Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand

Arsalan Emami-Khoyi,Hossein Alizadeh,Peter R Teske,Elaine C Murphy,James G Ross,Bettine Jansen Van Vuuren,Isma Benmazouz,Jennifer Bothwell,Adrian M Paterson

doi:10.3390/d12070278

Abstract

All multicellular organisms host a wide diversity of microorganisms in and on their bodies, which are collectively known as their microbiome. Characterising microbial communities that inhabit different body niches in wild animals is critical to better understand the dynamics of microbiome diversityand its functional significance. The current study is the first to apply massively parallel sequencing of 16S rRNA to characterise the microbial diversity and functional content of oral microbiota in two of New Zealand’s most important invasive mammals, the omnivorous common brushtail possum (Trichosurus vulpecula) and the carnivorous stoat (Mustela erminea). In total, strains of bacteria belonging to 19 different phyla, 27 classes, 52 orders, 103 families, 163 genera and 51 known species were identified from the oral cavities of the study species. Strains of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria dominated the core oral microbial diversity in both species, while other taxa were comparatively less abundant. Despite invasive populations typically demonstrating limited genetic variation, intraspecific variation of the core bacterial taxa in the oral microbiota was considerable. This suggests that a complex interaction between genetic, physiological, and environmental factors determines the diversity of the study species’oral microbiome.

Highlights

Microbes have dominated Earth’s evolutionary landscape for billions of years and have developed a plethora of biochemical adaptations to exploit all conceivable ecological niches on the planet
This idea is the foundation of the hologenome theory of evolution [17], which maintains that eukaryotic organismal fitness is the product of the integrated activities of both the hosts and all their associated microorganisms at any given point in time
Intricate and interdependent relationships between eukaryotic organisms and their microbiomes create a situation where the two evolve as a single entity, known as a holobiont [3]

Summary

Introduction

Microbes have dominated Earth’s evolutionary landscape for billions of years and have developed a plethora of biochemical adaptations to exploit all conceivable ecological niches on the planet. Intricate and interdependent relationships between eukaryotic organisms and their microbiomes create a situation where the two evolve as a single entity, known as a holobiont [3] This idea is the foundation of the hologenome theory of evolution [17], which maintains that eukaryotic organismal fitness is the product of the integrated activities of both the hosts and all their associated microorganisms at any given point in time. The Australian common brushtail possum (Trichosurus vulpecula), hereafter the brushtail possum, and a predatory placental mammal, the stoat (Mustela erminea), have had destructive impacts Soon after their introduction in the 1800s, these species spread rapidly in their new environments and preyed on native species that possessed no prior adaptations to evade mammalian land predators. Such knowledge holds unprecedented therapeutic, environmental, and socio-economic promises that reach beyond the realm of wildlife genomics [43]

Animal Ethics Statements

Sample Collection and Genomic Library Preparation

Results

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Conclusion