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We have previously shown that combinations of antibacterial plants alleviate postweaning diarrhea caused by ETEC. Here, we evaluated the effect of feeding garlic combined with either apple pomace or blackcurrant on the gastrointestinal microbial ecosystem of organic weaners three weeks after an ETEC challenge at weaning. The study involved two blocks of 32 pigs (7 weeks; 20 kg BW) per block housed in pairs. The pairs were randomly assigned to four treatments: non-challenged control (NC); ETEC-challenged control (PC); ETEC-challenged fed garlic and apple pomace (3% w\/w each; GA); and ETEC-challenged fed garlic and blackcurrant (3% w\/w each; GB). One pig per pen was euthanized on days 21\u201322 after weaning for digesta and mucosa sampling. Digesta was analyzed for bacterial counts (qPCR), microbial profiling (16S rRNA), and metabolites, while jejunal and ileal mucosa were assessed for antioxidant enzyme activity. The treatments did not influence the number of F18 fimbriae\u2019s gene, <jats:italic>E. coli<\/jats:italic>, <jats:italic>Lactobacillus<\/jats:italic> and total bacteria in the gut digesta, nor the jejunal and ileal mucosa expression of OCNL, ZO-1, and <jats:italic>NF-\u03baB<\/jats:italic> genes. Compared to NC, PC did not alter the overall gut microbiota composition but increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) <jats:italic>Campylobacter<\/jats:italic> and reduced <jats:italic>Roseburia <\/jats:italic>relative abundance. Compared to NC and PC, GA increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) <jats:italic>Weissella<\/jats:italic> relative abundance and reduced lactic acid and cadaverine concentrations in the stomach and jejunum. Both GA and GB increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) superoxide dismutase and glutathione peroxidase activities in the small intestinal mucosa. GA and GB increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) <jats:italic>Catenibacterium<\/jats:italic> and <jats:italic>Holdemanella<\/jats:italic> in the cecum and colon, with GB additionally increasing (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) short-chain fatty acid concentrations. Compared to NC and PC, GA increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) <jats:italic>Faecalibacterium<\/jats:italic> abundance in the cecum. GA and GB increased (<jats:italic>P<\/jats:italic>\u2009\u2264\u20090.05) the proportion of butyric acid in the colon. In conclusion, the combination of garlic with either apple pomace or blackcurrant increased the abundance of beneficial gut bacteria, leading to improved hindgut fermentation activity and oxidative status in the small intestine of pigs three weeks after weaning.<\/jats:p>","DOI":"10.1186\/s12866-025-04247-2","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T11:54:06Z","timestamp":1759406046000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Effects of supplementation of garlic with apple pomace or blackcurrant on the gastrointestinal microbial ecosystem of organic pigs after weaning"],"prefix":"10.1186","volume":"25","author":[{"given":"Kevin","family":"Jerez-Bogota","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Jensen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ole","family":"H\u00f8jberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nuria","family":"Canibe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,10,2]]},"reference":[{"key":"4247_CR1","doi-asserted-by":"publisher","unstructured":"Burrin D, Stoll B. 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