Analysis of microbial community difference between sand and rubber bedding in dairy farm by high throughput sequencing technology

doi:10.3969/j.issn.1004-1524.2022.07.04

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (7): 1377-1385.DOI: 10.3969/j.issn.1004-1524.2022.07.04

• Animal Science • Previous Articles Next Articles

Analysis of microbial community difference between sand and rubber bedding in dairy farm by high throughput sequencing technology

LYU Qian¹^,²(), LUO Qiao¹, LUO Xue¹, CHEN Jiubing¹, MA Li¹, LUO Zhengzhong², YAO Xueping¹, YU Shumin¹, SHEN Liuhong¹, CAO Suizhong¹^,^*()

1. College of Veterinary Medicine,Sichuan Agricultural University,Chengdu 611130,China
2. College of Animal Science and Technology,Chongqing Three Gorges Vocational College,Chongqing 404155,China

Received:2020-08-26 Online:2022-07-25 Published:2022-07-26
Contact: CAO Suizhong

Abstract

Abstract:

In order to explore the characteristics and differences of the microbial flora of the sand bedding and rubber bedding of dairy farms, 6 samples of sand bedding and rubber bedding were collected from two dairy farms in Sichuan Province,and the sequencing and bioinformatics of 16S rRNA gene in V4 area was analyzed by high-throughput sequencing technology. The results showed that a total of 1 443 818 clean reads were obtained from the 12 samples of the bedding material of the two dairy farms. The effective sequences with a similarity of 97% were subjected to operational taxonomic units (OTUs), and a total 2 311 OTUs were produced. At the level of genus classification, the dominant bacteria in the sand bedding were Acinetobacter, Marinobacter, Riemerella, Corynebacterium, Arthrobacter. The dominant bacteria in the rubber bedding were Corynebacterium, Luteimonas, Fusobacterium,Halomonas, and Vibrio. The relative abundance of Acinetobacter and Riemerella in the sand bedding samples was significantly higher than that of the rubber bedding samples (P<0.05), but the relative abundance of Fusobacterium in the rubber bedding samples was significantly higher than that of the sand bedding sample (P<0.05). Chao index, Ace index, Shannon index and Simpson index were not significantly different between the two groups (P>0.05). The results indicated that difference of the microbial flora between sand bedding samples was greater than the rubber bedding samples, whether it was sand or rubber bedding, there were pathogenic bacteria in environmental conditions.

Key words: dairy cow, environmental pathogen, high-throughput sequencing, microbial community

CLC Number:

S823

LYU Qian, LUO Qiao, LUO Xue, CHEN Jiubing, MA Li, LUO Zhengzhong, YAO Xueping, YU Shumin, SHEN Liuhong, CAO Suizhong. Analysis of microbial community difference between sand and rubber bedding in dairy farm by high throughput sequencing technology[J]. Acta Agriculturae Zhejiangensis, 2022, 34(7): 1377-1385.

Figures/Tables 9

Table 1 Bedding selection standard and cleaning standard

垫料选择标准Bedding selection standard	风干河沙Sand bedding	橡胶垫Rubber bedding
水分Moisture	≤5%	—
含土率Soil content	≤5%	—
杂质Impurities	≤5%	—
厚度Thickness	≥15 cm	上层为1 cm橡胶,下层为3~4 cm海绵The upper layer is 1 cm rubber and the lower layer is 3-4 cm sponge
清理频次Cleaning frequency	每天2次Twice per day	每天2次Twice per day

Fig.1 Distribution of bedding sampling points

Table 2 Average temperature and humidity from July to September in two dairy farms

月份 Month	平均温度Average temperature/ ℃		平均湿度Average humidity/%
月份 Month	F1	F2	F1	F2
7月July	25.2±1.8 $1 A A$	26.0±1.7 $7 A A$	80.8±3.1 $7 A A$	80.1±2.1 $5 A A$
8月August	26.2±2.1 $5 A A$	27.4±2.1 $1 B A$	78.9±3.4 $1 a A$	81.0±1.6 $7 A a$
9月September	21.3±1.5 $0 B A$	21.7±1.9 $3 C A$	76.0±2.9 $3 B A$	81.5±2.4 $5 A a$

Table 2 Average temperature and humidity from July to September in two dairy farms

月份 Month	平均温度Average temperature/ ℃		平均湿度Average humidity/%
月份 Month	F1	F2	F1	F2
7月July	25.2±1.8 $1 A A$	26.0±1.7 $7 A A$	80.8±3.1 $7 A A$	80.1±2.1 $5 A A$
8月August	26.2±2.1 $5 A A$	27.4±2.1 $1 B A$	78.9±3.4 $1 a A$	81.0±1.6 $7 A a$
9月September	21.3±1.5 $0 B A$	21.7±1.9 $3 C A$	76.0±2.9 $3 B A$	81.5±2.4 $5 A a$

Fig.2 OTUs Venn diagram

Fig.3 Composition of microbial community at genus level The abscissa is the sample name (F1 and F2 represent field 1 and field 2), and the ordinate is the relative abundance of the annotated species. The classification level is that the annotations are merged into Unclassified, and the species whose abundance is less than 0.5% in all samples merged into Others.

Fig.4 Histogram of key species differences The abscissa is the species of the top 10 abundances, the ordinate is the relative abundance, and * represents the significance of the difference test (if P<0.001, marked by “***; for example, 0.001≤P<0.01, marked by “**”; 0.01≤P≤0.05, marked by “*”;P>0.05, no mark.

Fig.5 Alpha diversity estimates of the bacterial communities The five lines from bottom to top are: minimum, first quartile, median, third quartile and maximum. Outliers are represented by “。”.

Fig.6 Alpha diversity dilution curve The abscissa represents the amount of sequencing data, and the ordinate represents the Alpha diversity index corresponding to the Chao index.

Fig.7 Heatmap of β diversity The larger the index, the greater the difference between samples. The closer the evolutionary tree, the greater the similarity of the samples.

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Analysis of microbial community difference between sand and rubber bedding in dairy farm by high throughput sequencing technology

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