Most companies in this industry start from a catalogue. A strain has already been discovered, named and published somewhere — Lacticaseibacillus rhamnosus GG, Bacillus subtilis FZB42 — and the manufacturer's job is to produce it reliably at scale. That's a real and useful capability, and it's most of what contract manufacturing is. It is not, however, the same capability as finding a new strain in the first place.
EmerrBio does both. The isolation-to-characterisation pipeline below is the same one that feeds every EmerrGrow, EmerrAqua, EmerrThrive and EmerrBiome product on this site, and it's also available directly as a CRO service for a client who brings their own sample or target trait.
Step 1 — Isolation
Everything starts with a sample: soil, plant material, a gut source, or a traditional fermented food. Candidate organisms are cultured out of that sample using selective and enrichment culturing techniques designed to favour the type of organism we're looking for — a spore-forming Bacillus tolerant of heat and desiccation, say, or a lactic-acid bacterium suited to a specific gut environment. Most of what grows out at this stage will not end up going anywhere; isolation is a filtering step, not a discovery in itself.
Step 2 — Morphological & Biochemical Identification
Each isolate that survives Step 1 is examined under a microscope and run through a panel of biochemical tests — Gram staining, colony morphology, cell shape, metabolic reactions. This narrows a candidate to a likely genus and species long before any sequencing happens, and it's fast enough to rule out obviously uninteresting isolates early.
Step 3 — Molecular Identification (16S rRNA)
Morphology can get you to "probably a Bacillus." It can't reliably get you to a specific species or strain — several species in this genus look almost identical under a microscope. 16S rRNA sequencing (and whole-genome sequencing where the project calls for it) settles the question with a certainty morphology alone can't provide, confirming exactly what the organism is before any further work is invested in it.
Step 4 — Functional & Safety Characterization
Identity isn't the finish line. A confirmed strain still has to be screened for whatever functional trait it's being considered for — phosphate solubilisation, a specific antimicrobial activity, gut colonisation — and, just as importantly, for safety: antibiotic-resistance screening and pathogenicity screening, at minimum. This is the step that decides whether a strain is actually viable, not just correctly identified.
What Happens After Characterisation
A completed engagement typically produces a full characterisation report — taxonomic identification plus a functional and safety profile — with strain banking and a scale-up fermentation trial available as an optional next step. Timelines depend entirely on the sample and the target trait, so we scope each project individually rather than quoting a fixed turnaround.
We'll also say plainly what a lot of marketing in this space won't: not every isolation attempt yields a commercially viable candidate. That possibility is part of any genuine discovery process. We'd rather tell a client that upfront than promise a guaranteed outcome we can't back up.
If you have a sample worth characterising, or a target trait you're trying to solve for, our CRO Services page covers how an engagement is scoped, and what comes after a strain is characterised — including scale-up from shake flask to 10,000-litre commercial fermentation.