基于全基因组测序的丁酸梭菌安全性评价

doi:10.19586/j.2095-2341.2023.0075

生物技术进展 ›› 2023, Vol. 13 ›› Issue (5): 755-759.DOI: 10.19586/j.2095-2341.2023.0075

基于全基因组测序的丁酸梭菌安全性评价

高应瑞¹(), 康福忠², 孟铁健¹, 刘珂飞¹, 王调调¹, 陈金艳¹, 孙彤¹

^1.天津生机集团股份有限公司，天津 300384
^2.天津市农业生态环境监测与农产品质量检测中心，天津 300193

收稿日期:2023-05-31 接受日期:2023-07-24 出版日期:2023-09-25 发布日期:2023-10-10
作者简介:高应瑞E-mail:gaoyr84@163.com

Safety Evaluation of Clostridium butyricum Based on Whole Genome Sequencing

Yingrui GAO¹(), Fuzhong KANG², Tiejian MENG¹, Kefei LIU¹, Tiaotiao WANG¹, Jinyan CHEN¹, Tong SUN¹

^1.Tianjin Shengji Group Limited Liability Co. ，Ltd，Tianjin 300384，China
^2.Tianjin Agricultural Ecological Environment Monitoring and Agricultural Product Quality Testing Center，Tianjin 300193，China

Received:2023-05-31 Accepted:2023-07-24 Online:2023-09-25 Published:2023-10-10

摘要/Abstract

摘要：

丁酸梭菌为革兰氏染色阳性专性厌氧菌，其主要代谢产物为丁酸，其次为乳酸、乙酸等有机酸，广泛分布于动物和人的肠道中。丁酸梭菌作为益生菌，在人以及动物的疾病预防、肠炎等疾病的治疗中均有良好的效果^[1]。开展了丁酸梭菌全基因组测序，从耐药性、毒力基因、致病性等方面综合评价了丁酸梭菌的安全性能。结果显示，丁酸梭菌基因组DNA总长度4 709 567 bp，其中包含1条环状染色体DNA、1条环状质粒和2条线性质粒DNA。环状染色体DNA大小为3 873 131 bp，G+C摩尔百分含量为28.86%，环状质粒DNA大小为769 297 bp，G+C含量为28.33%，线性质粒1 DNA大小为49 922 bp，G+C含量为28.26%，线性质粒2 DNA大小为17 217 bp，G+C含量为27.89%。基因组中共检测到4 285个基因、87个tRNA基因、44个rRNA 基因和3个sRNA 基因；通过与CARD和ARDB数据库相比较，丁酸梭菌全基因组中未检测到数据库中已经收录的耐药基因及致病性相关基因的存在，分析结果为今后进行安全性评价试验奠定了基础。

关键词: 丁酸梭菌, 全基因组测序, 安全性, 耐药, 毒力

Abstract:

Clostridium butyricum is a specialized anaerobic bacterium with Gram positive. Its main metabolites include not only butyric acid， but also organic acids， such as lactic acid and acetic acid. As a probiotic， clostridium butyricum is widely distributed in the intesines of animals and humans， and has shown good effects in disease prevention and treatment of enteritis and other diseases. Conducting whole genome sequencing of Clostridium butyricum to analyze its resistance， virulence genes and pathogenicity， which comprehensively evaluate its safety performance. The results showed that the total length of the genomic DNA of Clostridium butyricum was 4 709 567 bp， including a circular chromosomal DNA， a circular plasmid and two linear plasmid DNA. The size of circular chromosome DNA is 3 873 131 bp， the molar percentage of G+C is 28.86%， the size of circular plasmid DNA is 769 297 bp， the G+C content was 28.33%， the size of linear plasmid 1 DNA was 49 922 bp， the G+C content was 28.26%， the size of linear plasmid 2 DNA was 17 217 bp， and the G+C content was 27.89%. A total of 4 285 genes， 87 tRNA genes， 44 rRNA genes， and 3 sRNA genes were detected in the genome. Compared with CARD and ARDB databases， no drug resistance genes and pathogenicity related genes included in the database were detected in the whole genome of Clostridium butyricum， which laid the foundation for its future safety evaluation tests.

Key words: Clostridium butyricum, whole genome sequencing, safety, drug resistance, virulence

中图分类号:

高应瑞, 康福忠, 孟铁健, 刘珂飞, 王调调, 陈金艳, 孙彤. 基于全基因组测序的丁酸梭菌安全性评价[J]. 生物技术进展, 2023, 13(5): 755-759.

Yingrui GAO, Fuzhong KANG, Tiejian MENG, Kefei LIU, Tiaotiao WANG, Jinyan CHEN, Tong SUN. Safety Evaluation of Clostridium butyricum Based on Whole Genome Sequencing[J]. Current Biotechnology, 2023, 13(5): 755-759.

