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The chicken caecal microbiome: from baselines to biological impact

鸡盲肠微生物组：从基线到生物影响

基本信息

批准号：
BB/H019340/1
负责人：
Mark Pallen
金额：
$ 52.35万
依托单位：
University of Birmingham
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2010
资助国家：
英国
起止时间：
2010 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FH019340%2F1
关键词：
chicken caecal microbiome baselines biological

项目摘要

The intestinal tracts of animals are populated by hundreds, perhaps thousands of bacterial species in vast numbers - tens of billions of bacterial cells per gram of intestinal contents. Collectively these bacteria make up the microbiota, and in its overall composition and genetic makeup, the population is called the microbiome. The metagenome can be defined as the totality of DNA sequences of all the component organisms. Many of these species have not been cultured in the laboratory and most are poorly characterised. Yet they are crucial partners to their animal hosts in nutrition and health - and include the so-called 'good bacteria' of the digestive tract. For the first time, a new approach, high-throughput DNA sequencing (HTS), makes it possible to identify and count on a large scale each bacterial species in a microbiome using specific sequence 'signatures'. These are obtained from a gene, present in all bacteria, that codes for an RNA molecule that is part of the protein synthesis machinery. This gene (16S rDNA) includes both near-constant regions, useful for its specific enrichment from the metagenome, and highly variable regions where the sequence is characteristic of the bacterial species concerned. It is these variable sequence 'signatures' that will identify component bacteria. It is also feasible to infer the biochemical activities of the microbiome by using HTS to identify genes in the metagenome that encode enzymes, capable of digesting dietary substances that could enhance the nutrition of the host organism. For HTS analysis, DNA is extracted from intestinal (caecal) contents or faeces. The16SrDNA sequences are enriched by amplification, using a method called PCR, to create a pool of fragments representing all the bacteria present. These fragments are then individually analysed and their sequences, amounting to one million or more per analysis run, matched computationally to those of all known bacterial species. In this way the bacteria from which they were derived can be identified. If there is no exact match, the closest known relative can be identified. 'Proof of principle' experiments have established the practicality of this approach to unravel the complexities of intestinal microbiology. However few published studies have rigorously defined the variability inherent in the technology, or between individuals, or from day to day and as dietary intake changes. Such data are essential if the enormous power of the technology is to be exploited in rational, hypothesis-based scientific studies. We propose to obtain these data using broiler chickens, so that groups of birds of defined and matched age, breed and diet can be accessed at relatively low cost. Having established robust baselines for analysis, we will tackle some key questions about the role of the microbiota. How does the microbiome change as birds age and change diet? What is the effect of colonisation of the intestinal tract by food borne pathogens such as Campylobacter, and can this information be used to enhance levels of bacteria that may suppress the invading pathogen? We will also assess the potential of sequencing the entire metagenome, the gene pool representing the microbiota as a whole. We will seek evidence for bacterial enzymes that may add to the digestive capacity of the host and thus enhance growth and productivity of the birds. We believe this proposal will firmly establish the scientific credentials of intestinal microbiome research on food animals, and prepare the way for future research into the role of the microbiome in animal health and welfare, efficient utilisation of feed, emergence of antibiotic resistance, and the establishment of intestinal pathogens.

动物的肠道中有成百上千种细菌，数量巨大--每克肠道内容物中有数百亿个细菌细胞。这些细菌共同组成了微生物区系，在其总体组成和基因构成上，这个种群被称为微生物群。元基因组可以定义为所有组成生物的DNA序列的总和。这些物种中的许多还没有在实验室中培养，而且大多数的特征都很差。然而，在营养和健康方面，它们是动物宿主的重要合作伙伴--包括所谓的消化道“有益细菌”。第一次，一种新的方法--高通量DNA测序(HTS)--使人们能够使用特定的序列“签名”大规模地识别和计数微生物组中的每个细菌物种。它们是从存在于所有细菌中的一种基因中获得的，该基因编码一种RNA分子，该分子是蛋白质合成机制的一部分。该基因(16S RDNA)包括近恒定区和高度变异区，前者有助于从后基因组中特异地丰富其序列，后者的序列是相关细菌物种的特征。正是这些可变序列‘签名’将识别组成细菌。通过使用HTS来识别元基因组中编码酶的基因，从而推断微生物组的生化活动也是可行的，这些基因能够消化能够增强宿主有机体营养的饮食物质。对于HTS分析，从肠道(盲肠)内容物或粪便中提取DNA。通过使用一种称为聚合酶链式反应的方法，通过扩增来丰富16SrDNA序列，以创建代表所有存在的细菌的片段池。然后对这些片段进行单独分析，并将它们的序列与所有已知细菌物种的序列进行计算匹配，每次分析总计100万或更多。通过这种方式，可以识别出它们的来源细菌。如果没有完全匹配的，可以识别出最接近的已知亲属。“原则主张”实验已经确定了这种方法在揭开肠道微生物学复杂性方面的实用性。然而，很少有发表的研究严格定义这项技术固有的可变性，或个人之间的可变性，或每天和饮食摄入量变化时的可变性。如果要在理性的、基于假设的科学研究中利用这项技术的巨大力量，这些数据是必不可少的。我们建议使用肉鸡来获得这些数据，这样就可以以相对较低的成本获得确定和匹配的年龄、品种和饮食的禽类群。在建立了可靠的分析基线后，我们将解决有关微生物区系作用的一些关键问题。随着鸟类年龄的增长和饮食的改变，微生物群会发生怎样的变化？肠道被弯曲杆菌等食源性病原体定植的影响是什么？这些信息能否被用来提高细菌水平，从而抑制入侵的病原体？我们还将评估对整个元基因组测序的潜力，整个元基因组是代表整个微生物区系的基因库。我们将寻找细菌酶的证据，以增加宿主的消化能力，从而促进鸟类的生长和生产力。我们相信，这项建议将奠定食用动物肠道微生物组研究的科学资质，并为未来研究微生物组在动物健康和福利、饲料的有效利用、抗生素耐药性的出现和肠道病原体的建立方面的作用铺平道路。