| Literature DB >> 30073560 |
Tianshu Lyu1, Guangshuai Liu1, Huanxin Zhang2, Lidong Wang1, Shengyang Zhou1, Huashan Dou3, Bo Pang3, Weilai Sha1, Honghai Zhang4.
Abstract
Wolves (Canis lupus) and their domesticated and close relatives, dogs (Canis lupus familiaris), have great differences in their diets and living environments. To the best of our knowledge, the fundamental question of how the abundance and function of the gut microbiota of domestic dogs evolved to adapt to the changes in host feeding habits has yet to be addressed. In this study, our comparative analyses of gut metagenomes showed that the abundance of gut microbiota between the two species have some significant differences. Furthermore, a number of taxa observed in higher numbers in domestic dogs are related to carbohydrate metabolism, which may be because that there were more complicated polysaccharides in dogs diets than that in wolves diets. A significant difference in the abundance of genes encoding glycosyltransferase family 34 (GT34), carbohydrate-binding module family 25 (CBM25), and glycoside hydrolase family 13 (GH13) between the gut microbiota metagenomes of domestic dogs and gray wolves also supported this observation. Furthermore, the domestic dog gut microbiota has greater valine, leucine and isoleucine biosynthesis and nitrogen metabolism. This result showed that compared with wolves, the domestic dog diet contains a smaller amount of animal protein, which is consistent with the dietary composition of wolves and dogs. Our results indicate that the function and abundance of gut microbiota of domestic dogs has been adapted to domestication, which is of great significance for the ability of domestic dogs to adapt to changes in food composition.Entities:
Keywords: Canis lupus; Canis lupus familiaris; Function comparison; Gut microbiota; Metagenomic
Year: 2018 PMID: 30073560 PMCID: PMC6072643 DOI: 10.1186/s13568-018-0652-x
Source DB: PubMed Journal: AMB Express ISSN: 2191-0855 Impact factor: 3.298
Sample information
| Sample name | Sex | Age | Local |
|---|---|---|---|
| CL1.1 | Male | 7 | Dalai Lake National Nature Reserve |
| CL1.2 | Female | 7 | Dalai Lake National Nature Reserve |
| CL1.3 | Male | 4 | Dalai Lake National Nature Reserve |
| CL1.4 | Female | 4 | Dalai Lake National Nature Reserve |
| CL2.1 | Female | 6 | Dalai Lake National Nature Reserve |
| CL2.2 | Male | 4 | Dalai Lake National Nature Reserve |
| CL2.3 | Male | 4 | Dalai Lake National Nature Reserve |
Basic information of the gene catalog
| Basic information | |
|---|---|
| ORFs NO. | 307,207 |
| Integrity:enda | 56,321 (18.33%) |
| Integrity:start | 67,985 (22.13%) |
| Integrity:allb | 159,718(51.99%) |
| Integrity:none | 23,183 (7.55%) |
| Total Len. (Mbp)c | 218.5 |
| Average Len. (bp)d | 711.26 |
| GC percente | 42.29 |
aGenes that only contain termination/initiation codons
bGenes that contain none/all codons
cOverall length of genes
dAverage length of genes
eEstimate of the total GC content of genes
The statistical table of data
| Sample | Insert size (bp) | Raw data | Clean data | GC % | Effective % |
|---|---|---|---|---|---|
| CL1.1 | 350 | 6407.94 | 6403.51 | 43.83 | 99.931 |
| CL1.2 | 350 | 6636.36 | 6628.6 | 42.97 | 99.883 |
| CL1.3 | 350 | 6787.35 | 6771.63 | 38.61 | 99.768 |
| CL1.4 | 350 | 6210.43 | 6201.88 | 43.65 | 99.862 |
| CL2.1 | 350 | 6327.63 | 6323.43 | 42.04 | 99.934 |
| CL2.2 | 350 | 6459.95 | 6449.21 | 44.28 | 99.834 |
| CL2.3 | 350 | 6229.68 | 6192.29 | 42.39 | 99.4 |
Fig. 1Correlation coefficient between samples, the ANOSIM analysis based on species, and the cluster analysis based on Bray–Curtis distance. a Correlation coefficient. The different colors represent the different Spearman correlation coefficient, the deeper the color is, the greater the absolute value of the correlation between samples; b ANOSIM analysis at the phylum level. The x-axis for grouping information, y-axis for distance information, R-value is between (− 1, 1) and R-value is greater than 0, indicating there are significant differences between groups; c the cluster analysis at the family level; and d the cluster analysis at the genus level
Fig. 2The relative abundances of dominant bacteria in each sample at a the phylum level and b the genus level
Fig. 3The abundance clustering based on significant differences in species at a the family level and b the genus level. Horizontal represents sample information; vertical information represents annotated information of species; the cluster tree on the left is the species cluster tree. The values corresponding to the intermediate heat map are the Z values of the relative abundance of each row of species after standardized treatment
Fig. 4The relative abundance of functionally annotated genes at level 1 a based on the CAZy database and b based on the KEGG database. The vertical axis represents the relative proportion of comments to a functional class. The horizontal axis represents the sample name. The functional categories corresponding to each color block are shown in the figure on the right
Fig. 5The PCA and NMDS dimension reduction analysis based on the functional gene abundance using KEGG databases. a PCA analysis; b NMDS dimension reduction analysis
Fig. 7Significantly different enzymes based on the CAZy database
Fig. 6The annotated pathway of amino acids biosynthesis