Uncovering the molecular strategies that allow human gut symbionts to degrade insoluble dietary and host glycans

揭示人类肠道共生体降解不溶性膳食和宿主聚糖的分子策略

• 批准号: BB/L009951/1
• 负责人: Harry Flint
• 金额: $ 40.7万
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL009951%2F1
• 关键词: Uncovering; molecular; strategies; allow; human

The human intestine harbours enormous numbers (100 trillion) of resident gut micro-organisms that have important consequences for many aspects of health. The energy sources that support the growth of this complex community derive largely from carbohydrates (glycans) that are not degraded by host enzymes, in particular from dietary plant polysaccharides and host-secreted mucin. Much of the non-digestible carbohydrate that enters the large intestine is in the form of insoluble material such as starch particles, plant cell wall fragments and secreted mucus. Rather few bacterial species have the ability to degrade these insoluble substrates. Those that do must be considered 'keystone species', responsible for releasing energy to the rest of the microbial community, and also, via the uptake of microbially-produced short fatty acid products across the gut wall, providing around 10% of the host's energy supply from the diet. Understanding of microbial glycan utilization is therefore fundamental to understanding the impact of diet upon health, and for developing approaches to manipulate the gut microbiota for health benefit. Almost all of the detailed work so far on glycan metabolism by the human gut microbiota has focussed on gram-negative Bacteroides and there is very little information on the equally numerous gram-positive bacteria belonging to the Firmicutes phylum. Recent evidence indicates however that it is certain Firmicutes, especially Ruminococcus spp., that play 'keystone' roles in initiating the degradation of insoluble substrates, whereas human colonic Bacteroides spp. tend to favour soluble carbohydrates. This proposal will therefore investigate for the first time the molecular mechanisms that enable human colonic species of Ruminococcus to degrade particulate resistant starch (R. bromii), cereal bran rich in plant cell wall polysaccharides (R. champanellensis) and insoluble mucin (R. gnavus). The work will exploit the available genome sequences to enable functional studies on extracellular enzymes, enzyme complexes and substrate attachment mechanisms. Preliminary work already shows that organization at the level of the genome and enzyme systems (including likely extracellular enzyme complexes) is completely different from that in Bacteroides spp. A second main element of the proposal will examine interactions of these primary degraders with other species that are likely to compete for solubilized products of insoluble substrates (including Bacteroides spp.), or to modify metabolism by utilizing fermentation products (acetogenic bacteria). These interactions will be explored in vitro and also in vivo by using gnotobiotic animal models (colonised by single, or combinations of, Ruminococcus strains). The project will substantially advance our understanding of the interdependency of different groups within the human gut microbiota and the impact of variations in gut microbiota composition, and will help to test and predict the fermentability of different types of plant material in the gut. Results from this work will help us understand how to keep a beneficial relationship with our gut bacteria and should lead to the development of novel strategies to maintain a 'healthy' gut microbiota and to re-adjust the microbial community following disturbance ('dysbiosis') eg. caused by antibiotics or disease states.

人类肠道内栖息着大量（100 万亿）的肠道微生物，它们对健康的许多方面都有重要影响。支持这个复杂群落生长的能量来源主要来自不被宿主酶降解的碳水化合物（聚糖），特别是来自膳食植物多糖和宿主分泌的粘蛋白。进入大肠的大部分不可消化的碳水化合物以不溶性物质的形式存在，例如淀粉颗粒、植物细胞壁碎片和分泌的粘液。很少有细菌物种具有降解这些不溶性底物的能力。那些做到这一点的物种必须被视为“关键物种”，负责向微生物群落的其他部分释放能量，并且通过肠壁吸收微生物产生的短脂肪酸产物，提供宿主饮食中约 10% 的能量供应。因此，了解微生物聚糖的利用对于了解饮食对健康的影响以及开发控制肠道微生物群以获得健康益处的方法至关重要。迄今为止，几乎所有关于人类肠道微生物群聚糖代谢的详细工作都集中在革兰氏阴性拟杆菌上，而关于同样数量的属于厚壁菌门的革兰氏阳性细菌的信息却很少。然而，最近的证据表明，某些厚壁菌门，特别是瘤胃球菌属，在启动不溶性底物的降解中发挥着“关键”作用，而人类结肠拟杆菌属则在启动不溶性底物的降解过程中发挥着“关键”作用。倾向于可溶性碳水化合物。因此，该提案将首次研究人类结肠瘤胃球菌能够降解颗粒抗性淀粉（R. bromii）、富含植物细胞壁多糖的谷麸（R. champanellensis）和不溶性粘蛋白（R. gnavus）的分子机制。这项工作将利用可用的基因组序列来进行细胞外酶、酶复合物和底物附着机制的功能研究。初步工作已经表明，基因组和酶系统（包括可能的细胞外酶复合物）水平的组织与拟杆菌属完全不同。该提案的第二个主要内容将检查这些初级降解剂与其他物种的相互作用，这些物种可能会竞争不溶性底物（包括拟杆菌属）的溶解产物，或通过利用发酵产物（产乙酸菌）来改变代谢。这些相互作用将通过使用无菌动物模型（由单一或组合的瘤胃球菌菌株定殖）在体外和体内进行探索。该项目将极大地增进我们对人类肠道微生物群内不同群体的相互依赖性以及肠道微生物群组成变化的影响的理解，并将有助于测试和预测肠道中不同类型植物材料的发酵能力。这项工作的结果将帮助我们了解如何与肠道细菌保持有益的关系，并应导致开发新的策略来维持“健康”的肠道微生物群，并在干扰（“生态失调”）后重新调整微生物群落。由抗生素或疾病状态引起。

项目成果

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

• DOI: 10.1111/1462-2920.13158
• 发表时间: 2016-07
• 期刊: Environmental microbiology
• 影响因子: 5.1
• 作者: Duncan SH;Russell WR;Quartieri A;Rossi M;Parkhill J;Walker AW;Flint HJ
• 通讯作者: Flint HJ

Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates.

• DOI: 10.3389/fmicb.2018.02558
• 发表时间: 2018
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Crost EH;Le Gall G;Laverde-Gomez JA;Mukhopadhya I;Flint HJ;Juge N
• 通讯作者: Juge N

Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria.

• DOI: 10.1111/1462-2920.14454
• 发表时间: 2019-01
• 期刊: Environmental microbiology
• 影响因子: 5.1
• 作者: Laverde Gomez JA;Mukhopadhya I;Duncan SH;Louis P;Shaw S;Collie-Duguid E;Crost E;Juge N;Flint HJ
• 通讯作者: Flint HJ

Biomass utilization by gut microbiomes.

• DOI: 10.1146/annurev-micro-092412-155618
• 发表时间: 2014-09
• 期刊: Annual review of microbiology
• 影响因子: 10.5
• 作者: B. White;R. Lamed;E. Bayer;H. Flint

Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii.

• DOI: 10.1128/mbio.01058-15
• 发表时间: 2015-09-29
• 期刊: mBio
• 影响因子: 6.4
• 作者: Ze X;Ben David Y;Laverde-Gomez JA;Dassa B;Sheridan PO;Duncan SH;Louis P;Henrissat B;Juge N;Koropatkin NM;Bayer EA;Flint HJ
• 通讯作者: Flint HJ