肠道微生物组与宿主的表观遗传修饰

高通量测序技术已经增加了人们对肠道微生物组和表观遗传学修饰的理解,将肠道微生物组和宿主表观遗传学修饰紧密联系起来,阐明了很多疾病的发生过程如免疫、代谢、心血管疾病甚至是癌症。肠道微生物组与宿主具有相互作用,与人体密不可分,相辅相成。肠道微生物组的生态失调可能诱导疾病的发生并能调控宿主表观遗传学修饰。宿主表观遗传学调控和肠道微生物组(或其代谢产物)变化的相互关系在很多疾病中都有报道。因此,肠道微生物组可作为某些疾病的诊断标记,健康肠道微生物组的移植会逆转这种微生态失调,可作为一种有效的治疗策略。本文主要探讨了肠道微生物组直接调控宿主表观修饰和通过小分子生物活性物质和其他酶辅因子间接影响表观修饰,以及基于肠道微生物组调控宿主表观修饰的诊断和治疗应用等。     

膳食脂肪、肠道微生物与宿主健康的研究进展

作为三大主要营养物质之一,膳食脂肪为人体提供能量和营养。膳食脂肪摄入不当会破坏肠道微生物的稳态,影响宿主的代谢状况,增加慢性疾病发生的风险。建立疾病动物模型是研究肠道微生物与宿主健康的重要手段。文中综述了膳食脂质的数量和种类、肠道微生物和宿主代谢之间的相互作用及其可能的作用机制,阐述了基于不同的疾病动物模型,膳食脂质影响肠道微生物的结构和功能,以及对宿主代谢的调节,为深入了解膳食脂质、肠道微生态和宿主健康三者之间的关系提供了依据。     

肥胖相关的肠道微生物群落结构动力学与功能解析研究

肥胖及相关的慢性代谢性疾病近年来已经成为威胁全球的公共健康问题。越来越多的证据表明,在宿主的营养、免疫和代谢中有不可替代的作用的肠道菌群不仅可以通过调节宿主脂肪吸收存储相关的基因,影响后者的能量平衡,更重要的是其结构失调导致宿主循环系统中内毒素增加,诱发慢性、低水平炎症,导致肥胖和胰岛素抵抗。运用微生物分子生态学、元基因组学和代谢组学的方法,揭示与代谢性疾病相关的菌群结构失调,并鉴定出相关的特定细菌类群及其功能,使得通过以菌群为靶点的营养干预手段防止慢性代谢性疾病成为可能,将带来代谢性疾病预防和控制策略的革命性的变化。     

Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome

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人类肠道微生物组与相关疾病研究进展

人体肠道共生着数以万亿计的微生物,肠道微生物在维持宿主正常生理功能中发挥重要作用,其成分和功能变化可导致严重的肠道和全身性疾病。以新一代测序技术和生物信息学分析为基础的元基因组学研究不仅极大地推动了对人类肠道微生物的整体认识,还加深了对肠道微生物代谢产物促进人类健康机理的理解,为肠道炎症、代谢性疾病和癌症等人类疾病的诊断与治疗提供了新思路。就肠道微生物元基因组学与肠道相关疾病的研究进展作一综述。     

Save your gut save your age: The role of the microbiome in stem cell ageing

The tremendous importance of microbiota in microbial homoeostasis, alterations in metabolism and both innate and adaptive immune systems has been well established. A growing body of evidence support that dysbiosis or compositional changes in gut microbiota is linked to the ageing of stem cells in terms of dysregulations of metabolism, aberrant activation of the immune system as well as promoting epigenetic instability of stem cell. In this concise review, we elucidate recent emerging topics on microbiotic alterations and underlying mechanisms in stem cell ageing.     

