The plots of principal component analysis of microbiota composition and biodiversity from faecal samples.

<p>(A) Principal component analysis of the DGGE data for the fecal bacterial community compositions of the CD patients and controls. Each circle is representative of a single sample and shaded according to the abundance of DGGE bands. The plot shows different bacterial community composition in the faeces from the patients and controls. The percentage of variation explained by each principal component is shown in brackets. (B) Band numbers and bacterial diversity obtained from the faecal profiles of CD patients. For each group, the mean values and standard deviation (bars) are shown. Bacterial diversity of CD patients was significantly lower compared with the controls. **, <i>p</i><0.01.</p

The sequence analysis of DGGE bands from the faeces of controls.

<p>The sequence analysis of DGGE bands from the faeces of controls.</p

Experimental design.

<p>This study includes five groups. After undergoing the trauma-hemorrhagic shock (T-HS) operation, rats received either standard enteral nutrition (EN) (T-HS/SE), essential amino acid (EAA) enriched high-protein EN (T-HS/EAA), or a continue infusion of isotonic saline but on normal chow diet (T-HS/Ctr). Food intake in a pair-fed group (PF) was restricted to the T-HS/Ctr group. A normal control group (NC) without T-HS and fed <i>ad libitum</i> chow was also included. Six individuals in each group were harvested on days 2, 4, and 6, respectively.</p

Phylogenetic tree generated from the 16S rDNA sequences of predominant bacterial species in the faeces.

<p>The sequences were aligned with closely related 16S rDNA sequences retrieved from GenBank database using the BLAST. The dominant sequences from the faeces of CD patients and healthy subjects were divided into 4 clusters: Firmicutes, Bacteroidetes, γ-Proteobacteria and ε-Proteobacteria. The scale bar represents the genetic distance.</p

The dysbiosis of faecal microbiota in the patients with Crohn's disease (CD).

<p>(A) Representative DGGE profiles of the faecal samples from CD patients and healthy controls. CD represents Crohn's disease patients and HC is healthy controls. (B) Dendrogram illustrating the similarity correlation of fingerprints between the patients and healthy subjects by means of the clustering algorithm of UPGMA. Scale bar describes DGGE similarity between profiles.</p

Comparison of skeletal muscle mass.

<p>Wet masses of gastrocnemius (A), extensor digitorum longus (B), and soleus (C) in each group were measured following 2, 4, and 6 days of recovery from T-HS. Values are presented as mean ± SE. Groups with different letters at each time point indicate a significant difference (<i>p</i><0.05). T-HS, trauma-hemorrhagic shock.</p

Observations of diarrhea and food intake in normal or T-HS injured animals.

<p>Diarrhea times (A) and food intake (B) in specific groups were recorded daily during study period. Values are presented as mean ± SE. Marker indicates a significant difference from NC group. *, <i>p</i><0.05; ^#, <i>p</i><0.01. T-HS, trauma-hemorrhagic shock.</p

Phylogenetic distribution of meaningful bacterial 16S rDNA sequences and related clones from GenBank.

<p>The bar indicates 5% sequence divergence.</p

Histological characteristics of the ileal mucosa from CD patient.

<p>H&E staining showed normal epithelial architecture and few infiltrated inflammatory cells in the nonulcerated tissues (A). The mucosal specimen from ulcerated ileum revealed the disrupted mucosal architecture and the infiltration of inflammatory cells in (B). Magnifications: ×100.</p

16S rRNA gene primers for real-time PCR.

<p>16S rRNA gene primers for real-time PCR.</p