Profiling of the Bacterial Microbiota along the Murine Alimentary Tract

Abstract

Here, the spatial distribution of the bacterial flora along the murine alimentary tract was evaluated using high throughput sequencing in wild-type and Tff3-deficient (Tff3^KO) animals. Loss of Tff3 was linked to increased dextran sodium sulfate-induced colitis. This systematic study shows the results of 13 different regions from the esophagus to the rectum. The number of bacterial species (richness) increased from the esophagus to the rectum, from 50 to 200, respectively. Additionally, the bacterial community structure changed continuously; the highest changes were between the upper/middle and lower gastrointestinal compartments when comparing adjacent regions. Lactobacillus was the major colonizer in the upper/middle gastrointestinal tract, especially in the esophagus and stomach. From the caecum, a drastic diminution of Lactobacillus occurred, while members of Lachnospiraceae significantly increased. A significant change occurred in the bacterial community between the ascending and the transverse colon with Bacteroidetes being the major colonizers with relative constant abundance until the rectum. Interestingly, wild-type and Tff3^KO animals did not show significant differences in their bacterial communities, suggesting that Tff3 is not involved in alterations of intraluminal or adhesive microbiota but is obviously important for mucosal protection, e.g., of the sensitive stem cells in the colonic crypts probably by a mucus plume.

Keywords: TFF3; colitis; esophagus; gut bacteria; gut microbiome; intestine; microbiota; mucus; stomach; trefoil factor.

Figure 1

Richness (top) and Simpson index (down) in wild-type (left panel, in blue) and Tff3^KO (right panel, in red) mice through the gastrointestinal tract; esophagus (Eso), forestomach (FS), stomach corpus (SC), stomach antrum (SA), proximal duodenum (PD), distal duodenum (DD), jejunum (J), ileum (I), caecum (Cae), ascending colon (CA), transverse colon (CT), descending colon (CD), and rectum (Rec).

Figure 2

Relative abundance of bacterial microbiota along the alimentary tract of wild-type mice: esophagus (Eso), forestomach (FS), stomach corpus (SC), stomach antrum (SA), proximal duodenum (PD), distal duodenum (DD), jejunum (J), ileum (I), caecum (Cae), ascending colon (CA), transverse colon (CT), descending colon (CD), and rectum (Rec). Top: abundance of taxa detected at least in one region. Pairwise comparison between adjacent regions were calculated with PERMANOVA (n.s., no significant differences; ***, significant differences). Bottom: abundance of taxa belonging to unclassified Bacteroidales (light green), unclassified Bacteroidetes (dark green), Lactobacillus (blue), and unclassified Lachnospiraceae (yellow) detected in the different regions. Differences between taxa in adjacent regions were calculated with Kruskal–Wallis test (Benjamin and Hochberg correction); p < 0.05: *; p < 0.01: **; p < 0.001: ***.

Figure 3

Relative abundance of bacterial microbiota along the alimentary tract of Tff3^KO mice. For details see the legend of Figure 2.

Figure 4

Group-average agglomerative hierarchical clustering of 197 samples, based on the global bacterial profiles at phylotype level and Bray-Curtis similarities. Each sample is termed by its anatomical region (for details see the legend of Figure 2), the number of the animal (from 1 to 18), and the mouse strain (wild-type or Tff3^KO).

Figure 5

Relative abundance of phylotypes belonging to L. murinus, L. gasseri/taiwanensis and L. reuteri in each mouse and in each region; esophagus (Eso), forestomach (FS), stomach corpus (SC), stomach antrum (SA), proximal duodenum (PD), distal duodenum (DD), jejunum (J), ileum (I), caecum (Cae), ascending colon (CA), transverse colon (CT), descending colon (CD), and rectum (Rec).