Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.)

Abstract

In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to better understand the relationship between the gene expression level and bacterial abundance in the gut, we studied the growth performance, gut bacterial structure, and transcriptome profile in the 4th generation of the new carp strain (selection group) at harvesting time, and compared them with the control line (traditional Huanghe carp). Body weight, depth, width, and length increased 14.58, 7.14, 5.04, and 5.07%, respectively. The gut microbiome of the selection group also exhibited significantly higher species diversity parameters (Shannon, Simpson, and chao1). Both PCA and phylogenetic analyses divided all gut samples into two parts: control and selection group. Aeromonas was the dominant taxon in the control group, followed by Firmicutes and Roseomonas; in the selection group, Roseomonas was the dominant taxon, followed by Firmicutes and then Aeromonas. Among the 249 significantly differentially expressed genes, 194 were downregulated and 55 were upregulated. Functional GO annotation produced 13 terms in the biological process, 8 in the cellular component, and 7 in the molecular function categories. KEGG annotation indicated that most of these genes were associated with the immune-related pathways. A total of 2,892 pairs of genes (245) and baceterial genera (256) were analyzed using Pearson’s correlation analysis. Most of the identified associations were mapped to the immune system, bacterial community, and cell differentiation categories. The top-10 bacterial genera identified by these analyses were Methylocystis, Ohtaekwangia, Roseomonas, Shewanella, Lutispora, GpVI, Desulfovibrio, Candidatus_Berkiella, Bordetella, and Azorhizobium. Genes paired with bacteria flora were divided into four functional categories: immune, growth, adipocyte differentiation, and nerve regulation. These genes may be related to the comparatively fast growth and high muscle polyunsaturated fatty acid content of the Huanghe carp new strain. Meanwhile, nerve regulation-related genes may be a reflection of the microbiota-gut-brain axis. These results illustrate that gut bacterial community structure is associated with the growth performance and gene expression in the Huanghe carp new strain.

Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens

“…To determine significant differences in β-diversity among different field strains, PERMANOVA was carried out using the "adonis" function of the VEGAN package 49 . Spearman correlation between genes transcripts, LC 50 of each insecticide (All data were used in correlation analysis between insecticide susceptibilitytranscriptome-microbiome, only field strains data were used in environmental abiotic factors correlation analysis because we do not have information on their origins or environment histories) and microbial abundance (bacteria and fungi) was calculated using corAndPvalue 50 in WGCNA package (version 1.69) and P was corrected by Benjamini and Hochberg FDR (BH) method, set threshold as P(adj) < 0.05 in subsequent use to remove weak interactions 51 . The network was made in Gephi (version 0.9.2) based on the spearman correlation metrics.…”

Optimization of in vitro culture conditions of common carp germ cells for purpose of surrogate production

“…The gut of common carp carries symbiotic bacteria. Thus, removing gut contents during germ cell processing may release bacteria into the body cavity, which can contaminate germ cell cultures (19). To address this issue, we have compared two methods to dissect and open the body cavity of common carp.…”

Transcriptome, intestinal microbiome and histomorphology profiling of differences in the response of Chinese sea bass (Lateolabrax maculatus) to Aeromonas hydrophila infection

“…The important role of the human intestinal microbiota in regulating host gene expression and manipulating the microbiome composition may be useful in future treatments (Richards et al, 2019). Other studies have also confirmed that the intestinal microbiota and the host intestinal epithelium should be regarded as an interrelated entity (Shi et al, 2021) and that the percentages of Aeromonas and Rosemonas and the differential expression of IL12 are associated with the disease resistance of Huanghe carp to new strains (Su et al, 2021). Our results indicated that some of the top 10 differentially expressed genes related to the genus level of intestinal microorganisms were involved in the immune response, such as cell adhesion molecule 1 (CADM1) and thrombospondin-4-b (thbs4b).…”