Bioproject ID: PRJNA580128

bioproject id PRJNA580128      to NCBI
key word Challenge; Gut microbiota; Citrobacter freundii; Immune response; Goblet cells; Grass carp; COMPLEMENT; INFECTION; STRINGTIE; SYSTEM; HEALTH; HISAT
experiment type challenge
publication Xiong F et al., "Gut microbiota modulation and immunity response induced by Citrobacter freundii strain GC01 in grass carp (Ctenopharyngodon idellus)", Aquaculture, 2020; 521(15):735010.
description Gut microbiota modulation and immunity response induced by Citrobacter freundii in grass carp
abstract The effect of Citrobacter freundii, an opportunistic pathogen of fish, on the gut microbiota and immune responses in fish remains unknown. We fed grass carp (Ctenopharyngodon idellus) with two different concentrations of this bacterium (experimental Low and High groups, plus Control group). No signs of acute inflammatory response were found in either of the experimental groups using the intestinal HE staining method, but the number of intestinal goblet cells was much higher in the High group. Furthermore, we found that feeding C. freundii significantly decreased the alpha diversity and altered beta diversity of gut microbiota in both groups, and significantly promoted the relative abundance of Enterobacteriales, Pasteurellales, Neisseriales and Citrobacter in the High group. Spleen transcriptome showed that the expression pattern of immune system-related genes varied significantly between the Control group and High group. Several immunity-related pathways and two infectious diseases-related pathways were significantly enriched in the High group. Many complement system genes, including c3, c4, c5, c7, c8a, c8b and c1s, were also up-regulated in the High group. Overall, our results indicate that C. freundii did not trigger acute intestinal inflammation, but it changed the diversity and population structure of gut microbiota, and triggered the host's innate mucosal immune system. The enrichment of two infectious diseases-related pathways also suggested a higher risk of infection in the High group. These results contribute to our understanding of the effects of opportunistic fish pathogens on gut microbiota and host's immune responses.

Sample Information

sample id sample name tissue strain treatment description
1. SRR11613380 High3 spleen Citrobacter freundii Fed with high concentration Citrobacter freundii Fed with high concentration Citrobacter freundii, replicate 3
2. SRR11613381 High2 spleen Citrobacter freundii Fed with high concentration Citrobacter freundii Fed with high concentration Citrobacter freundii, replicate 2
3. SRR11613382 High1 spleen Citrobacter freundii Fed with high concentration Citrobacter freundii Fed with high concentration Citrobacter freundii, replicate 1
4. SRR11613383 Con2 spleen Citrobacter freundii untreatment Control, replicate 2
5. SRR11613384 Con1 spleen Citrobacter freundii untreatment Control, replicate 1
6. SRR11613385 Low5 spleen Citrobacter freundii Fed with low concentration Citrobacter freundii Fed with low concentration Citrobacter freundii, replicate 5
7. SRR11613386 Low4 spleen Citrobacter freundii Fed with low concentration Citrobacter freundii Fed with low concentration Citrobacter freundii, replicate 4
8. SRR11613387 Low3 spleen Citrobacter freundii Fed with low concentration Citrobacter freundii Fed with low concentration Citrobacter freundii, replicate 3
9. SRR11613388 Low2 spleen Citrobacter freundii Fed with low concentration Citrobacter freundii Fed with low concentration Citrobacter freundii, replicate 2
10. SRR11613389 Low1 spleen Citrobacter freundii Fed with low concentration Citrobacter freundii Fed with low concentration Citrobacter freundii, replicate 1
11. SRR11613390 Con5 spleen Citrobacter freundii untreatment Control, replicate 5
12. SRR11613391 Con4 spleen Citrobacter freundii untreatment Control, replicate 4
13. SRR11613392 Con3 spleen Citrobacter freundii untreatment Control, replicate 3
14. SRR11613393 High5 spleen Citrobacter freundii Fed with high concentration Citrobacter freundii Fed with high concentration Citrobacter freundii, replicate 5
15. SRR11613394 High4 spleen Citrobacter freundii Fed with high concentration Citrobacter freundii Fed with high concentration Citrobacter freundii, replicate 4