Analysis of Microbial Diversity in Feces of Adult Nycticebus bengalensis by High-throughput Sequencing

doi:10.12300/j.issn.1674-5817.2023.140

Abstract

Abstract:

Objective To analyze the composition of microbial community in gut of elderly male Nycticebus bengalensis, aiming to explore the health impact factors associated with artificial captivity. Methods Fecal samples of 4 adult male Nycticebus bengalensis were collected and the V4 region was amplified using bacterial 16S rDNA universal primers. Illumina NovaSeq sequencing platform was used for microbial sequencing analysis. The complexity and similarity of the samples were analyzed using the QIIME software analysis tool. The species structure and abundance of the intestinal flora were analyzed at the phylum and genus levels based on validated data. The PICRUSt software was applied to predict the metabolic function of the flora. Results The results showed that the diversity index (Shannon index) of the flora in the youngest Nycticebus bengalensis was higher than that of the others. PCoA analysis showed that the bacterial community compositions of the four samples had a certain degree of similarity. Bacteria identified in the Nycticebus bengalensis feces included 12 phyla, 18 classes, 28 orders, 49 families, 93 genera, and 59 species. Among them, the dominant phyla were Bacteroidetes and Firmicutes with average relative abundances of 46% and 28%, respectively; The genera Bacteroides, Bifidobacterium, and Fusobacterium had higher abundances, with relative abundances of 33%, 6%, and 6%, respectively; The beneficial genus Bifidobacterium was found in all samples, with the highest relative abundance found in the younger Nycticebus bengalensis. PICRUSt function prediction analysis showed that the abundance of the functional genes related to amino acid transport and metabolism, carbohydrate transport and metabolism,was relatively high. Conclusion The use of Illumina NovaSeq high-throughput sequencing technology can comprehensively detect the fecal microbial community of the Nycticebus bengalensis. The bacterial composition of Nycticebus bengalensis has rich diversity. Many bacteria are not identified and have higher relative abundance, which need further study.

Key words: Nycticebus bengalensis, Feces, High-throughput sequencing, Dominant bacteria, Function prediction

CLC Number:

R-332

Feiyan ZHANG,Chao LIU,Longbao Lü. Analysis of Microbial Diversity in Feces of Adult Nycticebus bengalensis by High-throughput Sequencing[J]. Laboratory Animal and Comparative Medicine, 2024, 44(3): 297-304. DOI: 10.12300/j.issn.1674-5817.2023.140.

Figures/Tables 4

Figure 1 Analysis of the complexity of microbial communities in fecal samples of Nycticebus bengalensisNote： A， Venn diagram based on OTUs （Each circle represents a sample， the numbers in overlapping circles represents the number of OTUs shared between samples， and the numbers in non-overlapping parts represent the number of unique OTUs of the samples）； B， Rarefaction curves of observed index； C， Beta diversity index heatmap. N1, N2, N3, and N4 are the sample numbers for the 4 Nycticebus bengalensis. N1， N2， and N4 were 12-year-old Nycticebus bengalensis and N3 was an 8-year-old Nycticebus bengalensis.

Table 1 Statistical table of microbial Alpha diversity indices in the fecal samples of 4 Nycticebus bengalensis

Alpha多样性指数 Alpha diversity indices	蜂猴粪便样本编号 Fecal sample number of Nycticebus bengalensis				平均值±标准误 Mean±standard error
Alpha多样性指数 Alpha diversity indices	N1	N2	N3	N4	平均值±标准误 Mean±standard error
Observed species	260.00	243.00	256.00	243.00	250.50±8.81
shannon	5.30	5.39	5.75	4.95	5.35±0.33
simpson	0.95	0.96	0.96	0.93	0.95±0.02
chao1	275.83	248.67	259.44	269.64	263.39±11.92
ACE	270.28	251.79	260.40	274.87	264.33±10.31
goods_coverage	1.00	1.00	1.00	1.00	1.00±0.00

Figure 2 Relative abundance of microbial communities in Nycticebus bengalensis fecal samples at the phylum （A） and genus （B） levelsNote：N1， N2， N3， and N4 were the sample numbers of the 4 Nycticebus bengalensis. N1， N2， and N4 were 12-year-old Nycticebus bengalensis and N3 was an 8-year-old Nycticebus bengalensis.

Figure 3 Functional analysis of the gut microbial communities in Nycticebus bengalensis fecal samplesNote： A， PICRUSt functional annotation clustering heatmap； B，Statistical chart of predicted results from KEGG database.

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