Animal scats (faeces)

​Application for Scientific Permit – Available for Public Comment

Public comment on the following application for a Scientific Resear​ch (Fauna) Permit is open until 28 May 2019.
Applicant: Augmanity Nano Ltd research institute and the Weizmann Science institute
Species/Taxon: Birds, mammals, reptiles, amphibians, terrestrial and marine animals.
Location: Reserved land including Maria Island National Park, Narawntapu National Park, Cradle Mountain National Park, Freycinet Peninsula (Freycinet National Park), Tasman peninsula.

Title of research: Tasmania Wildlife Biome Database Project
Aim of ​project:
1. Identification of major players and population dynamics within wildlife biomes that improve survival, individuals through ecosystems, and consequently protect biodiversity
2. To characterize and document microbial signatures of endangered and rare species for monitoring and conservation purposes
3. To identify new metabolic pathways, functions, antibiotics etc. within the biomes for human health and veterinary medicine

Wild animals exhibit remarkable adaptations allowing for unusual features of survival, such as resisting pathogens, eating poisonous food, or hunting prey by infecting it with disease. The present research proposal is driven by the hypothesis that some of these functions are adaptations occurring at the level of microbiomes living on or in the animal. In order to identify, isolate, and characterise such skills, our research will focus on constructing a unique, fully-annotated database of microbiomes collected from wild animals of different classes - reptilia, aves, mammalia, osteichthyes and more. Identified skills and functions could contribute to a new understanding of host-microbiome relationships and the role of microbiomes in animal evolution. Drawing a clearer picture of those dynamics would enable us a better practice protecting wildlife and habitats of Tasmania.
Maximum likely​ numbers of individuals involved:
Only faecal material will be collected; no animals will be involved. Determining how many samples or from which species they will be collected is unpredictable, thus it depends on which samples will be found in the field and parks by the principal investigator and staff.

Activities ​undertaken and methods:
Sample collection. In order to construct a fully annotated database of wildlife biomes, fresh faecal samples will be collected and fixed in OMNIgene-gut kits (Genotek) according to manufacturer’s instructions. Feaces will be collected from the ground in a non-invasive method which does not include any contact or disturbance to wild animals.
DNA extraction. Samples will be extracted using MagAttract Microbial DNA Kit (Qiagen), according to manufacturer’s protocol optimized for Tecan automated platform. Next, quality control will be performed, DNA will be tested for purity and quantity using a Nanodrop and run on a gel electrophoresis for quality and integrity.

Library prep, sequencing and analysis. llumina compatible libraries will be prepared using TruSeq DNA PCR-free kits and sequenced on the Illumina NextSeq platform with a read length of 80bp PE. Analysis will include a customized pipeline designed for whole-genome and de-novo assembly.

Bioinformatic analysis and​ database construction. A customized bioinformatics pipeline will be designed for wildlife metagenomic samples and will include taxonomic identification and gene annotation. Next, metagenomic data and meta-data (of host species and field data) will be merged into a database.

Fate of a​​nimals:
No animals will be disturbed during this project.

Likely impact on species involved (including any by-catch):


Scientific Research Permits
Natural Values Conservation Branch
134 Macquarie Street
Hobart TAS 7000

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