Microbiome Projects in the Baltimore Longitudinal Study of Aging

2008年，美国国立卫生研究院(NIH)启动了NIH人类微生物组项目(HMP)，其使命是产生研究资源，使之能够全面描述人类微生物区系并分析其在人类健康和疾病中的作用。在HMP项目中，300名年龄在18岁到40岁之间的健康人从这些人那里获得了口腔、鼻孔、皮肤、胃肠道和阴道的标本(男性15例，女性18例)。来自HMP的数据激发了人们对了解体内微生物群落如何影响我们的健康的兴趣。该项目揭示了人体内存在多种微生物，包括细菌、真菌和病毒。在不同的身体部位有不同的微生物群落。此外，各种环境和生物因素也促进了微生物的多样性，然而这些关系还没有得到充分的探索。到目前为止，细菌是已经被广泛研究的微生物，关于健康状况的几个有趣的发现已经被报道。 一些研究表明，肠道微生物群的组成随着年龄的增长而发生显著变化。据报道，在生命的不同阶段，细菌的数量、酶的丰度或途径的丰度随着年龄的不同而不同。出生后，婴儿在三年内就会形成类似成人的细菌群落。与成年人相比，儿童也有更大的β多样性。然而，个体内的细菌多样性，或称阿尔法多样性，似乎随着年龄的增长而增加。在耳朵后面的皮肤中，随着年龄的增长，后基因组衍生的乙氧基酸循环途径丰富，细菌数量减少。在肠道中，随着年龄的增长，细菌数量也会增加，而放线杆菌和细菌数则会减少。在大多数情况下，这些关联所解释的差异的大小和数量都很低，这表明还有其他因素导致了这种差异。研究发现，在老年人中，与年轻人相比，个体间的差异更大。这可能是由于影响饮食状况的各个方面的下降，包括牙列、唾液功能、消化、吸收和肠道转运时间的下降，这些都可能是微生物组成的原因。此外，环境差异和健康状况等外部因素也可能导致老年人的变异性。在这方面，研究表明，细菌群落可能因地理位置、饮食、炎症和脆弱状态而不同。这些初步研究表明，肠道中的细菌群落与衰老表型密切相关。 为了进一步了解衰老和微生物群落之间的关系，我们建议调查巴尔的摩老龄化纵向研究(BLSA)受试者的肠道微生物群落。自2015财年提交以来，我们已经从930名年龄在24岁和101岁之间的人中鉴定出粪便样本。对于513名受试者，有重复访问的样本，重复访问的次数最多为6次。随访期为0.96~5.96年，平均3.08年。我们建议进行元基因组测序，而不是16S测序，后者一直是大多数流行病学微生物组项目的标准。元基因组学的优势在于，除了原核生物(细菌、古生菌)外，全基因组鸟枪法还能捕获真核生物(真菌)和病毒。此外，与16S测序相比，元基因组测序在物种水平上提供了更多的细节。使用BLSA样本的另一个优点是我们可以研究微生物群落的横截面和纵向轨迹。这将使我们能够检查微生物组和疾病之间的因果关系，以确定治疗目的的潜在靶点。

In 2008, National Institutes of Health (NIH) launched the NIH Human Microbiome Project (HMP) with the mission of generating research resources enabling comprehensive characterization of the human microbiota and analysis of their role in human health and disease. For the HMP project, 300 healthy individuals between the ages of 18 to 40 years old were enrolled and specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women) were obtained from these individuals. Data from HMP have fueled the interest in understanding how communities of microbes that harbor in bodies affect our health. This project revealed that the human body is occupied by a diversity of microbes including bacteria, fungus, and viruses. There are different communities of microbes on different body locations. Further various environmental and biological factors contribute to the diversity of microbes, however these relationships are yet to be fully explored. To date, bacteria are the microbes that have been widely studies, and several interesting discoveries with respect to health status have been reported. Several studies have shown that the gut microbiome composition change significantly with age. Several differences in bacterial number, enzymatic or pathway abundance by age through different stages of lifespan have been reported. After birth, infants acquire bacterial communities that are adult-like within three years. Children, compared to adults, also have greater beta diversity. However, the bacterial diversity within an individual, or alpha diversity, appears to increase with age. In the skin behind the ear, there was an enrichment of the metagenomically derived glyoxylate cycle pathway as well as a decrease in abundance of bacteria firmicutes with increasing age. In the gut there is also an increase in firmicutes with age and a decrease in actinobacteria and bacteriodetes. In most cases the magnitude and the amount of variance explained by these associations were low suggesting that there are other factors that contribute to the variability. In older adults, studies have observed that there are greater inter-individual variability compared to younger individuals. This may be explained by the decline in various aspects that influence dietary status from decline in dentition, salivary function, digestion, absorption and intestinal transit times which can all contribute to microbial composition. In addition, there are external factors can also contribute to the variability in elderly including environmental differences and health status. In this respect, studies have shown that bacterial communities can differ based on geographical location, diet, inflammatory and frailty status. These preliminary studies suggest that bacterial communities in the gut are intimately associated with aging phenotypes. To further understand the relationship between aging and microbial communities, we propose to investigate gut microbiome communities in subjects of Baltimore Longitudinal Study on Aging (BLSA). In the time since the FY2015 submission, we have identified fecal samples from 930 individuals between 24 101 years of age. For 513 subjects, there are repeated samples available with number of repeat visits of up to 6 visits. The follow up period ranged from 0.96 and 5.96 years, with the average follow up being 3.08 years. We propose to conduct metagenomics sequencing rather than the 16S sequencing that has been the standard for most epidemiological microbiome projects. The strength of metagenomics is that the whole-genome shotgun sequence approach captures eukaryotes (fungus) and viruses in addition to the prokaryotes (bacteria, archae). Furthermore, metagenomics sequencing provides more details at the species levels as compared to the 16S sequencing. Another advantage of using BLSA samples is that we can study both cross sectional and longitudinal trajectories of microbiome communities. This will allow us to examine causal association between microbiome and diseases to identify potential target for therapeutic purposes.