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Analysis of Diversity and Composition of Apis Cerana Gut Microbiome in Overwintering Period

Nannan Liu

Nannan Liu

Jilin Agricultural Science and Technology UniversityJilin, PR China
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Liu, Nannan
, 
Wenming Lv

Wenming Lv

Jilin Agricultural Science and Technology UniversityJilin, PR China
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Lv, Wenming
, 
Hongying Lv

Hongying Lv

Jilin Agricultural Science and Technology UniversityJilin, PR China
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Lv, Hongying
, 
Zhihao San

Zhihao San

Jilin Agricultural Science and Technology UniversityJilin, PR China
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San, Zhihao
, 
Yulan Piao

Yulan Piao

Jilin Agricultural Science and Technology UniversityJilin, PR China
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Piao, Yulan
 and 
Fenglin Li

Fenglin Li

Jilin Agricultural Science and Technology UniversityJilin, PR China
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Li, Fenglin
  
Dec 22, 2023
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Article Category: Original Article
Published Online: Dec 22, 2023
Page range: 135 - 146
Received: Aug 08, 2023
Accepted: Oct 19, 2023
DOI: https://doi.org/10.2478/jas-2023-0009
Keywords
© 2023 Nannan Liu et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

Fig. 1.

Distribution of amplicon sequence variants (ASVs) in samples collected from October 2022 (YD_10) to March 2023 (YD_03). Each color represents a group, the number of exclusive ASVs in each month is shown in ellipses, and the number of shared ASVs is shown in circles.
Distribution of amplicon sequence variants (ASVs) in samples collected from October 2022 (YD_10) to March 2023 (YD_03). Each color represents a group, the number of exclusive ASVs in each month is shown in ellipses, and the number of shared ASVs is shown in circles.

Fig. 2.

Linear discriminant analysis (LDA) effect size analysis of differentially abundant (log10 LDA scores >2) bacterial taxa.
Linear discriminant analysis (LDA) effect size analysis of differentially abundant (log10 LDA scores >2) bacterial taxa.

Fig. 3.

Alpha diversity indexes in samples collected from October 2022 (YD_10) to March 2023 (YD_03).
Alpha diversity indexes in samples collected from October 2022 (YD_10) to March 2023 (YD_03).

Fig. 4.

Principal component analysis (PCA) and principal coordinate analysis (PCoA). Each point is a sample, and each color represents the samples collected from October 2022 (YD_10) to March 2023 (YD_03). The lines indicate relative distances.
Principal component analysis (PCA) and principal coordinate analysis (PCoA). Each point is a sample, and each color represents the samples collected from October 2022 (YD_10) to March 2023 (YD_03). The lines indicate relative distances.

Fig. 5.

Functional classification of proteins in a sample collected in December 2022 based on the Clusters of Orthologous Groups database.
Functional classification of proteins in a sample collected in December 2022 based on the Clusters of Orthologous Groups database.

Fig. 6.

Relative abundance of Kyoto Encyclopedia of Genes and genomes (KEGG), KEGG Orthology, and MetaCyc pathways. The bars indicate relative abundances.
Relative abundance of Kyoto Encyclopedia of Genes and genomes (KEGG), KEGG Orthology, and MetaCyc pathways. The bars indicate relative abundances.

Statistical table of sequence before and after quality control

Sample ID Input Filtered Percentage of input passed filter Denoised Merged Percentage of input merged Non-chimeric Percentage of input non-chimeric
YD_10_1 88539 76474 86.37 76230 75379 85.14 69127 78.08
YD_10_2 81862 71466 87.30 71173 70707 86.37 65069 79.49
YD_10_3 96019 73865 76.93 73617 73020 76.05 67709 70.52
YD_11_1 86631 74613 86.13 74311 73526 84.87 68256 78.79
YD_11_2 83855 73638 87.82 73365 72576 86.55 67742 80.78
YD_11_3 84939 74215 87.37 74000 73202 86.18 67951 80.00
YD_12_1 81283 70421 86.64 70147 69237 85.18 64245 79.04
YD_12_2 110139 96774 87.87 96181 94097 85.43 65177 59.18
YD_12_3 84101 73780 87.73 73324 72304 85.97 66716 79.33
YD_01_1 92436 80547 87.14 80054 79032 85.50 67321 72.83
YD_01_2 81970 71802 87.60 71398 70603 86.13 64468 78.65
YD_01_3 84961 74332 87.49 73994 73303 86.28 66340 78.08
YD_02_1 89603 78158 87.23 77797 76893 85.82 69627 77.71
YD_02_2 84113 73750 87.68 73377 72468 86.16 65430 77.79
YD_02_3 85446 74825 87.57 74473 73703 86.26 68538 80.21
YD_03_1 86101 75922 88.18 75540 74479 86.50 67065 77.89
YD_03_2 85007 72912 85.77 72556 71671 84.31 63921 75.19
YD_03_3 80454 70818 88.02 70503 69839 86.81 64284 79.90
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