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, 10 (1), 234

Integrative Analysis of Blood and Gut Microbiota Data Suggests a Non-Alcoholic Fatty Liver Disease (NAFLD)-related Disorder in French SLA dd Minipigs

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Integrative Analysis of Blood and Gut Microbiota Data Suggests a Non-Alcoholic Fatty Liver Disease (NAFLD)-related Disorder in French SLA dd Minipigs

Marco Moroldo et al. Sci Rep.

Abstract

Minipigs are a group of small-sized swine lines, which show a broad range of phenotype variation and which often tend to be obese. The SLAdd (DD) minipig line was created by the NIH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. In this report, we characterized the physiological status of a herd of French DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. Three datasets were produced, i.e. complete blood counts (CBCs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (NAFLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
(A) Plot of the first two components of the PCA based on the CBC data. (B) Plot of the first two components of the PCA based on the expression values of all the genes expressed in the blood. (C) Plot of the first two components of the PCA based on the faecal microbiota data. (D) Plot of the first two components of the IFM obtained from the MFA analysis performed on CBCs, genes, and the microbiota data.
Figure 2
Figure 2
Representation of the functionally connected networks obtained using ClueGO 2.3.4. Each node corresponds to an enriched GO term, and each colour corresponds to a GO group. The same term can be included in several groups, and its size reflects its statistical significance (refer to Supplementary Table 6). The 13 nodes at the bottom left of the picture are not connected to the network. Line width is proportional to k-score values.
Figure 3
Figure 3
(A) Histogram representing the relative abundance (%) of phyla in DD (on the right) and LW (on the left) pigs. (B) Histogram representing the relative abundance (%) of microbial taxa in DD (on the right) and LW (on the left) pigs.
Figure 4
Figure 4
(A) A clustered image map (CIM) based on the association values obtained from the first two dimensions of the sPLS analysis integrating CBCs and DE genes. The CBCs parameters are plotted on the X-axis, and the genes are plotted on the Y-axis. The red and the blue coloured blocks indicate a positive or a negative association respectively, while the yellow colour indicates weak levels of association. (B) A clustered image map (CIM) based on the association values obtained from the first two dimensions of the sPLS analysis integrating DE genes in the blood and faecal microbial taxa. The DE genes are plotted on the X-axis, and the microbial taxa are plotted on the Y-axis. The red and the blue coloured blocks indicate a positive or a negative association respectively, while the yellow colour indicates weak levels of association.

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