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Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing

View Article: PubMed Central - PubMed

ABSTRACT

Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements. Taxonomic analysis indicated that the predominant phyla were distinct with different dietary treatments. The phyla Firmicutes (51.4%), Bacteroidetes (29.55%) and Proteobacteria (7.90%) were dominant in the CK group, but Bacteroidetes (65.19% and 67.29%,) Firmicutes (18.01% and 17.39%), Proteobacteria (8.72% and 10.18%), Synergistete (2.51% and 1.76%) and Spirochaetes (2.60% and 1.46%) were dominant in CF5 and CF10 groups. The abundance of Firmicutes was negatively correlated with the supplementation of cassava foliage. However, the abundance of Bacteroidetes and Proteobacteria were positively correlated with the supplementation of cassava foliage. Our study also revealed that the microbial communities were significantly different at genus levels. Genes related to nutrient and energy metabolism, immunity and signal transduction pathways were primarily enriched by the microbiome.

No MeSH data available.


KEGG enrichment analysis of the difference groups.(A): CK-VS-CF5; (B): CK-VS-CF10; (C): CF5-VS-CF10. Rich Factor: The ratio of the number of differentially expressed genes and the total number genes which located in the pathway genes. The greater the Factor Rich, the higher the degree of enrichment. P-value closer to 0, the more significant enrichment.
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f6: KEGG enrichment analysis of the difference groups.(A): CK-VS-CF5; (B): CK-VS-CF10; (C): CF5-VS-CF10. Rich Factor: The ratio of the number of differentially expressed genes and the total number genes which located in the pathway genes. The greater the Factor Rich, the higher the degree of enrichment. P-value closer to 0, the more significant enrichment.

Mentions: In the present study, we found that the relative abundances of genera were also affected by the addition of cassava foliage. Figure 2 shows the 14 most abundant genera. The relative abundances of Bacteroides, Prevotella, Desulfovibrio, Treponema and Phascolarctobacterium were significantly increased with the addition of cassava foliage. However, the relative abundances of Oscillospira, Faecalibacterium, Megamonas, Dorea, Peptococcus, Collinsella and Ruminococcus were significantly decreased (P < 0.05). The relative abundance of Parabacteroides in the CF5 group was significantly higher compared with the CK and CF10 groups (P < 0.05). However, the relative abundance of Sutterella was not significantly different among all groups. Based on the functionality prediction, we detected a clear difference in the KEGG Orthologs (KO) composition in caecum. There were 104,109 and 87 differential enrichment KEGG pathways between CK and CF5, CK and CF10, CF5 and CF10, respectively. Figure 6 shows the top 20 pathway enrichment of different groups. Cecal microbial pathways were also detected, which were related to amino acid metabolism pathways (e.g. valine, leucine and isoleucine degradation, phenylalanine metabolism, glycine, serine and threonine metabolism, glutathione metabolism, arginine biosynthesis, taurine and hypotaurine metabolism, histidine metabolism, glutathione metabolism, nitrogen metabolism, lysine degradation), sugar and nucleotide sugar metabolism pathways (e.g. pentose phosphate pathway, glycosaminoglycan degradation, ribosome biogenesis in eukaryotes, phosphotransferase system (PTS), glycolysis/gluconeogenesis, galactose metabolism), fatty acid degradation pathways (e.g. fatty acid degradation, butanoate metabolism, degradation of aromatic compounds, glyoxylate and dicarboxylate metabolism), immunity and signal transduction (e.g. cationic antimicrobial peptide (CAMP), ascorbate and aldarate metabolism, African trypanosomiasis, two-component system, inositol phosphate metabolism, carotenoid biosynthesis, seleno compound metabolism), bacterial proliferation and colonization (e.g. bacterial secretion system and bacterial chemotaxis), sulfur metabolism pathways (e.g. sulfur relay system and sulfur metabolism), energy metabolism (methane metabolism), respectively. Notably, the two-component system pathway showed significant difference in the three groups, and the ABC transporter pathway showed significant difference in CF5 and CF10 groups.


Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing
KEGG enrichment analysis of the difference groups.(A): CK-VS-CF5; (B): CK-VS-CF10; (C): CF5-VS-CF10. Rich Factor: The ratio of the number of differentially expressed genes and the total number genes which located in the pathway genes. The greater the Factor Rich, the higher the degree of enrichment. P-value closer to 0, the more significant enrichment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382919&req=5

f6: KEGG enrichment analysis of the difference groups.(A): CK-VS-CF5; (B): CK-VS-CF10; (C): CF5-VS-CF10. Rich Factor: The ratio of the number of differentially expressed genes and the total number genes which located in the pathway genes. The greater the Factor Rich, the higher the degree of enrichment. P-value closer to 0, the more significant enrichment.
Mentions: In the present study, we found that the relative abundances of genera were also affected by the addition of cassava foliage. Figure 2 shows the 14 most abundant genera. The relative abundances of Bacteroides, Prevotella, Desulfovibrio, Treponema and Phascolarctobacterium were significantly increased with the addition of cassava foliage. However, the relative abundances of Oscillospira, Faecalibacterium, Megamonas, Dorea, Peptococcus, Collinsella and Ruminococcus were significantly decreased (P < 0.05). The relative abundance of Parabacteroides in the CF5 group was significantly higher compared with the CK and CF10 groups (P < 0.05). However, the relative abundance of Sutterella was not significantly different among all groups. Based on the functionality prediction, we detected a clear difference in the KEGG Orthologs (KO) composition in caecum. There were 104,109 and 87 differential enrichment KEGG pathways between CK and CF5, CK and CF10, CF5 and CF10, respectively. Figure 6 shows the top 20 pathway enrichment of different groups. Cecal microbial pathways were also detected, which were related to amino acid metabolism pathways (e.g. valine, leucine and isoleucine degradation, phenylalanine metabolism, glycine, serine and threonine metabolism, glutathione metabolism, arginine biosynthesis, taurine and hypotaurine metabolism, histidine metabolism, glutathione metabolism, nitrogen metabolism, lysine degradation), sugar and nucleotide sugar metabolism pathways (e.g. pentose phosphate pathway, glycosaminoglycan degradation, ribosome biogenesis in eukaryotes, phosphotransferase system (PTS), glycolysis/gluconeogenesis, galactose metabolism), fatty acid degradation pathways (e.g. fatty acid degradation, butanoate metabolism, degradation of aromatic compounds, glyoxylate and dicarboxylate metabolism), immunity and signal transduction (e.g. cationic antimicrobial peptide (CAMP), ascorbate and aldarate metabolism, African trypanosomiasis, two-component system, inositol phosphate metabolism, carotenoid biosynthesis, seleno compound metabolism), bacterial proliferation and colonization (e.g. bacterial secretion system and bacterial chemotaxis), sulfur metabolism pathways (e.g. sulfur relay system and sulfur metabolism), energy metabolism (methane metabolism), respectively. Notably, the two-component system pathway showed significant difference in the three groups, and the ABC transporter pathway showed significant difference in CF5 and CF10 groups.

View Article: PubMed Central - PubMed

ABSTRACT

Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements. Taxonomic analysis indicated that the predominant phyla were distinct with different dietary treatments. The phyla Firmicutes (51.4%), Bacteroidetes (29.55%) and Proteobacteria (7.90%) were dominant in the CK group, but Bacteroidetes (65.19% and 67.29%,) Firmicutes (18.01% and 17.39%), Proteobacteria (8.72% and 10.18%), Synergistete (2.51% and 1.76%) and Spirochaetes (2.60% and 1.46%) were dominant in CF5 and CF10 groups. The abundance of Firmicutes was negatively correlated with the supplementation of cassava foliage. However, the abundance of Bacteroidetes and Proteobacteria were positively correlated with the supplementation of cassava foliage. Our study also revealed that the microbial communities were significantly different at genus levels. Genes related to nutrient and energy metabolism, immunity and signal transduction pathways were primarily enriched by the microbiome.

No MeSH data available.