Taxonomy of the anaerobic gut fungi (Neocallimastigomycota): a review of classification criteria and description of current taxa

Members of the anaerobic gut fungi (<i>Neocallimastigomycota</i>) reside in the rumen and alimentary tract of larger mammalian and some reptilian, marsupial and avian herbivores. The recent decade has witnessed a significant expansion in the number of described <i>Neocallimastigomycota</i> genera and species. However, the difficulties associated with the isolation and maintenance of <i>Neocallimastigomycota</i> strains has greatly complicated comparative studies to resolve inter- and intra-genus relationships. Here, we provide an updated outline of <i>Neocallimastigomycota</i> taxonomy. We critically evaluate various morphological, microscopic and phylogenetic traits previously and currently utilized in <i>Neocallimastigomycota</i> taxonomy, and provide an updated key for quick characterization of all genera. We then synthesize data from taxa description manuscripts, prior comparative efforts and molecular sequence data to present an updated list of <i>Neocallimastigomycota</i> genera and species, with an emphasis on resolving relationships and identifying synonymy between recent and historic strains. We supplement data from published manuscripts with information and illustrations from strains in the authors' collections. Twenty genera and 36 species are recognized, but the status of 10 species in the genera <i>Caecomyces, Piromyces</i>, <i>Anaeromyces</i> and <i>Cyllamyces</i> remains uncertain due to the unavailability of culture and conferre (<i>cf</i>.) strains, lack of sequence data, and/or inadequacy of available microscopic and phenotypic data. Six cases of synonymy are identified in the genera <i>Neocallimastix</i> and <i>Caecomyces</i>, and two names in the genus <i>Piromyces</i> are rejected based on apparent misclassification.