A practical guide to collecting and shipping fecal samples

Microbiome assays can reveal patterns in bacterial communities, antimicrobial resistance genes and gastrointestinal dysfunction, but the result is only as reliable as the specimen behind it. In dogs and cats, collection timing, contamination, temperature and transit conditions can all alter the microbial profile before DNA extraction begins.

A consistent workflow helps veterinary teams compare samples across consultations, research projects and chronic enteropathy cases. The same principles apply whether a specimen is collected in a Melbourne referral hospital, a suburban Brisbane practice or a regional clinic sending material to a laboratory several hours away.

Define the clinical and laboratory purpose

Start by identifying what the assay is designed to measure. 16S rRNA sequencing provides a broad view of bacterial community composition, while shotgun metagenomics can assess organisms, functional pathways and antimicrobial resistance genes. A faecal sample intended for pathogen testing may require different handling from one collected for a longitudinal microbiome study.

Confirm the laboratory’s requirements before taking the sample. Some services supply stabilisation tubes or preservatives, while others request fresh faeces frozen promptly. The required amount, container type, minimum volume and acceptable transport temperature should be recorded in the practice’s sampling protocol.

Prepare the patient and collection materials

For a routine specimen, collect freshly passed faeces wherever possible. A clean examination room, disposable gloves, a sterile scoop and a labelled, leakproof container are usually sufficient. Avoid material that has contacted soil, grass, litter, kennel flooring or disinfectant, since these sources can introduce environmental DNA and dilute the host-associated signal.

Ask the owner about recent antibiotics, probiotics, dewormers, dietary changes and gastrointestinal treatments. These details do not necessarily prevent testing, but they are essential for interpretation. In Australia, where many dogs accompany owners on beach walks, parks and camping trips, exposure to soil, wildlife faeces or untreated water may also be clinically relevant.

Collect a representative specimen

Use several portions from the interior of the stool rather than sampling only the dry outer surface. If mucus or blood is present, note its location and follow the laboratory’s instructions about whether to include it. For longitudinal monitoring, collect samples at a similar time of day and under comparable dietary and treatment conditions when clinically practical.

Do not pool faeces from different animals unless the study protocol specifically requires it. Record the animal identification, date and time of defaecation, collection time, stool consistency and any visible abnormalities. A fresh sample taken from a clean surface is preferable to one retrieved after prolonged outdoor exposure, especially during hot Australian summers.

Stabilise the microbial signal

Time and temperature are central pre-analytical variables. If the laboratory requests an untreated sample, place it in the refrigerator promptly and avoid repeated warming and cooling. Freezing may be necessary for some assays, but the laboratory should specify whether a household freezer is acceptable and whether the specimen must remain continuously frozen.

Preservative tubes can simplify field collection and regional transport, but they are assay-specific. Do not transfer faeces into a different medium or top up a tube beyond its fill line. When a practice is comparing repeated samples, use the same container and stabilisation method each time. Guidance on educational library resources can help veterinary teams build consistent microbiome sampling procedures.

Label and document every tube

Labels should remain legible at low temperature and include a unique patient code, specimen number, collection date and time. Avoid relying on the animal’s name alone, particularly when several patients from the same household are being tested. Match the physical label with the electronic submission form before dispatch.

The accompanying clinical information should include species, age, sex, breed, relevant diagnosis, diet, medication exposure and recent travel or hospitalisation. Include the requested assay and the laboratory contact details. A clear chain of custody is especially important when samples are part of a research project or are being shipped between a city practice and a university laboratory.

Package samples for Australian transport

Use triple packaging: a primary leakproof container, absorbent material and a durable secondary container inside a rigid outer package. Place paperwork in a separate waterproof sleeve rather than inside the specimen bag. Follow the receiving laboratory’s instructions for ice packs, dry ice or frozen gel packs, and ensure the package can withstand courier handling.

Australian clinics must consider heat, distance and delivery schedules. A sample travelling from Darwin or regional Western Australia may face longer transit and higher ambient temperatures than one moving across inner Sydney. Arrange collection early in the week, avoid public-holiday delays and confirm whether the courier accepts biological specimens. If dry ice or other regulated materials are used, packaging, labelling and transport must comply with current carrier and dangerous-goods requirements.

Interstate and international movements may also involve biosecurity controls. Check the laboratory and courier requirements under relevant Australian biosecurity and state or territory rules rather than assuming ordinary parcel services are suitable. The receiving laboratory remains the final authority on acceptable packaging and documentation.

Review quality before interpreting results

On arrival, inspect the container for leakage, incorrect identification, thawing or an excessive delay between collection and receipt. Record deviations instead of silently discarding them. A compromised specimen may still provide useful information, but the limitation should accompany the result.

Microbiome data describe a community shaped by the patient, diet, medication, disease and sampling method. They should be interpreted alongside history, examination, laboratory findings and clinical response. For teams investigating antimicrobial exposure, resources discussing fecal metagenomics findings can provide relevant context, while careful sampling preserves the evidentiary value of the test.

Build a repeatable practice workflow

Assign responsibility for collection, freezing, dispatch and result tracking. Keep a small sampling kit ready with sterile containers, gloves, labels, absorbent material and submission forms. Staff training should cover contamination prevention, temperature control and the difference between diagnostic faecal testing and research-grade microbiome sampling.

A written workflow improves consistency across nurses, veterinarians and locations. It also makes results easier to compare when a dog or cat is followed over several weeks. Reliable microbiome science begins before sequencing, with a specimen that is correctly collected, stabilised, documented and delivered in a condition the laboratory can trust.