What we measure from a single sample.

What we measure

The composition and relative abundance of the bacterial community in your pet's gut. Shotgun metagenomic NGS reads every microbial DNA fragment in the sample, not just a fixed marker region, so coverage extends from highly abundant Firmicutes and Bacteroidetes down to low-abundance taxa that smaller assays miss.

How we measure it

We extract total DNA from a small faecal sample, sequence it on Oxford Nanopore (MinION and PromethION platforms), and classify the reads against the GTDB r214 reference database using a long-read metagenomic classifier. Diversity metrics are computed in QIIME 2. The output is a taxonomic table with relative abundance estimates, resolved to species, and to strain for organisms with enough coverage to support it.

• Long reads from Oxford Nanopore allow species-level resolution rather than the genus-level resolution typical of short-read marker-gene assays, and strain-level resolution for organisms abundant enough to be covered deeply.
• Untargeted sequencing means no fixed marker region, so coverage is not limited to a single gene.
• The same workflow handles dogs and cats.

What it tells you

How your pet's gut bacterial community compares to wellness ranges for their species, age class, and breed size. The report flags taxa that are unusually high or low, summarises diversity metrics, and identifies organisms of interest worth discussing with your vet.

What we measure

The bacterial community in your pet's mouth, sampled by swabbing the gumline and inner cheek. Like the gut, the oral microbiome shifts with age, diet, and dental health. It is also a different ecosystem from the gut, governed by different selection pressures, and changes there can show up before gut changes do.

The oral cavity is a well-characterised system. The species that separate healthy gingiva from periodontitis in dogs and cats are already named in the published literature, so an open-ended read of the whole community is not what the sample needs. A defined panel measured accurately is more useful than a broad panel measured loosely.

How we measure it

Quantitative PCR, not sequencing. An aliquot of the swab eluate is run across a 11-target panel plus a universal bacterial 16S reaction, on the same QuantStudio 1 platform used for the parasite screen. Every target is quantified against a synthetic DNA standard curve, so the result is an absolute quantity for that species rather than a share of a read pool. The universal reaction gives total bacterial load, which each target is normalised against.

Disease-associated, with reported diagnostic performance in dogs

• Peptostreptococcaceae XI [G-4] sp. COT-019
• Clostridiales sp. COT-028
• Porphyromonas gulae COT-052
• Tannerella forsythia COT-023

Health-associated, validated canine assays

• Capnocytophaga sp. COT-339
• Moraxella sp. COT-017
• Bergeyella zoohelcum COT-186
• Porphyromonas cangingivalis COT-109

Cat-relevant targets

• Prevotella nigrescens
• Aggregatibacter actinomycetemcomitans
• Prevotella intermedia

Normaliser

• Universal bacterial 16S rRNA, for total bacterial load

The COT numbers are Canine Oral Taxon designations. They are not decoration. Only about 16 per cent of canine oral taxa are shared with the human mouth, so a panel built from human periodontal species names does not transfer, and the assays with demonstrated canine performance are species-level and canine-specific. Where a target is listed with a COT number, a validated canine assay for that exact organism exists in the published literature.

• Sample collection: oral swab, included in the Bundle kit or available as the Oral Add-on for existing customers.
• Panel composition is drawn from published canine and feline oral microbiome studies and is subject to change during development. The final target list will be published on this page before ordering opens.

What it tells you

How much of each target species is present in your pet's mouth, as a quantity rather than a percentage, and how the health-associated group compares with the disease-associated group once both are normalised against total bacterial load. That ratio drives the periodontal risk score, which flags whether a dental review is worth raising with your vet.

Because every figure is an absolute quantity measured against a standard curve, it does not move simply because something else in the sample moved. A relative abundance does: a species can appear to rise only because another fell away. That makes an absolute number the better measurement.