肠道菌群与肾脏疾病相关性研究进展

人体是一个有机的整体,不同系统之间存在着相互影响。近年来,随着科学的不断发展,肠道菌群与人体健康的关系也逐渐受到重视。肠道菌群虽然居住于肠道,但其作用已经不仅仅局限于消化系统。通过对人体代谢和免疫功能的影响,肠道菌群对人体产生的作用是全身性的。肾脏是体内代谢产物排泄的主要器官,也是免疫复合物沉积的重要部位。因此,肠道菌群在肾脏疾病发展和治疗中都起着至关重要的作用。现如今,两者的关系已经成为科学研究的热点话题。本文总结了近5年的文献,从中西医的角度,针对肠道菌群与肾脏疾病之间的相互关系作一综述。     

蝗虫肠道微生物研究进展

蝗虫自古以来是我国农林牧业的一大害虫,蝗虫聚集成灾对农业造成了巨大的损失,国内外学者也因此对其进行了深入的研究。随着科研工作者对昆虫肠道微生态学理论的逐渐重视,蝗虫的肠道微生物也成为了研究的重点,同时测序技术的迅速发展促进了蝗虫肠道微生物的研究。本文从蝗虫肠道菌群的多样性、功能及研究方法入手,对近年来蝗虫肠道微生物的研究进展进行总结,并对今后的研究进行展望。     

Long term methionine restriction: Influence on gut microbiome and metabolic characteristics

The Methionine restriction (MR) diet has been shown to delay aging and extend lifespan in various model organisms. However, the long-term effects of MR diet on the gut microbiome composition remain unclear. To study this, male mice were started on MR and control diet regimens at 6 months and continued until 22 months of age. MR mice have reduced body weight, fat mass percentage, and bone mineral density while having increased lean mass percentage. MR mice also have increased insulin sensitivity along with increasing indirect calorimetry markers such as energy expenditure, oxygen consumption, carbon dioxide production, and glucose oxidation. Fecal samples were collected at 1 week, 18 weeks, and 57 weeks after the diet onset for 16S rRNA amplicon sequencing to study the gut microbiome composition. Alpha and beta diversity metrics detected changes occurring due to the timepoint variable, but no changes were detected due to the diet variable. The results from LEfSe analysis surprisingly showed that more bacterial taxa changes were linked to age rather than diet. Interestingly, we found that the long-term MR diet feeding induced smaller changes compared to short-term feeding. Specific taxa changes due to the diet were observed at the 1 or 18-week time points, including Ileibacterium, Odoribacter, Lachnoclostridium, Marinifilaceae, and Lactobacillaceae. Furthermore, there were consistent aging-associated changes across both groups, with an increase in Ileibacterium and Erysipelotrichaceae with age, while Eubacterium_coprostanoligenes_group, Ruminococcaceae, Peptococcaceae, and Peptococcus decreased with age.     

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

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Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome

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基于机器学习的肠道菌群数据建模与分析研究综述

人体肠道菌群与人类的健康和疾病存在密切关系,对肠道菌群的宏基因组数据进行建模和分析,在疾病预测及诊断相关领域科学研究和社会应用方面均具有重要意义。本文从大数据分析和机器学习的角度,对人体肠道菌群数据的建模、分析和预测算法的原理、过程以及典型研究应用实例进行综述,以期推动肠道菌群分析相关研究发展以及探索结合机器学习算法进行肠道菌群分析的有效方式,同时也为开发基于肠道菌群数据的新型诊疗手段提供借鉴,推动我国精准医疗事业发展。     

Convergent evolution of the gut microbiome in marine carnivores

The gut microbiome can help the host adapt to a variety of environments and is affected by many factors. Marine carnivores have unique habitats in extreme environments. The question of whether marine habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores remains unanswered. In the present study, we compared the gut microbiomes of 16 species from different habitats. Principal component analysis (PCA) and principal coordinate analysis (PCoA) separated three groups according to their gut microbiomes: marine carnivores, terrestrial carnivores, and terrestrial herbivores. The alpha diversity and niche breadth of the gut microbiome of marine carnivores were lower than those of the gut microbiome of terrestrial carnivores and terrestrial herbivores. The gut microbiome of marine carnivores harbored many marine microbiotas, including those belonging to the phyla Planctomycetes, Cyanobacteria, and Proteobacteria, and the genus Peptoclostridium. Collectively, these results revealed that marine habitats drive the convergent evolution of the gut microbiome of marine carnivores. This study provides a new perspective on the adaptive evolution of marine carnivores.     

