Looking to translate qPCR microbiome data into biologically meaningful and actionable insights? The Alimetrics qPCR microbial target portfolio organises assays into functional and ecological categories, simplifying assay selection and interpretation across poultry, swine, and ruminant applications.
Choose your taxa of interest for your assay based on their primary role in the gastrointestinal ecosystem (e.g., fibre degradation, fermentation stability, butyrate production, lactate metabolism, protein fermentation, gut health, pathogen pressure).
Where it helps?
- Enables function-based interpretation of qPCR data, linking microbes to performance and gut health (ADG, FCR, resilience).
- Simplifies assay selection by grouping targets into biologically relevant categories.
- Supports mode-of-action understanding for feed additives and nutritional strategies.
How does it work?
Alimetrics qPCR assays are grouped into functional categories, each reflecting key biological processes in the gut ecosystem.
You can mix and match your qPCR panel per your needs.
We help you to interpret the results in the context of:
- Animal species
- Production stage
- Diet composition
- Environmental and study context
Functional classification of qPCR assays
1. Fibre degraders, fermentation efficiency & butyrate production
Microbes supporting carbohydrate fermentation and VFA-L production, contributing to gut health and nutrient utilisation.
Examples:
- Ruminococcaceae / Clostridial Cluster IV
- Lachnospiraceae / Clostridial Cluster XIVa
- Prevotella spp., Blautia spp.
- Faecalibacterium prausnitzii
- Clostridium butyricum, Butyricicoccus pullicaecorum
Typical applications: fibre enzymes, prebiotics, VFA-L-targeting additives.
2. Lactate producers
Microbes producing lactic acid, involved in rapid fermentation and microbial competition.
Examples:
- Lactobacillus spp. (multiple species groups)
- Bifidobacterium spp.
- Enterococcus spp.
- Streptococcus spp.
Note: beneficial at balanced levels; excessive abundance may indicate rapid fermentation or imbalance.
Typical applications: probiotics, DFM evaluation, microbiome modulation.
3. Lactate utilisers & fermentation stabilisers
Microbes converting lactate into VFA-Ls, helping maintain pH balance and fermentation stability.
Examples:
- Megasphaera elsdenii
- Selenomonas ruminantium
- Veillonella spp.
Typical applications: rumen health, acidosis prevention, high-energy diet studies.
4. Protein fermenters & BCFA-associated taxa
Microbes associated with protein and amino acid fermentation, including pathways linked to BCFA formation, aromatic putrefactive metabolites, and nitrogen metabolism. qPCR target data should be interpreted together with metabolite profiles to distinguish microbial potential from actual fermentation outputs.
Examples:
- Peptostreptococcaceae
- Clostridium sensu stricto
- Bacteroides spp., Alistipes spp.
Typical applications: protease evaluation, protein optimisation, BCFA interpretation, putrefactive metabolite follow-up, and gut health studies.
5. Major enteric & production pathogens
Targets associated with disease, performance loss, and biosecurity risk.
Examples:
- Poultry: Clostridium perfringens, APEC, Salmonella spp., Eimeria spp.
- Swine: Lawsonia intracellularis, Brachyspira hyodysenteriae, E. coli F4/F18
- Multi-species: Salmonella spp., Campylobacter jejuni, Listeria monocytogenes
Typical applications: pathogen surveillance, challenge trials, additive validation.
6. Rumen & hindgut ecosystem markers
Markers reflecting overall microbial ecosystem activity and structure.
Examples:
- Total eubacteria
- Methanogens
- Yeasts and protozoa
Typical applications: rumen efficiency, methane studies, ecosystem balance.
7. Direct-fed microbials, probiotics & additive monitoring
Targets used to track probiotic strains and microbial interventions.
Examples:
- Bacillus spp.
- Saccharomyces cerevisiae
- Lactobacillus spp., Bifidobacterium spp.
Typical applications: DFM verification, colonisation tracking, mode-of-action studies.
We can support assay panel selection based on your study objectives, species, and desired functional insights.
How to Order
- Contact us either by email diagnostics@alimetrics.com or alternatively use the contact form below.
- Indicate your interest in the BioFreeze™ sample collection solution, one or more of our unique gut health panels or a customized selection of analyses.
- We can help you plan a solution best suited to your needs.
- We will provide you with a quotation and further instructions within two business days.
Request Service
Use this form to request information of our analysis services. We’ll get back to you within two business days.
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