图/表 3

图1 丁酸梭菌的基因组完成图与预测基因COG功能分类图

Fig. 1 Genome completion map and predicted gene COG functional classification map of Clostridium butyricum

图2 ANI热图注：C. butyricum—本实验室分离丁酸梭菌；C. butyricum1—宿主来源为健康鸡肠道；C. butyricum2—宿主来源为鸡肠道；C. butyricum3—宿主来源为人类粪便；C. butyricum4—宿主来源为人类；C. butyricum5—宿主来源为猪。

Fig. 2 ANI heat map

图3 系统进化树注：C. butyricum—本实验室分离丁酸梭菌；C. butyricum1—宿主来源为健康鸡肠道；C. butyricum2—宿主来源为鸡肠道；C. butyricum3—宿主来源为人类粪便；C. butyricum4—宿主来源为人类；C. butyricum5—宿主来源为猪。

Fig. 3 System evolution tree

参考文献 16

1	张善亭,史燕,张淑丽,等.丁酸梭菌的研究应用进展[J].生物技术通报,2013(9):27-33.
2	NAKANISHIS, TANAKA M. Sequence analysis of a bcteriocino genic plasmid of Clostridium butyricum and expression of the bacteriocin gene in Escherichia coli [J]. Anaerobe, 2010, 16(3): 253-257.
3	傅云扉,魏琦麟,袁明贵,等.丁酸梭菌及产丁酸代谢改造[J].中国生物工程杂志,2022,42(1/2):37-45.
4	中国食品科学技术学会益生菌分会. 益生菌的科学共识(2020年版)[J].中国食品学报,2020,20(5):303-307.
5	KANEHISA M, SATO Y, KAWASHIMA M, et al.. KEGG as a reference resource for gene and protein annotation[J]. Nucleic Acids Res., 2016, 44(1): 457-462.
6	FAINO L, SEIDL M F, DATEMA E, et al.. Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome[J]. MBio, 2015, 6(4): 9-15.
7	SIT C S, RUZZINI A C, VAN ARNAM E B, et al.. Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants[J]. Proc. Natl. Acad. Sci. USA, 2015, 112(1): 31-50
8	TSUJI M, KUDOH S, HOSHINO T. Draft genome sequence of cryophilic basidiomycetous yeast Mrakia blollopis SK-4, isolated from an algal mat of Nagaike Lake in the Skarvsnes ice-free area, East Antarctica[J]. Genome Announ., 2015, 3(1): 1-14
9	BADOUIN H, HOOD M E, GOUZY J, et al.. Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae[J]. Genetics, 2015, 200(4): 1275-1284.
10	DELCHER A L, HARMON D, KASIF S O, et al.. Improved microbial gene identification with GLIMMER[J]. Nucleic Acids Res.,1999, 27(23): 4636-4641.
11	SALZBERG S, DELCHER A, KASIF S, et al.. Microbial gene identification using interpolated Markov models[J].Nucleic Acids Res., 1998, 26(2): 544-548.
12	DELCHER A L, BRATKE K A, POWERS E C, et al.. Identifying bacterial genes and endosymbiont DNA with Glimmer[J]. Bioinformatics, 2007, 23(6): 673-679.
13	BARD J, WINTER R. Gene ontology: tool for the unification of biology[J]. Nat. Genet., 2000, 25: 25-29.
14	PHILIP J, DAVID B, HSIN Y C, et al.. InterProScan 5: genome-scale protein function classification[J]. Bioinformatics, 2014, 30(9): 1236-1240.
15	KANEHISA M, SATO Y, KAWASHIMA M, et al.. KEGG as a reference resource for gene and protein annotation[J]. Nucleic Acids Res., 2016, 44(1): 457-462.
16	MAKAROVA, KIRA S, YURI I, et al.. Archaeal clusters of orthologous genes (arCOGs): an update and application for analysis of shared features between thermococcales, methanococcales, and methanobacteriales[J]. Life, 2015, 5(1): 818-840.

[1]	刘婷婷, 仝涛, 黄昆仑. 转基因玉米的研究进展和食用安全性评价[J]. 生物技术进展, 2022, 12(4): 523-531.
[2]	张凤, 贺晓云, 黄昆仑, 汪其怀. 转基因耐除草剂大豆的食用安全评价研究进展[J]. 生物技术进展, 2021, 11(4): 489-495.
[3]	王杰明,石雅丽,刘安礼,刘占英,兰辉,郝健霞,姚梽鹏,张清翠. 生物技术生产丁酸的研究进展[J]. 生物技术进展, 2020, 10(1): 53-59.
[4]	黄荣才,高胜涛,范士杰,马露,卜登攀,. 畜禽粪污源抗生素及耐药基因在环境中的归趋[J]. 生物技术进展, 2019, 9(2): 146-151.
[5]	于艳琴,杜京旗,赵君,杨卫民. 枣皮红色素理化性质及其食品添加剂研制[J]. 生物技术进展, 2014, 4(2): 129-134.
[6]	高岳. 氨基糖苷类抗生素应用的新机遇[J]. 生物技术进展, 2014, 4(2): 102-106.
[7]	陈亮,郝东云. 转基因作物的食用与环境安全性问题及其对策[J]. 生物技术进展, 2011, 1(2): 81-83.

基于全基因组测序的丁酸梭菌安全性评价

Safety Evaluation of Clostridium butyricum Based on Whole Genome Sequencing

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 3

参考文献 16

相关文章 7

编辑推荐

Metrics

本文评价