It does not make a difference between two tests automatically meaningful. In healthy dogs followed for six months after a dental scale, the quantity of P. gulae rose roughly a hundredfold, and between-dog spread in healthy animals alone runs to fifteen or twenty-five fold. No published study reports within-dog variation in an untreated animal, so the size of change that counts as real is not yet established. We report the number and the direction; we do not claim a threshold for meaningful change, because nobody has measured one.

What we measure

Fungal organisms present in the sample, identified by their genomic DNA picked up during shotgun metagenomic sequencing. Panel-based commercial tests detect a defined list of fungal species; because BAARK sequences untargeted, fungal DNA appears in the read pool whenever it is present at detectable abundance, including species not on any commercial panel.

How we measure it

No separate workflow. Reads are taxonomically classified across kingdoms, so fungal hits emerge from the same sequencing run as bacterial hits. The pipeline uses fungal reference databases to assign reads to genera and species where the evidence supports it.

• Malassezia, Candida, Aspergillus and other clinically relevant species are flagged when present at detectable abundance.
• Fungal sensitivity depends on relative abundance in the sample; very low-abundance fungi may not produce enough reads for confident species-level assignment.

What it tells you

Whether named fungi of clinical interest were detected in the sample and at what relative abundance. This adds context to skin, ear, or gut concerns where fungal involvement is plausible from the published veterinary literature.

What we measure

The presence and relative quantity of seven gut parasites that account for the bulk of canine and feline parasitic burden in Australia. Shotgun NGS catches parasites when they are abundant; targeted qPCR adds sensitivity for low-abundance infections that the broader sequencing might miss.

How we measure it

The faecal sample is split: most of the DNA goes into the shotgun NGS workflow, and an aliquot is run through a qPCR panel on a QuantStudio 1 platform. The seven targets are:

• Giardia duodenalis
• Cryptosporidium spp.
• Toxocara spp. (roundworm)
• Ancylostoma spp. (hookworm)
• Trichuris vulpis (whipworm)
• Cystoisospora spp.
• Dipylidium caninum (flea tapeworm)

What it tells you

Whether DNA from any of the seven target parasites was detected in the sample, and at what relative quantity. A positive result is a flag for veterinary review and possible follow-up testing; a negative result indicates the seven targets were below the detection threshold on this sample.

What we measure

Three things are computed at this stage. First, a dysbiosis score that summarises how far your pet's bacterial community sits from the wellness range for their species, age, and breed size. Second, a list of organism-of-interest flags for any taxa unusually high or low. Third, a set of dietary and supplement recommendations grounded in published veterinary microbiome research, calibrated to the individual sample.

How we measure it

Bioinformatics first, AI second. Read classification against GTDB r214 and abundance estimation do the heavy lifting. The Biome Health Engine then takes that taxonomic table and applies a set of rule-based and learnt scoring functions developed by our scientific team, drawing on the published veterinary microbiome literature.

• Dysbiosis scoring is calibrated to species, age class, and breed size.
• Recommendations are generated per sample, not pulled from a generic list.
• The engine is updated periodically as the published literature and our reference cohort grow.

What it tells you

A summary you can read in five minutes and bring to a vet appointment. The dysbiosis score gives a single high-level read; the organism-of-interest flags give specifics; the recommendations give starting points for dietary and supplement discussion.

What it tells you

Whether your pet's microbiome is moving in the direction you and your vet are aiming for, after a diet change, antibiotic course, probiotic supplementation, or a deliberate weight or wellness intervention. The trajectory is the answer to "is this working?"

How it works

Order another Gut Health or Bundle test on the cadence that suits your pet (typically 3, 6, or 12 months). Each sample is processed exactly the same way, so results are directly comparable. The portal shows the change over time alongside the absolute values.

What you get

A PetTrials account that matches your pet to active veterinary research studies based on species, age, breed, and (with your permission) the health context you shared with us at order. Studies range from nutrition trials and probiotic intervention research to specific-condition cohorts.

How participation works

Matching is opt-in: you receive notifications about studies your pet might qualify for, and you decide whether to enrol. PetTrials is a separate platform; BAARK shares only the metadata you authorise. Most studies offer participation incentives or free testing.