Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was 74\%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.
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RBINS Staff Publications 2025
Trophobiotic interactions between ants and honeydew-providing hemipterans are widespread and are one of the key mechanisms that maintain ant super-abundance in ecosystems. Many of them occur inside ant nests. However, these cryptic associations are poorly understood, particularly those with hoppers (suborder Auchenorrhyncha). Here, we study tree-dwelling ant and Hemiptera communities in nests along the Mt. Wilhelm elevational gradient in Papua New Guinea and report a new case of this symbiosis between Pseudolasius Emery, 1887 ants and planthoppers. Furthermore, we provide a worldwide review of other ant-hopper interactions inside ant-built structures and compare their nature (obligate versus facultative) and distribution within the suborder Auchenorrhyncha. The novel interactions were observed in nests located at the tree trunk bases or along the whole trunks. Only immature planthopper stages were found inside nests, so full species identifications were not possible. However, nymph morphology and molecular data (18S and COI genes) indicated four related species of the family Flatidae (infraorder Fulgoromorpha) associated with Pseudolasius. Ant-planthopper occurrences were relatively rare (6% of all trophobiotic interactions) and peaked at mid-elevation (900 m above sea level). Pseudolasius was the only genus associated with planthoppers in the communities, with most cases monopolised by a single species, P. breviceps Emery, 1887. In contrast, all other ant genera tended various scale insects (Sternorrhyncha: Coccoidea). This apparent partner-specificity is rare: Worldwide, there are only about ten reported cases of obligate symbiosis in ant nests, distributed in five of the thirty-three Auchenorrhyncha families. Those trophobioses are randomly dispersed across the Auchenorrhyncha phylogeny, and thus likely originated multiple times independently. Further research on both adult and nymph hopper life history is needed to answer how these symbioses, notably rare in hoppers compared with other hemipterans, are maintained.
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RBINS Staff Publications 2018
