Herptile Microbiomes

Herptile Microbiomes at MSA2023

The Mycological Society of America (MSA) is a group of mycologists interested in all aspects of research focused on fungi. Every year, MSA’s elected officers organize a meeting that bring together mycologists from different backgrounds interested in sharing their research. This year, the team attended and the main focus of the project, research about the herptile microbiome and Basidiobolus genomics was presented through talks and posters. Specifically, in a session on animal-fungal interactions there were three talks on Basidiobolus work and one on snake fungal disease.

Joey Spatafora from OSU (Spatafora Lab), presented to the MSA members, our Understanding Rules of Life project, explaining how the herptile gut microbiome works as an incredible system for investigating the evolution and ecology of Basidiobolus-bacterial interactions. His presentation included some results about the phylogenetic ITS diversity of all the Basidiobolus strains isolated from the fecal samples obtained during the 2022 sampling campaing; also, mentioned about the immense ITS gene copy number that can be found in a single Basidiobolus strain and how this complicates the assessment of diversity of this fungus in the fecal microbiome analyses. Also, the incredible secondary metabolism machinery of Basidiobolus was mentioned and how some classes of these may be associated with a bacterial origin. Beyond explaining about the main focus and results of the project, Joey covered the challeges that we have been facing during our fisrt year of the project, related to the fungus and some interesting and surprissingly results obtained.

Javier Tabima from Clark University (Tabima Lab), presented the first report of Basidiobolus diversity in the American Northeast, specifically from urbanized and contaminated zones, and conservation management areas in uniques sites of Massachusetts. Different watershed sites were selected to collect amphibians and sampling sediment cores and water. The detection of the fungus was performed by traditional culturing and target-gene sequencing techniques. When analyzing the isolates collected from the amphibians samples, any of the results indicated a host-specific relationship between Basidiobolus and the host. Also, Javier demonstrated the presence of the fungus in both water and sediments from all the different collected sites, indicating an ubiquitous presence of Basidiobolus in environmental samples. Javier highlighted the importance to keep studying the distribution of the fungus in the environment and to characterize relationships between urban disturbance and Basidiobolus diversity recovered.

Lluvia Vargas, Postdoc in the Spatafora Lab, gave a presentation about the first sequenced Basidiobolus genome of this project. It was indicated during the presentation that this genome was sequenced through Nanopore, a long-read sequencing technology, being able to get a good quality assembly comparable with other Basidiobolus genomes available in public databases. An interesting feature of this new genome was the length, of ~107 Mb, and the presence of a high number of gene models in comparison with the other assemblies. Lluvia also mentioned that some preliminary results showed that this Basidiobolus genome had high number of byosinthetic gene clusters, specifically NPRS and NRPS-like, and that some of them may have a signal of bacterial origin, which may suggest an horizontal gene transfer event ocurred.

Alexander Romer, from Middle Tenneesee State University (Walker Lab), presented the latest results of their research on the snake fungal disease caused by the fungal pathogen Ophidiomyces ophidiicola. The main take-home message of the presentation was that this fungal pathogen induced dysbiosis to the host microbiome. Through the extensive analysis of more than 700 skin microbiome samples from more than 30 snake species, it was demonstrated that the severity of the disease have a significat effect on the bacterial abundance and composition. Alex mentioned that these results provide insights of the effect of pathogen load in the snake native microbiome and more research is needed to implement better disease management techniques.

During poster presentations, Leila, from Stajich Lab (Stajich lab), explained the results from Metagenome Assembled Genomes (MAGs) obtained from different fecal samples of a variety of herptiles species sampled in this project. From MAGs results, different fungal genera as Pichia, Saccharomyces, Rhodotorula and Candida, and some bacterial groups as Klebsiella, Serratia, Enterococcus, Cetobacterium, Providencia and Acinetobacter were identified. Also, it has been suggested that Pichia, one of the most abundant genera found in samples from captive frogs, may have some antagonistic interaction against Basidiobolus. Some others interesting key points from Leila’s research, is that 1) looking into evolutionary relationships, the Bacteroidetes found in herptiles, clustered in a different group that those that came from human gut microbiomes; 2) differences in bacterial taxonomic composition were found across frogs from a captive environment and those that came from the wild.

In a related project for a different focus, graduate student Mark Yacoub (Stajich lab) presented research on discovery of a novel mycovirus, a DNA Circovirus, that is associated with the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis Preprint.