Accumulating evidence suggests that bacteriocin production represents a probiotic trait for intestinal strains to afford dominance, fight infection and even signal the immune system. In this respect, in a previous study, we isolated a strain of Streptococcus hyointestinalis DPC6484 from the porcine intestine which displays antimicrobial activity against a wide range of Gram-positive bacteria and produces a bacteriocin with a mass of 3453 Da. Interestingly, the strain was found to be also immune to a nisin-producing strain. Genome sequencing revealed the genetic determinants responsible for a novel version of nisin, designated nisin H, consisting of the genes nshABTCPRKGEF, with transposases located between nshP and nshR and between nshK and nshG. The same gene cluster is also found in S. hyointestinalis LMG14581. Notably, the cluster lacks an equivalent of the nisin immunity gene, nisI. Nisin H is proposed to have the same structure as the prototypical nisin A, but differs at 5 amino acid positions, namely (nisin A to H) Ile1Phe, Leu6Met, Gly18DHB, Met21Tyr and His31Lys, and appears to represent an intermediate between the lactococcal nisin A and the streptococcal nisin U variants of nisin. Purified nisin H inhibits a wide range of Gram positive bacteria including staphylococci, streptococci, Listeria, bacilli and enterococci. It represents the first example of a natural nisin variant produced by an intestinal isolate of streptococcal origin.