高通量测序和宏基因组学：在非培养条件下分析食品微生物生态学的前进。
High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.
机构信息
Department of Agriculture, University of Naples Federico II, Portici, Italy.
出版信息
Appl Environ Microbiol. 2013 May;79(10):3148-55. doi: 10.1128/AEM.00256-13. Epub 2013 Mar 8.
Abstract
Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.
摘要
受环境微生物学领域近期发展趋势的影响，食品微生物学从分子生物学的进步中受益，并采用了新策略来检测、鉴定和监测食品中的微生物。现在，通过直接从待研究样本中提取核酸，然后使用高通量测序（HTS）方法，就可以深入研究食品中的微生物多样性。在本文中，我们描述了将非培养依赖型 HTS 应用于食品基质的工作流程。介绍了 HTS 用于研究食品微生物组的当前情况和未来展望，并描述了做出决策的过程，以选择最佳的工作条件来满足食品研究的具体需求。
相似文献
1
High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.高通量测序和宏基因组学：在非培养条件下分析食品微生物生态学的前进。
Appl Environ Microbiol. 2013 May;79(10):3148-55. doi: 10.1128/AEM.00256-13. Epub 2013 Mar 8.
2
Metagenomics insights into food fermentations.宏基因组学对食品发酵的见解。
Microb Biotechnol. 2017 Jan;10(1):91-102. doi: 10.1111/1751-7915.12421. Epub 2016 Oct 6.
3
Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.基于短读宏基因组学的食源性病原体细菌生态与抗药组学分析的生物信息学流程
Methods Mol Biol. 2025;2852:289-309. doi: 10.1007/978-1-0716-4100-2_19.
4
Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.当代基于宏基因组学的环境研究中采样与数据分析的实际考量
J Microbiol Methods. 2018 Nov;154:14-18. doi: 10.1016/j.mimet.2018.09.020. Epub 2018 Oct 1.
5
Recent Past, Present, and Future of the Food Microbiome.食物微生物组的过去、现在和未来。
Annu Rev Food Sci Technol. 2018 Mar 25;9:589-608. doi: 10.1146/annurev-food-030117-012312. Epub 2018 Jan 18.
6
Translating Omics to Food Microbiology.将组学转化到食品微生物学中。
Annu Rev Food Sci Technol. 2017 Feb 28;8:113-134. doi: 10.1146/annurev-food-030216-025729. Epub 2017 Jan 11.
7
Species classifier choice is a key consideration when analysing low-complexity food microbiome data.在分析低复杂度食品微生物组数据时，物种分类器的选择是一个关键考虑因素。
Microbiome. 2018 Mar 20;6(1):50. doi: 10.1186/s40168-018-0437-0.
8
A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods.一个整合了预测宏基因组分析的生物信息学流程，用于分析源自食品的 16S rDNA/rRNA 测序数据。
Food Microbiol. 2018 Dec;76:279-286. doi: 10.1016/j.fm.2018.05.009. Epub 2018 May 24.
9
Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area - A pilot study.高通量焦磷酸测序在美国大都市地区大小零售商店采购的食品商品中微生物群落分析的应用 - 一项初步研究。
Food Res Int. 2018 Mar;105:29-40. doi: 10.1016/j.foodres.2017.10.057. Epub 2017 Oct 31.
10
Metagenomic insights into the dynamics of microbial communities in food.宏基因组学对食品中微生物群落动态的见解。
Int J Food Microbiol. 2015 Nov 20;213:31-9. doi: 10.1016/j.ijfoodmicro.2015.09.010. Epub 2015 Sep 16.
引用本文的文献
1
Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities.格拉纳·帕达诺奶酪和帕尔马干酪的微生物群分析揭示了奶酪特异性生物标志物、精神益生菌潜力和生物保护活性。
NPJ Biofilms Microbiomes. 2025 Aug 27;11(1):177. doi: 10.1038/s41522-025-00815-6.
2
Can Metagenomic Analyses Be Used Effectively in Safe Food Production?宏基因组分析能否有效地应用于安全食品生产？
Food Sci Nutr. 2025 Aug 7;13(8):e70772. doi: 10.1002/fsn3.70772. eCollection 2025 Aug.
3
Biosensors in Microbial Ecology: Revolutionizing Food Safety and Quality.微生物生态学中的生物传感器：革新食品安全与质量
Microorganisms. 2025 Jul 21;13(7):1706. doi: 10.3390/microorganisms13071706.
