人体微生物群与微生物组

随着微生物群(组)研究的兴起,人体微生物组对机体健康或疾病作用的探索一度呈井喷之势,但研究技术及分析方法仍处于起步阶段,需进一步深入。本文对微生物群和微生物组的概念进行了解释,阐述了人体微生物群与机体的相互作用模式,概括了微生物群与人体有关疾病的关系,提出了人体微生物组研究中的6个关键问题,并对未来的发展方向进行了展望。     

Human gut microbiota and bifidobacteria: from composition to functionality

The human gut is the home of an estimated 10(18) bacterial cells, many of which are uncharacterized or unculturable. Novel culture-independent approaches have revealed that the majority of the human gut microbiota consists of members of the phyla Bacteroidetes and Firmicutes. Nevertheless the role of bifidobacteria in gut ecology illustrates the importance of Actinomycetes and other Actinobacteria that may be underestimated. The human gut microbiota represents an extremely complex microbial community the collective genome of which, the microbiome, encodes functions that are believed to have a significant impact on human physiology. The microbiome is assumed to significantly enhance the metabolism of amino and glycan acids, the turnover of xenobiotics, methanogenesis and the biosynthesis of vitamins. Co-colonisation of the gut commensals Bifidobacterium longum and Bacteroides thetaiotaomicron in a murine model system revealed that the presence of bifidobacteria induced an expansion in the diversity of polysaccharides targeted for degradation by Bacteroides and also induced host genes involved in innate immunity. In addition, comparative analysis of individual human gut microbiomes has revealed various strategies that the microbiota use to adapt to the intestinal environment while also pointing to the existence of a distinct infant and adult-type microbiota.     

肠道噬菌体组与人体健康

噬菌体作为肠道微生物群落的重要组成部分,自生命初期即定植于肠道,在不同生命时期均以较为稳定的状态存在于人体。目前已知的肠道噬菌体主要是DNA噬菌体,且大多以前噬菌体形式存在。肠道噬菌体可通过多种机制优化其宿主微生物群的结构和组成,并以多种方式直接或间接影响人体的生理状态,其结构变化与多种疾病相关。利用测序方法,能够直接获取噬菌体组信息。本文基于噬菌体组的相关研究,综述了肠道噬菌体组与人体健康相关的研究进展,并对该领域的研究方法和发展方向做出展望。     

微生物组与动物疫病防控

微生物组研究的发展推动了人类不断探索人体微生物群与疾病之间的相关性。然而,微生物组学在动物疫病防控中的研究尚处于起步阶段。本文对动物疫病防控领域中微生物组研究所发挥的6个作用进行了阐述：揭示疾病与菌群的相关性,鉴定新发病原体,确立有益于维持机体健康生长的菌群,筛选疾病防控的新药物和新制剂,开发新疫苗或改进疫苗的使用效果,提出更简单有效的防控措施。     

Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs

Background

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptive defence system that provides resistance against alien replicons such as viruses and plasmids. Spacers in a CRISPR cassette confer immunity against viruses and plasmids containing regions complementary to the spacers and hence they retain a footprint of interactions between prokaryotes and their viruses in individual strains and ecosystems. The human gut is a rich habitat populated by numerous microorganisms, but a large fraction of these are unculturable and little is known about them in general and their CRISPR systems in particular.

Results

We used human gut metagenomic data from three open projects in order to characterize the composition and dynamics of CRISPR cassettes in the human-associated microbiota. Applying available CRISPR-identification algorithms and a previously designed filtering procedure to the assembled human gut metagenomic contigs, we found 388 CRISPR cassettes, 373 of which had repeats not observed previously in complete genomes or other datasets. Only 171 of 3,545 identified spacers were coupled with protospacers from the human gut metagenomic contigs. The number of matches to GenBank sequences was negligible, providing protospacers for 26 spacers.Reconstruction of CRISPR cassettes allowed us to track the dynamics of spacer content. In agreement with other published observations we show that spacers shared by different cassettes (and hence likely older ones) tend to the trailer ends, whereas spacers with matches in the metagenomes are distributed unevenly across cassettes, demonstrating a preference to form clusters closer to the active end of a CRISPR cassette, adjacent to the leader, and hence suggesting dynamical interactions between prokaryotes and viruses in the human gut. Remarkably, spacers match protospacers in the metagenome of the same individual with frequency comparable to a random control, but may match protospacers from metagenomes of other individuals.

