Gut Microbiome Test (Baby)
Your baby's gut is run by trillions of bacteria — and when that bacterial balance is off, the symptoms show up everywhere except where you'd expect. This at-home test maps your baby's microbiome so you can finally see what's actually going on, with paediatric reference ranges and clinical commentary on every finding.
Is this test right for your baby?
Tap any sign you've noticed in your baby. Each one can trace back to imbalances in the developing infant gut microbiome — the test maps which organisms are driving the picture.
Infant eczema is closely linked to the gut–skin axis. Low Bifidobacterium and high Proteobacteria in the early microbiome are associated with atopic flare-ups and food-driven skin reactions.
Repeat ENT infections often track back to a poorly seeded immune system. Beneficial flora in the gut train mucosal immunity in the first 1,000 days — when these are depleted, recurrent infections follow.
Even one course of antibiotics can wipe out Bifidobacterium and Lactobacillus in an infant's gut. This test maps exactly what's been lost and what's overgrown so recovery is targeted, not guesswork.
Infant colic is increasingly understood as a microbiome problem — excess gas-producing bacteria and low protective species drive the cramping, crying, and discomfort that classic colic looks like.
Infant constipation is regulated by gut motility hormones produced by the microbiome. Methane-producing organisms slow transit, while low SCFA production reduces the signals that drive normal bowel movement.
Persistent loose stools in babies are often driven by viral gastro pathogens (Adeno-, Noro-, Rotavirus) or opportunistic bacteria. This test screens directly for them so the cause is identified, not assumed.
Reactivity to formula, dairy, or solids often points to a compromised gut lining. Low beneficial flora and elevated zonulin let undigested proteins trigger the immune system.
The infant microbiome plays a direct role in nutrient extraction and the growth signals babies depend on. Low diversity and depleted Bifidobacterium are linked to faltering growth even when intake looks fine.
Infant reflux often coexists with upper GI dysbiosis and altered gastric motility. Mapping the wider gut ecosystem helps explain why reflux persists past the usual age window.
The first-1,000-days microbiome shapes how the immune system learns to tolerate (or react to) foods and environment. Low diversity and depleted protective flora are flagged as risk factors for the allergic march.
Not sure if this test is right for your baby?
Answer a few quick questions and our patient care team will respond within 24 hours with personalised guidance — no obligation, no sales pitch.
Got questions? Let us know.
Drop our patient care team a message and we’ll reply within 24 hours.
How it works
From your couch to the lab and back — four simple steps, no GP visit needed. Designed for parents collecting from a baby's nappy. Your baby's microbiome report arrives in 7–10 business days.
What's inside your baby's report
Your baby's 15-page paediatric microbiome report covers macroscopic findings, GIT functional markers (incl. PE-1, calprotectin, sIgA, zonulin, steatocrit, transglutaminase IgA), short-chain fatty acids, six phyla with diversity indices and ratios, parasites/worms/viruses, bacterial pathogens with full H. pylori virulence and resistance profiling, sixteen fungal species, and 33+ beneficial flora and probiotics — every marker with quantitative results, age-banded reference ranges for ages 0–3, and clinical commentary on every flagged finding.
| Test | Result | ||
|---|---|---|---|
| Stool Colour | Brown | ||
| Stool Form | Formed | ||
| Mucous | Present | ||
| Occult Blood | Negative | ||
Macroscopic findings are recorded by the lab on receipt and combined with the molecular data on the report. The mini phyla snapshot above mirrors the larger Phyla & Diversity tab.
| Marker | Result | Flag | Reference |
|---|---|---|---|
| Calprotectin | 60.0 | OK | (<100.0) µg/g |
| β-Glucuronidase | 3922 | OK | (100–8000) U/g |
| Pancreatic Elastase 1 (PE-1) | 355 | OK | (>200) µg/g |
| Stool pH | 5.4 | L | (5.5–7.5) |
| Secretory IgA | 800 | OK | (200–1500) ng/mL |
| Steatocrit | 0.5 | OK | (<15.0) % |
| Transglutaminase IgA | 25.0 | OK | (<100.0) µg/g |
| Zonulin | 32 | OK | (<180) ng/mL |
| Function | Result | Flag | Reference |
|---|---|---|---|
| Ammonia / Urease Production | 0.2110 | OK | (<0.5000) % |
| Histamine Production | 0.0990 | OK | (<1.0000) % |
| Lipopolysaccharides (LPS) Production | 1.0157 | OK | (<7.0000) % |
| Sulphate Production | 0.0405 | OK | (<3.0000) % |
Includes the two paediatric-specific markers — Steatocrit (fat malabsorption) and Transglutaminase IgA (coeliac antibody) — alongside the standard digestive function panel. All reference ranges are age-banded for ages 0–3.