亮斑扁角水虻对有机废弃物的应用及其肠道微生物研究进展

有机废弃物的安全处理与二次利用是当今社会发展进程中的一大难题,亮斑扁角水虻Hermetia illucens强大的生物转化能力可有效解决此类问题：一方面,亮斑扁角水虻可大量消耗有机废弃物,有效治理环境污染;另一方面,转化后的虫体营养价值高,广泛应用于养殖领域。然而,亮斑扁角水虻的生物转化作用机制目前尚不明确,可转化的有机废弃物范围及其转化效率的影响因素仍有待探讨。本文结合近年来关于亮斑扁角水虻领域的研究,主要从亮斑扁角水虻对有机废弃物的生物转化作用、转化效率的影响因素、虫沙的应用和肠道微生物的功能4个方面进行综述,同时对未来需要解决的问题进行了展望,以期为亮斑扁角水虻的综合开发利用提供参考依据。     

The effect of captivity on the primate gut microbiome varies with host dietary niche

Despite careful attention to animal nutrition and wellbeing, gastrointestinal distress remains relatively common in captive non‐human primates (NHPs), particularly dietary specialists such as folivores. These patterns may be a result of marked dietary differences between captive and wild settings and associated impacts on the gut microbiome. However, given that most existing studies target NHP dietary specialists, it is unclear if captive environments have distinct impacts on the gut microbiome of NHPs with different dietary niches. To begin to examine this question, we used 16S ribosomal RNA gene amplicon sequences to compare the gut microbiomes of five NHP genera categorized either as folivores (Alouatta, Colobus) or non‐folivores (Cercopithecus, Gorilla, Pan) sampled both in captivity and in the wild. Though captivity affected the gut microbiomes of all NHPs in this study, the effects were largest in folivorous NHPs. Shifts in gut microbial diversity and in the relative abundances of fiber‐degrading microbial taxa suggest that these findings are driven by marked dietary shifts for folivorous NHPs in captive settings. We propose that zoos and other captive care institutions consider including more natural browse in folivorous NHP diets and regularly bank fecal samples to further explore the relationship between NHP diet, the gut microbiome, and health outcomes.     

Age‐related changes in the marmoset gut microbiome

The gut microbiome is known to play a significant role in human health but its role in aging remains unclear. The objective of this study was to compare the gut microbiome composition between young adult and geriatric non‐human primates (marmosets) as a model of human health and disease. Stool samples were collected from geriatric (8+ years) and young adult males (2–5 years). Stool 16S ribosomal RNA V4 sequences were amplified and sequenced on the Illumina MiSeq platform. Sequences were clustered into operational taxonomic units and classified via Mothur's Bayesian classifier referenced against the Greengenes database. A total of 10 young adult and 10 geriatric marmosets were included. Geriatric marmosets had a lower mean Shannon diversity compared with young marmosets (3.15 vs. 3.46; p = 0.0191). Geriatric marmosets had a significantly higher mean abundance of Proteobacteria (0.22 vs. 0.09; p = 0.0233) and lower abundance of Firmicutes (0.15 vs. 0.19; p = 0.0032) compared with young marmosets. Geriatric marmosets had a significantly higher abundance of Succinivibrionaceae (0.16 vs. 0.01; p = 0.0191) and lower abundance of Porphyromonadaceae (0.07 vs. 0.11; p = 0.0494). In summary, geriatric marmosets had significantly altered microbiome diversity and composition compared with young adult marmosets. Further studies are needed to test microbiome‐targeted therapies to improve healthspan and lifespan.