Plantaricin EF (PlnEF) is a class IIb bacteriocin produced by Lactobacillus plantarum. We compared L. plantarum NCIMB8826 and LM0419, a plnEFI deletion mutant of that strain lacking plnEF and the gene for the cognate immunity protein plnI, in a 2,4,6-trinitrobenzenesulfonic acid (TNBS) induced mouse model of acute inflammatory bowel disease. Mice fed either L. plantarum NCIMB8826 or LM0419 were not protected against TNBS according to either disease activity or histology (Ameho) scores. Mice consuming NCIMB8826 exhibited intermediate (non-significant) levels of colonic tumour necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) that ranged between the TNBS-treated animals and healthy controls. By comparison, TNF-α and IL-6 quantities were elevated in mice given L. plantarum LM0419 and equivalent to mice given TNBS alone. Both strains survived digestive tract transit in equal numbers and did not result in global changes to the bacterial composition in the intestine according to 16S rRNA gene sequencing either prior to or after TNBS administration. Examination of intestinal taxa showed that mice consuming wild-type L. plantarum, but not LM0419 contained lower proportions of Mucispirillum (Deferribacteres phylum) in the faeces prior to TNBS administration and Parabacteroides (Bacteroidetes phylum) in the caecum after disease induction. Parabacteroides also positively correlated with disease activity and histology scores. These findings suggest a role for PlnEFI production by L. plantarum in benefiting digestive tract health.