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. 2022 Aug 10;12(16):2024.
doi: 10.3390/ani12162024.

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

Zhenwei Zhang  1 , Bingjian Huang  1 , Yonghui Wang  1 , Mingxia Zhu  1 , Changfa Wang  1
Affiliations

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

Zhenwei Zhang et al. Animals (Basel). .

Abstract

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys' oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.

Keywords: 16S rRNA; donkey foal; microbial function; oral microbiome; weaning.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Alpha diversity indices of oral bacteria between preweaning and postweaning donkeys. (a) Sobs index; (b) Chao index; (c) Shannon index; (d) Simpson index; PreW, preweaning group; PostW, postweaning group; *, p < 0.05.
Figure 2
Figure 2
Venn diagram presenting the distribution of oral bacteria community OTUs between preweaning and postweaning donkeys. PreW, preweaning group; PostW, postweaning group.
Figure 3
Figure 3
Composition of the predominant oral bacteria at phylum level between preweaning and postweaning donkeys (abundance of the phylum is expressed as %). PreW, preweaning group; PostW, postweaning group.
Figure 4
Figure 4
Difference in the predominant oral bacteria at phylum level between preweaning and postweaning donkeys (abundance of the phylum is expressed as %). Extended error bar plot was created by bioinformatics software (STAMP). Welch’s two-sided test was used and Welch’s inverted was 0.95; PreW, preweaning group; PostW, postweaning group. *, p < 0.05; **, p < 0.01.
Figure 5
Figure 5
Composition of the predominant oral bacteria at genus level between preweaning and postweaning donkeys (abundance of the genera was expressed as %). PreW, preweaning group; PostW, postweaning group.
Figure 6
Figure 6
Difference in the predominant oral bacteria at genus level between preweaning and postweaning donkeys (abundance of the genera was expressed as %). Extended error bar plot was created by bioinformatics software (STAMP). Welch’s two-sided test was used and Welch’s inverted was 0.95; PreW, preweaning group; PostW, postweaning group. *, p < 0.05; **, p < 0.01; ***, p < 0.001.
Figure 7
Figure 7
LEfSe analysis of the oral microbial composition of Dezhou donkeys in preweaning and postweaning stages. (a) Cladogram by the LEfSe method, visualizing the phylogenetic distribution of the oral bacteria. (b) Histogram of the LDA scores, showing the most differentially abundant taxa between two groups (LDA score > 3.5, n = 10). PreW, preweaning group; PostW, postweaning group.
Figure 7
Figure 7
LEfSe analysis of the oral microbial composition of Dezhou donkeys in preweaning and postweaning stages. (a) Cladogram by the LEfSe method, visualizing the phylogenetic distribution of the oral bacteria. (b) Histogram of the LDA scores, showing the most differentially abundant taxa between two groups (LDA score > 3.5, n = 10). PreW, preweaning group; PostW, postweaning group.
Figure 8
Figure 8
Principal component analysis (PCA, (a)) and nonmetric multidimensional scaling analysis (NMDS, (b)) of the oral bacteria community composition of the preweaning and postweaning donkeys at the OTU level. The Log10 transformed data were used for analysis, and the percentage values given on each axis represent the amount of total variation. PC1 or MNDS1, first axis; PC2 or MNDS2, second axis. PreW, preweaning group; PostW, postweaning group.
Figure 9
Figure 9
Comparison of enriched KEGG metabolic pathways of preweaning and postweaning donkeys. KEGG, Kyoto Encyclopedia of Genes and Genomes; PreW, preweaning group; PostW, postweaning group; ko00620, pyruvate metabolism; ko00010, glycolysis/gluconeogenesis; ko00520, amino sugar and nucleotide sugar metabolism; ko01210, 2-oxocarboxylic acid metabolism; ko00250, alanine, aspartate, and glutamate metabolism; ko00400, phenylalanine, tyrosine, and tryptophan biosynthesis; ko00030, pentose phosphate pathway; ko00061, fatty acid biosynthesis; ko00051, fructose and mannose metabolism; *, p < 0.05; **, p < 0.01.
Figure 10
Figure 10
Comparison of enriched KEGG module of preweaning and postweaning donkeys. KEGG, Kyoto Encyclopedia of Genes and Genomes; PreW, preweaning group; PostW, postweaning group; M00004, pentose phosphate pathway (pentose phosphate cycle); M00083, fatty acid biosynthesis (elongation); M00082, fatty acid biosynthesis (initiation); M00307, pyruvate oxidation, pyruvate => acetyl-CoA; M00116, menaquinone biosynthesis, chorismate => menaquinol; *, p < 0.05.
Figure 11
Figure 11
Comparison of COG functional abundance in oral microbiota between preweaning and postweaning donkeys. Proportion of COG abundance differences within the 95% confidence interval. COG, clusters of orthologous groups of proteins; PreW, preweaning group; PostW, postweaning group.
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