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

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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.


Shannon value and rarefaction curves of OUTs clustered at 97% sequence identity across different samples.
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f1: Shannon value and rarefaction curves of OUTs clustered at 97% sequence identity across different samples.

Mentions: A total of 712,593,146 qualified sequences were obtained from the 18 samples from 18 geese caecum. These sequences included an average of 77,100 reads per caecum sample, and the length of unique tag N50 is 460 bp. (Table 2 and Table S1 and 2). Shannon value and Shannon rarefaction curves for each sample reached the saturation plateau (Table 2 and Fig. 1), indicating that the sampling effort had sufficient sequence coverage to accurately describe the bacterial composition of each group. Indices of bacterial richness based on OTUs were estimated by the method of Ace and Chao, and indices of bacterial diversity were determined using the method of Simpson and Shannon (Table 2). Among the 18 samples, a total of 200,365 OTUs were detected by our analysis, with an average of 11,131 OTUs per sample (Table 2).


Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing
Shannon value and rarefaction curves of OUTs clustered at 97% sequence identity across different samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Shannon value and rarefaction curves of OUTs clustered at 97% sequence identity across different samples.
Mentions: A total of 712,593,146 qualified sequences were obtained from the 18 samples from 18 geese caecum. These sequences included an average of 77,100 reads per caecum sample, and the length of unique tag N50 is 460 bp. (Table 2 and Table S1 and 2). Shannon value and Shannon rarefaction curves for each sample reached the saturation plateau (Table 2 and Fig. 1), indicating that the sampling effort had sufficient sequence coverage to accurately describe the bacterial composition of each group. Indices of bacterial richness based on OTUs were estimated by the method of Ace and Chao, and indices of bacterial diversity were determined using the method of Simpson and Shannon (Table 2). Among the 18 samples, a total of 200,365 OTUs were detected by our analysis, with an average of 11,131 OTUs per sample (Table 2).

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.