4
Scalable genotyping of microbial colonies.微生物菌落的可扩展基因分型
Microb Genom. 2025 Mar;11(3). doi: 10.1099/mgen.0.001378.
5
16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases.应用于昆虫制品（新型食品）微生物组的16S rRNA元条形码分析：三个参考数据库的比较分析
Ital J Food Saf. 2025 Jan 20;14(1). doi: 10.4081/ijfs.2025.13171. Epub 2025 Jan 16.
6
kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.kMetaShot：一种用于宏基因组组装基因组的快速且可靠的分类学分类器。
Brief Bioinform. 2024 Nov 22;26(1). doi: 10.1093/bib/bbae680.
7
Understanding the role of microbes in health and disease of farmed aquatic organisms.了解微生物在养殖水生生物健康与疾病中的作用。
Mar Life Sci Technol. 2024 Sep 19;6(4):579-609. doi: 10.1007/s42995-024-00248-8. eCollection 2024 Nov.
8
Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.比较基因组分析及新型高质量煤炭宏基因组草图的特性描述。
World J Microbiol Biotechnol. 2024 Nov 1;40(12):370. doi: 10.1007/s11274-024-04174-w.
9
Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.真菌鉴定器（FId）：一种更新的聚合酶链反应-限制性片段长度多态性方法，用于简化生态研究中子囊酵母菌分离株的鉴定。
J Fungi (Basel). 2024 Aug 23;10(9):595. doi: 10.3390/jof10090595.
10
Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.揭示巴西开菲尔乳杆菌微生物组：新型发酵乳杆菌（LkefirU）基因组的发现及其具有潜在抗阿尔茨海默病特性的生物活性肽的计算机预测。
BMC Genomics. 2024 Sep 20;25(1):884. doi: 10.1186/s12864-024-10695-3.
本文引用的文献
1
Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities.改进的内转录间隔区特异性引物选择可实现真菌群落的定量、超高通量分析。
Appl Environ Microbiol. 2013 Apr;79(8):2519-26. doi: 10.1128/AEM.03870-12. Epub 2013 Feb 1.
2
The effect of marination on lactic acid bacteria communities in raw broiler fillet strips.腌制对生鸡胸肉片中原生乳酸菌群落的影响。
Front Microbiol. 2012 Oct 18;3:376. doi: 10.3389/fmicb.2012.00376. eCollection 2012.
3
"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese.通过高通量测序对水牛乳马苏里拉奶酪生产过程中涉及的微生物群落进行“重制”。
Appl Environ Microbiol. 2012 Nov;78(22):8142-5. doi: 10.1128/AEM.02218-12. Epub 2012 Aug 31.
4
Next-generation approaches to the microbial ecology of food fermentations.下一代食品发酵微生物生态学方法。
BMB Rep. 2012 Jul;45(7):377-89. doi: 10.5483/bmbrep.2012.45.7.148.
5
Comparison of next-generation sequencing systems.新一代测序系统的比较。
J Biomed Biotechnol. 2012;2012:251364. doi: 10.1155/2012/251364. Epub 2012 Jul 5.
6
High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses.高通量测序检测先前与手工奶酪无关的细菌亚群。
Appl Environ Microbiol. 2012 Aug;78(16):5717-23. doi: 10.1128/AEM.00918-12. Epub 2012 Jun 8.
7
Spoilage microbiota associated to the storage of raw meat in different conditions.与不同条件下储存生肉相关的腐败微生物组。
Int J Food Microbiol. 2012 Jul 2;157(2):130-41. doi: 10.1016/j.ijfoodmicro.2012.05.020. Epub 2012 May 25.
8
Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics.利用宏基因组学比较腌制和未腌制鸡肉中的微生物群落。
Int J Food Microbiol. 2012 Jul 2;157(2):142-9. doi: 10.1016/j.ijfoodmicro.2012.04.016. Epub 2012 Apr 29.
9
Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis.采用 PCR-DGGE 和 pyrosequencing 分析技术评估巴西开菲尔粒的微生物多样性。
Food Microbiol. 2012 Sep;31(2):215-21. doi: 10.1016/j.fm.2012.03.011. Epub 2012 Apr 1.
10
Next-generation sequencing reveals significant bacterial diversity of botrytized wine.下一代测序技术揭示了受贵腐菌侵染葡萄酒的显著细菌多样性。
PLoS One. 2012;7(5):e36357. doi: 10.1371/journal.pone.0036357. Epub 2012 May 1.
Zotero 插件