| Short-Chain Fatty Acid | Result | Flag | Reference |
|---|---|---|---|
| Total SCFA — Beneficial | 73.5 | OK | (>8.0) µmol/g |
| Acetate | 68.30 | OK | (40.00–80.00) % |
| Butyrate | 10.80 | OK | (4.00–27.00) % |
| Propionate | 18.90 | OK | (0.00–20.00) % |
| Valerate | 2.00 | OK | (0.00–3.00) % |
SCFAs are the energy currency of the colon and the most actionable readout of fibre fermentation. Butyrate is the keystone short-chain fatty acid for gut barrier integrity in infants.
| Phylum | Result | Flag | Reference |
|---|---|---|---|
| Actinobacteria | 0.089 | L | (0.100–20.000) % |
| Bacteroidetes | 22.256 | OK | (20.000–55.000) % |
| Euryarchaeota | 0.028 | H | (<0.020) % |
| Firmicutes | 71.552 | H | (35.000–70.000) % |
| Proteobacteria | 6.063 | OK | (0.300–9.000) % |
| Verrucomicrobia | 0.093 | OK | (0.040–3.500) % |
| Index | Result | Flag | Reference |
|---|---|---|---|
| Shannon Diversity Index | 4.51 | H | (1.80–4.10) |
| Simpson Diversity Index | 0.97 | OK | (0.70–0.98) |
| Ratio | Result | Flag | Reference |
|---|---|---|---|
| Firmicutes / Bacteroidetes | 3.21 | OK | (<4.00) |
| F. nucleatum / F. prausnitzii | N/A | (<3.00) | |
| Gram-Positive / Gram-Negative | 0.16 | OK | (<2.50) |
| Prevotella / Bacteroides | 0.52 | H | (<0.10) |
| Proteobacteria / Actinobacteria | 67.87 | H | (<14.00) |
| Organism | Result | Flag | Reference |
|---|---|---|---|
| Blastocystis hominis | 95.00 | H | (<1.00) ×10⁵ org/g |
| Cryptosporidium species | <DL | (<1.00) | |
| Cyclospora cayetanensis | <DL | (<1.00) | |
| Dientamoeba fragilis | 2.48 | H | (<1.00) |
| Entamoeba histolytica | <DL | (<1.00) | |
| Enterocytozoon species | <DL | (<1.00) | |
| Giardia intestinalis | <DL | (<1.00) |
| Subtype | Result | ||
|---|---|---|---|
| Subtype 1 | Negative | ||
| Subtype 2 | POSITIVE | ||
| Subtypes 3–9 | All Negative | ||
| Organism | Result | ||
|---|---|---|---|
| Ancylostoma species (Hookworm) | Not Detected | ||
| Ascaris species (Roundworm) | Not Detected | ||
| Enterobius vermicularis (Pinworm) | Not Detected | ||
| Hymenolepis spp. (Tapeworm) | Not Detected | ||
| Necator americanus (Hookworm) | Not Detected | ||
| Strongyloides spp. | Not Detected | ||
| Taenia species (Tapeworm) | Not Detected | ||
| Trichuris trichiura (Whipworm) | Not Detected | ||
| Virus | Result | ||
|---|---|---|---|
| Adenovirus 40/41 | Not Detected | ||
| Astrovirus (hAstro) | Not Detected | ||
| Norovirus GI/II | Not Detected | ||
| Rotavirus A | DETECTED | ||
| Sapovirus (I, II, IV, V) | Not Detected | ||
| Organism | Result | Flag | Reference |
|---|---|---|---|
| Aeromonas species | <DL | (<1.00) ×10³ CFU/g | |
| Campylobacter species | <DL | (<1.00) ×10⁵ CFU/g | |
| C. difficile, Toxin A | <DL | (<1.00) ×10⁴ CFU/g | |
| C. difficile, Toxin B | <DL | (<1.00) ×10⁴ CFU/g | |
| C. difficile, Hypervirulent | <DL | (<1.00) ×10³ CFU/g | |
| Enteroaggregative E. coli | <DL | (<1.00) ×10³ CFU/g | |
| Enteropathogenic E. coli | 0.78 | (<1.00) ×10³ CFU/g | |
| E. coli O157 | <DL | (<1.00) ×10² CFU/g | |
| Enteroinvasive E. coli / Shigella | <DL | (<1.00) ×10³ CFU/g | |
| Enterotoxigenic E. coli LT/ST | <DL | (<1.00) ×10⁵ CFU/g | |
| Salmonella species | <DL | (<1.00) ×10⁵ CFU/g | |
| Shiga toxigenic E. coli (stx1/2) | <DL | (<1.00) ×10³ CFU/g | |
| Vibrio species | <DL | (<1.00) ×10⁴ CFU/g | |
| Yersinia species | <DL | (<1.00) ×10⁵ CFU/g | |
| Helicobacter pylori | <DL | (<1.00) ×10³ CFU/g |
| Test | Result | ||
|---|---|---|---|
| H. pylori Antigen | Negative | ||
| Fungal Species (16 total) | Result | Flag | Reference |
|---|---|---|---|
| Candida albicans | <DL | (<1.00) ×10⁵ CFU/g | |
| Candida dubliniensis | <DL | (<1.00) | |
| Candida famata | <DL | (<1.00) | |
| Candida glabrata | <DL | (<1.00) | |
| Candida guilliermondii | <DL | (<1.00) | |
| Candida intermedia | <DL | (<1.00) | |
| Candida kefyr | <DL | (<1.00) | |
| Candida krusei | <DL | (<1.00) | |
| Candida tropicalis | 1.10 | H | (<1.00) ×10⁵ CFU/g |
| Geotrichum species | <DL | (<1.00) | |
| Rhodotorula species | <DL | (<1.00) | |
| Saccharomyces cerevisiae | <DL | (<1.00) |
Full panel screens 16 fungal species — 13 Candida species plus Geotrichum, Rhodotorula and Saccharomyces. Candida overgrowth in infants frequently presents as oral thrush, persistent nappy rash, or post-antibiotic flare-ups.
