nx_probiome.nx

nx_probiome.nx -- R6 of the FERMENTATION ladder: the cross-kingdom BENEFICIAL-MICROBE engine. The fermentation rungs (R0-R5) run the yogurt/cheese PROCESS safely; this rung models the CULTURES THEMSELVES as biology -- which organism confers which benefit to which host, and whether it is safe to use at all -- and generalises the yogurt/cheese "good bacteria" idea across all of life: PEOPLE (gut probiotics), PLANTS (rhizosphere PGPR, nitrogen fixers, mycorrhizae), ANIMALS (direct-fed microbials), and ORGANISMS-IN-GENERAL (soil nitrifiers, composters, bioremediators). One engine, four host kingdoms -- the "One Health" pattern (a single microbe can lift people AND plants AND soil). v2 (2026-07-09) widens beyond bacteria to ORGANISMS IN GENERAL: a microbe_domain axis (bacterium / yeast / mold / mycorrhizal fungus) so the engine covers the real biology of fermentation and plant health -- acetic-acid bacteria (kombucha/vinegar), probiotic + leavening yeasts, koji/tempeh/cheese molds, and arbuscular mycorrhizal fungi -- not just bacteria. Additive, never reductive: every earlier strain is kept. THE NEVER-HARM LAW (the cross-kingdom analog of nx_ferment_safety's never-poison law, Global Rule 26): a beneficial-microbe capability may NEVER recommend or admit an organism that is unsafe for its host. STRUCTURAL refusal, not a warning string: - a frank PATHOGEN (Listeria monocytogenes, ...) is ALWAYS refused; - an OPPORTUNIST / non-QPS organism (Enterococcus faecium, which can carry transferable vancomycin resistance and is a nosocomial pathogen) is refused for general use; - an organism that carries acquired ANTIBIOTIC RESISTANCE is refused (it could transfer the resistance in the gut/rumen/soil); - a TOXIGENIC organism is refused even though its genus contains QPS members -- a "qualified" strain must PASS its qualification. Two genus-level liar-kill pairs prove this MECHANICALLY: Bacillus subtilis (QPS) vs B. cereus (cereulide toxin), and Aspergillus oryzae (safe domesticated koji mold) vs A. flavus (aflatoxin); - a HOST MISMATCH is refused: a soil/plant nitrogen-fixer is NOT a human probiotic (do not eat Rhizobium as a gut culture), and the recommender will never hand you a strain outside the target host. Unknown strain ids FAIL CLOSED (treated as pathogens). THE EXCEED (measured, liar-killed by the gate -- see the _test):