ABSTRACT:The aim of this study was to use high throughput sequencing of piglet faeces to investigate if the favourable effects of sodium humate (HNa) and zinc oxide (ZnO) in post-weaning diarrhoea (PWD) treatment are related to changes in the faecal microbiota. Twenty four piglets weaned at 28 days of age were divided into three groups with eight animals per pen: a control group without any treatment (Control), a group treated with 2500 mg ZnO (ZnO), and a group treated with 20 g sodium humate and 1700 mg ZnO (HNa + ZnO) per kg of diet. Piglets of all three groups were challenged with two enterotoxigenic Escherichia coli (ETEC) strains (ETEC/O149/F4/LT and ETEC/O147/F18/LT) on Day 4 post-weaning. As a result very intense and severe diarrhoea with high mortality developed in the ETEC-infected control group, while the ZnO and HNa + ZnO dietary treatments both protected piglets from clinical signs of diarrhoea, mortality and depression of growth performance. A higher relative abundance of Gammaproteobacteria represented mainly by genus Escherichia on Day 10 postweaning in faeces of the ETEC-infected control group in comparison with ZnO and HNa + ZnO was detected. On Day 21, the highest relative increase of beneficial lactobacilli was observed in the HNa + ZnO group. Correlation analysis showed a positive correlation of the ETEC-infected control with the genera Turicibacter, Clostridium, Campylobacter, Dehalobacterium, Desulfuvibrio, Paludibacter and a negative correlation with the genera Prevotella, Blautia, Faecalibacterium, Lactobacillus, and Coprococcus. The opposite correlations with these genera were observed in the supplemented groups, especially in the HNa + ZnO group. The results indicate that dietary supplementation with HNa and ZnO affects the microbial composition of faeces while maintaining good health condition and growth performance of ETEC-infected weaned pigs.