Probiotics should bring 'balance' to the intestinal microbiota by stimulating beneficial bacteria, whilst mitigating adverse ones. Balance can also be interpreted as high alpha-diversity. Contrary, Escherichia coli is often regarded as an adverse component of the resident intestinal microbiota. The aim of the present study was to implement a mouse model for in vivo screening of Lactobacillus-strains for ability to increase gut-microbiota diversity and to mitigate E. coli. Mice were divided into six groups, two dietary control-groups and four groups administered strains of Lactobacillus fermentum and/or Lactobacillus plantarum. All animals were pre-treated with antibiotics, and E. coli in order to equalise the microbiota from the start. After 7 weeks of Lactobacillus administration, the animals were sacrificed: DNA was extracted from caecum tissue, and the microbiota composition was analysed with terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene sequencing. The diversity of the caecal microbiota decreased when the dietary carbohydrate source was limited to corn starch. Conversely, the diversity was restored by Lactobacillus-supplements. The tested combinations of two Lactobacillus strains exerted different influences, not only on the taxonomic level, but also on the inferred microbiome functions. The mixture of L. fermentum GOS47 and L. fermentum GOS1 showed potential for anti-inflammatory activity and short chain fatty acid production. On the other hand, co-administration of L. fermentum GOS57 and L. plantarum GOS42 significantly decreased the viable count of Enterobacteriaceae. These results warrant further investigation of the tested strains as candidates for probiotics. Furthermore, the findings demonstrated that the current experimental animal model is suitable for in vivo studies of the effect of bacterial supplements on the gut-microbiota.