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Basic sampling requirements


Samples should* come from individual captured animals, and host's metadata should also be gathered. *exceptions are possible.


Samples must be frozen within 14 days, and the time and conditions before freezing must be acknowledged.


Samples need to be obtained using gloves and following the best sampling practices guidelines of EHI to minimise human and cross-contamination.


Samples need to be obtained, preserved and shipped following the EHI guidelines. Any deviation must be acknoelwedged.

Hierarchical sampling design



Hologenomic analysis of individual animals requires enough genomic and metagenomic DNA to properly characterise host genomes and microbial metagenomes.



Not all field researchers have the same capacity to obtain samples from individual animals, due to animal's biological features, fieldwork conditions or sampling permit limitations.



We therefore implement a flexible hierarchical sampling design, that is adjusted to the capacities of field researchers and properties of the samples organisms.

Sampling options

From minimum to maximum additive requirements.


Faeces and/or Anal/Cloacal Swabs

Faeces and anal/cloacal swabs aim to capture the microbial community of the lower intestine. The appropriateness of using one or the other sample type will be determined by the host organisms. Both sample types contain host and microbial DNA, although the ratio between host and microbial DNA can vary drastically across sampled individuals and species. Thus, this sample types might not ensure correct host genotyping, mainly in small animals.


1 + Buccal Swabs

Buccal swabs aim to capture the oral microbial community as well as to provide a larger amount of host DNA for genomic characterisation. When combining with Type 1 samples, there is usually enough DNA to correctly genotype the host animal.


2 + Tissue/Blood samples

Tissue and blood samples are the best sample types for genomic characterisation of host animals. Obtaining this type of samples will ensure genomic characterisation is properly performed. Tissue samples are preferred in mammals (e.g. ear punch in micromammals, wing punch in bats), amphibians and reptiles, while blood samples are preferred in birds.


3 + Skin Swabs

Mainly relevant for amphibians. These type of samples enables characterising the skin microbiome of the organisms.


3/4 + Snap-frozen Glycerol samples

If field researchers are able to freeze the samples immediatelly, they are requested to obtain faecal samples or anal/cloacal/buccal/skin swabs in a buffer (provided by EHI) containing PBS and glycerol to keep microorganisms alive while frozen. This samples will contribute to the wild animal-associated microbial biobank on EHI.


In EHI, metadata are as important as the samples. We therefore request four types of metadata per sample.



Basic information about the sampling event: day, time, coordinates, method, researchers involved, etc.


Host animal

External morphological aspect, length and weight of the animal. Standard biometries vary across organisms. Photos are welcome.


Environment metadata

Information about the sampling site (e.g. habitat type) and meteorological conditions (e.g. temperature, rain). 



Basic information about the sample (e.g number of pellets), and time (hours or days) until freezing.

MIGS/MIMS data standards

EHI follows the GSC-developed data reporting standard designed for accurate reporting of contextual information for samples associated with genomic and metagenomic sequencing.

Frequently Asked Questions

If possible, should I get both faeces and anal swabs?

It is not necessary to do so with all the samples, but paired faecal and anal swab samples from the same individuals are welcome to 1) assess the differences between both sample types in different organisms, and 2) to increase the sample material. Obtaining both sample types is specially advised when the faecal material is very small (< 20-30 mg).

Should I get skin samples from non-amphibian vertebrates?

It is not prioritised, but such skin samples are welcome.


The GLOBE Institute
University of Copenhagen
Ă˜ster Farimagsgade 5, 7
1353 Copenhagen K


Antton Alberdi, PhD
Email: antton.alberdi[at]


GLOBE Institute
University of Copenhagen