Conclusions

The analysis of assembled contigs is complementary to the approach based on the analysis of original reads and hence provides additional data about composition and evolution of CRISPR cassettes, revealing the dynamics of CRISPR-phage interactions in metagenomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-202) contains supplementary material, which is available to authorized users.     

微生物群在变应性鼻炎发病机制中作用的研究进展

变应性鼻炎是耳鼻咽喉科常见的鼻腔变应性反应疾病,发病率高且严重影响患者的生活质量.因此,探讨该病的病因非常重要.近年来,微生物群在人类健康与疾病中作用的研究越来越受到重视,变应性鼻炎是研究的热点之一.微生物群是居住在于人体内外表面的所有微生物,包括病毒、真菌、原生动物、古生菌和细菌.越来越多的证据表明,微生物群在免疫介...     

21世纪初农业生态系统健康研究方向

农业生态系统健康是指农业生态系统免受发生“失调综合症”,处理胁迫的状态和满足持续生产农产品的能力,目前,农业生态系统健康研究范围主要涉及农业生态系统健康评价方法,土壤质量和水质与农业生态系统健康的联系,农业生态系统健康与人类健康的关系,害虫生态管理对农业生态系统健康的贡献,杂草综合管理在农业生态系统健康中的作用,从生态病理学到农业生态系统健康,线虫群落作为农业生态系统健康指示生物的研究,转基因作物对农业生态系统健康的生态影响评价,农业投入政策对农业生态系统健康的影响,景观生态学在农业生态系统健康评价中的应用,农业生态系统健康与绿色食品开发等,首先论述了农业生态系统健康研究的现状,介绍了农业生态系统健康研究实例-土壤健康的生物指标,最后提出了今后农业生态系统健康的研究方向,为保障农产品安全和增进人类健康提供依据。     

Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens

Fermenting microbial communities generate hydrogen; its removal through the production of acetate, methane, or hydrogen sulfide modulates the efficiency of energy extraction from available nutrients in many ecosystems. We noted that pathway components for acetogenesis are more abundantly and consistently represented in the gut microbiomes of monozygotic twins and their mothers than components for methanogenesis or sulfate reduction and subsequently analyzed the metabolic potential of two sequenced human gut acetogens, Blautia hydrogenotrophica and Marvinbryantia formatexigens in vitro and in the intestines of gnotobiotic mice harboring a prominent saccharolytic bacterium. To do so, we developed a generally applicable method for multiplex sequencing of expressed microbial mRNAs (microbial RNA-Seq) and, together with mass spectrometry of metabolites, showed that these organisms have distinct patterns of substrate utilization. B. hydrogenotrophica targets aliphatic and aromatic amino acids. It increases the efficiency of fermentation by consuming reducing equivalents, thereby maintaining a high NAD⁺/NADH ratio and boosting acetate production. In contrast, M. formatexigens consumes oligosaccharides, does not impact the redox state of the gut, and boosts the yield of succinate. These findings have strategic implications for those who wish to manipulate the hydrogen economy of gut microbial communities in ways that modulate energy harvest.     

人类微生物组产业发展态势及建议

近年来,各国政府、高校、企业和公众高度关注人类微生物组与健康研究,旨在全面系统地解析微生物组的结构和功能,以及生理调控机制,为解决健康问题提供新思路,相关研究带动了人类微生物组行业内益生菌、益生元类保健食品和膳食补充剂、粪菌移植产业的发展,也催生了微生物组检测及健康指导、微生态药物产业的崛起。通过梳理全球人类微生物组产业现状,分析相关产业发展面临的主要瓶颈及未来发展方向,并针对中国人类微生物组产业提出了具体的发展建议。     

