Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Sesilje Weiss,Ian Smith,Raphael Eisenhofer,Kristofer M Helgen,David Taggart

doi:10.1186/s42523-021-00074-8

Abstract

BackgroundMarsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages.ResultsUsing qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches.ConclusionsThis study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

Highlights

Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium to further their development
To further investigate the microbial component of the pouch environment, and to create a robust framework for future pouch microbiome research, we studied the Southern Hairy-nosed Wombat (SHNW), Lasiorhinus latifrons
To examine females and pouch young at different developmental stages, samples from 8 individuals and 1 joey were collected on the first trip in April 2019, 9 individuals and 1 joey were collected in August, and 9 individuals and 3 joeys were collected in October (Fig. 1)

Summary

Introduction

Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. The most salient difference is the birth of the marsupial neonate (joey) at a much earlier stage of (2021) 3:13 immune protection during their pouch life [3, 4]. Studies using molecular techniques on Tammar wallaby and brushtail possum (Trichosurus vulpecula) pouches found changes in microbial composition associated with reproductive stage [11, 12]. If and how microbes in the marsupial pouch influence the reproductive success of the host remains to be determined, there is increasing awareness that DNA contamination can confound NGS studies that target sample types with low microbial biomass [15, 16]. It is crucial to apply a robust authentication framework when exploring the microbiome of new sample types, or those that have been understudied such as the marsupial pouch [16]

Methods

Results

Conclusion