Traditional microbiology asks you to grow bacteria on a plate before you can understand what's living in a fermented meat sample. That approach has a serious blind spot: only the species that grow easily under laboratory conditions ever become visible. Many of the strains that actually dominate the microbiota of traditional products like sucuk and pastırma either fail to grow on standard media at all, or grow in proportions that don't reflect their real abundance.
Why culture-dependent methods fall short
Take a fermented sucuk sample. In the classical approach, you plate it, count colonies, and call the largest counts "dominant." But along the way:
- Slow-growing or less competitive species disappear from the picture
- Species adapted to anaerobic conditions may never show up on a standard aerobic medium
- The sample's true proportional makeup gets distorted by differences in growth rate on the plate
The result is that some bacteria treated as "primary species" in the literature can, in the actual product, turn out to be minor or even trace components.
Seeing the real picture through metagenomic sequencing
At İnovatif Biotech, our R&D process relies on culture-independent metagenomic sequencing using the Oxford Nanopore platform. DNA is extracted directly from the sample, and the genetic signature of every microorganism present is read — there's no need to grow anything, only for it to exist.
That lets us establish the true species composition of a fermented product independent of laboratory selection bias. In one sample we analyzed, for instance, Lactobacillus nagelii turned out to be dominant, while species that feature more prominently in the classical literature came in well below expectations.
How this data shapes BAKTOGARD® cultures
The data we get from metagenomic analysis becomes our reference point when deciding which strains to isolate and propagate in the lab. Our goal isn't to chase what the literature says "should" be there — it's to develop starter cultures that reflect the microbial profile that actually exists in Anatolia's own fermented products.
This approach makes a difference in three ways:
- Authenticity — Our cultures are built from strains that carry the genuine aroma and texture character of regional products.
- Safety — The pathogen-inhibition capacity and absence of biogenic amine production in dominant species are directly tested, not assumed.
- Scientific transparency — Every culture combination is backed by a dataset built on direct observation, not assumption.
Fermentation science is moving fast, and falling sequencing costs are making culture-independent analysis like this practical even for industrial-scale R&D programs. We've used this approach from day one in developing Turkey's first domestic fermented-sucuk starter culture.