THE COOL KID IN THE GAME! NGS FOR ANIMAL MICROBIOME
- Dr. Nihan
- 4 days ago
- 4 min read
For years, “the microbiome” in veterinary medicine meant culture plates, a few PCRs, and well... some of guesswork. In today’s technology and information capacity, animal clinics, diagnostic labs, and health companies are asking a different question:
“Instead of chasing one pathogen, what if we could see the whole community along with the balance, resistance genes and more in one read?”
That is where next-generation sequencing (NGS) quietly moved from our laboratories and research conferences into real clinical world, discussions, diagnosis and product decisions. Let me tell you (one of my top three sentences when it comes to science & industry): It is not magic and it will not replace every culture or sensitivity report! But when we use it correctly, it really changes how we think about gut health, skin microbiome, and even most chronic infections, and further; super excited part: antimicrobial stewardship in animals!
What Do We Mean By “NGS” in Animal Microbiome Work?
In simple words, NGS is a set of tools (rather than a single test) that gives us Three Layers of information: Composition (who is present there), Function (what they can do), Activity (what are they actually doing in this host, at this time). Isn’t it great?
Now… If you are in science terms and want to know more about the tools of this method, here is a short list:
16S rRNA gene sequencing (amplicon sequencing) is to target a conserved bacterial gene to identify which bacteria are present and in what relative proportions. This is still being used by most of the dog and cat gut studies as the main workhorse!
Full-length 16S or long-read sequencing gives much better species-level resolution. A recent work in 2024, presumed healthy dogs used full-length 16S to define a species-level core fecal microbiome in 286 home-living dogs. It was a true big step forward from just “genus-level” bar charts.
Shotgun metagenomic sequencing allows detection of pathogens, commensals, virulence factors, antimicrobial resistance genes in one go – since it basically sequences all DNA in the sample (bacterial, fungal, viral, host).
Metatranscriptomics is still mostly in the ‘research’ phase but the coolest guy in this game to me! It looks at which genes are active right now and what functions are they performing, instead of only “who is there”. Thus, it is highly relevant for understanding host-microbe interactions, responses to the environmental changes, treatment response and much more.
Why use NGS in microbiome work instead of “just culture”?
Well after reading the above intro, I really don’t think that you are questioning this- but here is one important thing to know: Classic culture and PCR are still essential, but they are narrow beams of light now. Because NGS widens the field of view in several ways:
Detects unculturable and fastidious organisms: A 2023 study comparing NGS with culture in 78 exotic animal patients found that culture missed 15% of putative bacterial and 81% of putative fungal pathogens that NGS picked up.
Catches mixed infections and community shifts: NGS does not force us to pick “one suspect” in advance. It shows whole communities, imbalance patterns, and co-infections that matter clinically, especially in chronic skin, ear, and GI disease.
Quantifies relative abundance: When the disease is dysbiosis or biofilm-driven, “how dominant and in what context” data really matters along with “present / absent.
Supports antimicrobial stewardship: Metagenomics can map resistance genes in the microbiome and help rationalize antibiotic choice as part of AMR and One Health strategies.
Enables truly data-driven product development: Feed, probiotic, and functional ingredient companies are already using NGS to track how formulations shift the microbiome in dogs, cats, pigs, poultry, and aquaculture species.
So, NGS is a different level of the main question in animal health comes with different answers we get from ‘just culture’. With NGS, we are driving from “what is causing this infection?” to “what ecosystem are we treating and how are we reshaping it?”
The next blog post on NGS will be exploring where animal microbiome NGS is actually being used, where is this going next, and what NGS means for veterinarians and animal health companies.
Until then, stay warm, take care of your-micro-biome-self!
References
Damerum, A., Malka, S., Lofgren, N., et al. (2023). Next-generation DNA sequencing offers diagnostic advantages over traditional culture testing. American journal of veterinary research, 84(8), ajvr.23.03.0054. doi:10.2460/ajvr.23.03.0054
Rojas, C.A., Park, B., Scarsella, E., et al. (2024). Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing. Frontiers in Veterinary Science. 11-2024. doi:10.3389/fvets.2024.1405470
Shah, H., Trivedi, M., Gurjar, T., Sahoo, D. K., et al. (2024). Decoding the gut microbiome in companion animals: impacts and innovations. Microorganisms, 12:(9), 1831. doi:10.3390/microorganisms12091831
Suchodolski, J.S. (2021). Analysis of the gut microbiome in dogs and cats. Veterinary Clinical Pathology. 50:6-17. doi:10.1111/vcp.13031
Van Borm, S., Belák, S., Freimanis, G., et al. (2015). Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods in molecular biology (Clifton, N.J.), 1247, 415–436. doi:0.1007/978-1-4939-2004-4_30
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