病变患者HPV感染情况、基因型分布及阴道微生态变化分析

摘要 目的：分析女性宫颈病变患者人乳头瘤病毒（HPV）感染情况、基因型分布及阴道微生态变化。方法：选取2022年6月至2023年6月期间92例女性宫颈病变患者（纳入观察组）,同时期无宫颈病变的健康体检者92例纳入对照组,比较观察组与对照组HPV感染情况、基因型分布、阴道微生态评估及功能学指标检测结果。结果：观察组HPV感染检出率为73.91%,高于对照组的13.04%,其中单一感染检出率54.35%、混合感染检出率19.56%,分别高于对照组的11.96%、1.09%,差异均有统计学意义（P<0.05）;观察组HPV基因型检出率最高的为HPV 16、HPV 18,检出率分别为45.65%、35.87%,均显著高于对照组（P<0.05）;观察组衣原体、支原体、滴虫、细菌性阴道炎检出率均高于对照组（P<0.05）,乳酸杆菌为优势菌、阴道pH值≤4.5的比例均低于对照组（P<0.05）;观察组白细胞酯酶、唾液酸甘酶、β-葡萄糖醛酸酶阳性检出率均高于对照组（P<0.05）。结论：宫颈病变患者高危型HPV感染率及HPV 16、HPV 18等基因型检出率显著高于正常人群,且患者的阴道微生态存在明显变化,病原体及白细胞酯酶、唾液酸甘酶、β-葡萄糖醛酸酶阳性检出率提高。     

快速发展中的环境微生物科学与技术—“第十二次全国环境微生物学学术研讨会”专刊序言

第十二次全国环境微生物学术研讨会于2009年11月在武汉华中科技大学顺利召开,本次会议围绕\"环境微生物与人类健康\"的主题,在环境微生物学前沿、微生物与环境健康及人类健康、环境微生物资源挖掘与利用,以及环境微生物技术与环境污染防治、生态修复、废弃物资源化利用和再生能源等诸多领域展开深入研讨,充分反映了我国环境微生物学界取得的最新进展,为了展现国内环境微生物及相关交叉领域科研工作者取得的最新进展,《微生物学通报》针对\"第十二次全国环境微生物学术研讨会\"组织出版了这期\"环境微生物专刊\",期望该专刊的出版有助于促进我国环境微生物学相关领域的交流和发展。     

Gut microbiota,host health,and polysaccharides

The intestinal microbiota is a complicated ecosystem that influences many aspects of host physiology (i.e. diet, disease development, drug metabolism, and regulation of the immune system). It also exhibits spatial patterning and temporal dynamics. In this review, the effects of internal and external (environmental) factors on intestinal microbiota are discussed. We describe the roles of the gut microbiota in maintaining intestinal and immune system homeostasis and the relationship between gut microbiota and diseases. In particular, the contributions of polysaccharides, as the most abundant diet components in intestinal microbiota and host health are presented. Finally, perspectives for research avenues relating to gut microbiota are also discussed.     

Potential of Transgenic Crops in Bangladesh: Findings from a Consultation of Bangladeshi Scientific Experts

This note summarizes the results of a consultation of scientific and regulatory experts in July 2005 on the potential of transgenic crops in Bangladesh. We find that Bangladeshi experts are optimistic on the potential of agricultural biotechnology to respond to biotic and abiotic stresses in their country in the future. Public research is constrained by human capacities, infrastructure and capital investment, and transgenic crop development will require the active involvement of outside partners, such as international organizations or collaboration with private companies. We also find that social acceptance of genetic engineering is not considered a major issue, but could become one, and prompted experts to call for a wider awareness campaign on the technology.This research project was conducted as part of the South Asia Biosafety Program (SABP), a project funded by the US Agency for International Development (USAID) and jointly managed by the International Food Policy Research Institute and AGBIOS Canada. The authors would like to thank the Bangladesh Agricultural Research Council and all the participants to the meetings in Dhaka and Mymensingh for their help.     

