R. F. Ismagilov

The paper uses 3D imaging to show that malnourished mice gavaged with bacteria have dense bacterial clusters on jejunum mucosa, suggesting colonization and potential villus loss.

This paper develops a 3D imaging approach to quantify spatial patterns of intestinal microbiota in mice, revealing dynamic colonization and taxonomic distribution patterns.

Epithelial GATA4 regulates intestinal regionalization of bacterial colonization, metabolic pathways, and tissue immunity.

The paper shows that multi-stability and hysteresis explain shifts to and persistence of aerobe-anaerobe microbiome states under changing oxygen and nutrient conditions.

This paper develops a quantitative framework to measure absolute microbial abundances in gut samples, revealing diet-induced changes in microbial loads across different GI locations.

This paper introduces a single-step method for quantitative 16S rRNA gene DNA copy quantification and amplicon barcoding, enabling broad microbial coverage and accurate quantification even in samples with high host DNA.

This study shows that high-molecular-weight dietary fiber polymers drive aggregation of particulates in the murine small intestine, independent of mucins and immunoglobulins.