| Organism | Result | Flag | Reference |
|---|---|---|---|
| Akkermansia muciniphila | 0.012 | (<3.500) % | |
| Faecalibacterium prausnitzii | 5.130 | OK | (1.000–14.000) % |
| Bacteroides thetaiotaomicron | 0.092 | (<5.000) % | |
| Bacteroides uniformis | 0.437 | (<10.000) % |
| Organism | Result | Flag | Reference |
|---|---|---|---|
| BIFIDOBACTERIUM TOTAL | 0.011 | L | (0.010–20.000) % |
| B. adolescentis | <DL | (<0.700) % | |
| B. animalis | 0.011 | (<0.100) % | |
| B. bifidum | <DL | (<12.000) % | |
| B. breve | <DL | (<10.000) % | |
| B. longum | <DL | (<15.000) % |
| Organism | Result | Flag | Reference |
|---|---|---|---|
| LACTOBACILLUS TOTAL | 0.0020 | (<3.0000) % | |
| L. acidophilus, L. casei, L. rhamnosus, L. plantarum, L. reuteri… | All <DL or trace | ||
| Organism | Result | Flag | Reference |
|---|---|---|---|
| Pediococcus acidilactici | 2.000 | H | (<0.090) % |
| Roseburia hominis | 0.024 | OK | (0.010–0.300) % |
| Roseburia inulinivorans | 0.065 | OK | (0.000–0.500) % |
| Lactococcus lactis | 0.007 | (<0.030) % | |
| Streptococcus thermophilus | <DL | (<1.000) % |
Full panel quantifies 33+ beneficial organisms including Akkermansia, Faecalibacterium, the Bifidobacterium family (total + 6 species), the Lactobacillus family (total + 13 species), Roseburia, Pediococcus, Clostridium butyricum, Lactococcus, and Oxalobacter formigenes. Low Bifidobacterium total in the first 1,000 days is the keystone clinical signal.
Everything parents ask about baby gut testing
Answers to the questions we hear most from parents considering the Baby Biome test for their child.
Book a free discovery call or email us at hello@themicrobiomeclinic.com.au
Yes. The test is completely non-invasive — there is no blood, no needles, and nothing introduced into your baby's body. You collect a small stool sample directly from your baby's nappy using the scoop and stabiliser tube provided. The sample is then analysed at NutriPATH, our NATA-accredited Australian pathology partner.
Wait until your baby has had a bowel motion in their nappy. Using the small scoop in the kit, transfer a portion of the stool into the stabiliser tube — about the size of a pea is enough. Seal the tube, label it, and place it inside the pre-paid Australia Post return satchel. The full process takes under five minutes and parent-friendly step-by-step instructions are included with every kit.
The Baby Biome panel is designed for children from birth up to 3 years of age. Reference ranges are age-banded so results are interpreted against what's normal for an infant microbiome — not against adult values. For children aged 3–17, the Paediatric Biome test (coming soon) is the right fit.
Yes — and that's often exactly the picture parents want to see. If your baby has recently been on antibiotics, the test will show what's been wiped out and what's overgrown in the aftermath, so recovery can be targeted rather than a guessing game. If you'd like a baseline microbiome snapshot instead, we recommend waiting at least 4 weeks after the last antibiotic dose before sampling.
You'll receive a comprehensive PDF report covering ~25 markers across 6 categories: phyla composition, beneficial flora (Bifidobacterium, Lactobacillus, Akkermansia, Faecalibacterium), viral pathogens (Adeno-, Noro-, Rotavirus), Candida, digestive function (PE-1, beta glucuronidase, zonulin, sIgA, calprotectin), and short-chain fatty acids. Every marker is shown with your baby's result, an age-banded reference range, a flag (low/normal/high), and clinical commentary explaining what it means.
Results are typically ready in 7–10 business days from when the lab receives your baby's sample. You'll be notified by email as soon as the report is available.
Your baby's report can be reviewed in a follow-up consultation with a Microbiome Doctor™ at The Microbiome Clinic™ — they will translate the lab data into a personalised plan that takes into account your baby's birth history, feeding, antibiotic exposure, and current symptoms.
No referral is needed — you can order directly as a parent. Your baby's report is a NATA-accredited pathology document (accreditation #20770) and can be shared with your child's paediatrician or GP.