägele, Hans-Joachim & M., Podmirseg Sabine