人类口腔微生物组学研究:现状、挑战及机遇

全球超过一半的人口患有口腔疾病,其医护费用与全球十大常见死亡病因的花费相当,而且口腔感染与早产、动脉粥样硬化、肝硬化、糖尿病、阿尔茨海默病等全身性或慢性疾病显著相关,因此,口腔微生物组一直是人类微生物组计划的主要研究对象之一。与人体其他部位比较,口腔微生物组研究具有取样快捷、宿主反应表征方便、干预手段直接有效等特点;同时,超过65%的口腔细菌类群已可培养,诸多代表性菌株的全基因组信息已破译。因此口腔微生物组在菌群内部调控网络及其与宿主互作机制、局部感染对远隔器官的影响机制、以及基于菌群的慢病早期预警等微生物组研究核心科学问题上具备作为模式研究体系与技术示范对象的重要优势。本文在分析口腔微生物组学国际、国内研究现状的基础上,建议尽快启动中国人口腔微生物组计划(China human oral microbiome project,CHOMP),通过产学研协同攻关,开拓基于口腔菌群的口腔及全身系统性疾病的个体化预防、诊断及治疗策略。     

Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism

Human colonic bacteria are necessary for the digestion of many dietary polysaccharides. The intestinal symbiont Bacteroides thetaiotaomicron uses five outer membrane proteins to bind and degrade starch. Here, we report the x-ray crystallographic structures of SusE and SusF, two outer membrane proteins composed of tandem starch specific carbohydrate-binding modules (CBMs) with no enzymatic activity. Examination of the two CBMs in SusE and three CBMs in SusF reveals subtle differences in the way each binds starch and is reflected in their K_d values for both high molecular weight starch and small maltooligosaccharides. Thus, each site seems to have a unique starch preference that may enable these proteins to interact with different regions of starch or its breakdown products. Proteins similar to SusE and SusF are encoded in many other polysaccharide utilization loci that are possessed by human gut bacteria in the phylum Bacteroidetes. Thus, these proteins are likely to play an important role in carbohydrate metabolism in these abundant symbiotic species. Understanding structural changes that diversify and adapt related proteins in the human gut microbial community will be critical to understanding the detailed mechanistic roles that they perform in the complex digestive ecosystem.     

松嫩平原黑土区不同养分循环结构农业经营制度比较研究

采用模拟养分循环开展长期定位试验的方法对黑土区不同养分循环结构农业经营制度进行了比较研究,结果表明,有机－无机相结合的农业制度包括传统农业与“石油农业”两者之长,是我国农业生产常久不衰、提高系统生产力和养分循环再利用的有效途径．     

基因治疗与人类健康

随着分子生物学及基因工程技术的迅猛发展 ,基因治疗已经成为治疗人类疾病的重要方法之一 ,同时也是维护人类健康最有发展前景的手段之一。诸如遗传病、肿瘤、和传染病与心血管病的基因治疗。遗传免疫方面 ,病毒性疾病和肿瘤的基因治疗 ,如将病毒抗原基因 (HBsAg)及一些肿瘤抗原基因 (CEA)直接注入人体内而产生抗体 ;人类亚健康状态 ,如肥胖、秃顶、疲劳、衰老等的基因治疗。然而基因治疗目前仍面临着许多困扰 ,如基因治疗的有效性、安全性、及社会伦理等诸多问题 ,因此在临床实际应用中要慎之又慎。只有对基因治疗合理规范和正确引导并遵循伦理原则 ,才能最终推动现代医学的发展。     

High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T))

Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon-chain length mycolic acids bound in the cell wall. S. rugosus is also a medically important species because it is an opportunistic pathogen associated with mammalian lung disease. This report represents the second species in the genus to have its genome sequenced. The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part of the NIH Roadmap for Medical Research, Human Microbiome Project.     

Emergence and development of agro-ecological engineering in China

Chinese agricultural eco-engineering is a newborn scientific field which emerged in the practices of sustainable development of agriculture. Based on the discussion of the emergence and development of China’s agricultural eco-engineering, this paper analyzes the characteristics and components of the system. As a case study, the paper introduces the application of ecotechnology and its comprehensive effect in Baiquan county, Helingjiang province, China.