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），其使命是生成研究资源，从而能够全面表征人类微生物群并分析其在人类健康和疾病中的作用。 对于HMP项目，招募了300名年龄在18至40岁之间的健康个体，并从这些个体中获得口腔、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健康的兴趣。该项目揭示了人体被多种微生物占据，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有助于微生物的多样性，但这些关系尚未得到充分探索。到目前为止，细菌是已经被广泛研究的微生物，并且已经报道了关于健康状况的几个有趣的发现。 几项研究表明，肠道微生物组的组成随着年龄的增长而发生显着变化。 已经报道了通过寿命的不同阶段，细菌数量、酶或途径丰度随年龄的几种差异。出生后，婴儿在三年内获得与成人相似的细菌群落。与成人相比，儿童也有更大的β多样性。然而，个体内的细菌多样性或α多样性似乎随着年龄的增长而增加。在耳后皮肤中，随着年龄的增加，宏基因组来源的乙醛酸循环途径富集，以及细菌厚壁菌门丰度减少。在肠道中，随着年龄的增长，厚壁菌门也会增加，放线菌和抑菌剂会减少。 在大多数情况下，由这些关联解释的方差的大小和数量都很低，这表明还有其他因素导致了变异性。在老年人中，研究观察到，与年轻人相比，个体间的变异性更大。 这可能是由于影响饮食状况的各个方面的下降，如牙列、唾液功能、消化、吸收和肠道通过时间的下降，这些都可能影响微生物组成。 此外，环境差异和健康状况等外部因素也会导致老年人的变异性。在这方面，研究表明，细菌群落可以根据地理位置，饮食，炎症和虚弱状态而有所不同。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与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，我们已经确定了930名年龄在24101岁之间的个体的粪便样本。对于513例受试者，有重复样本可用，重复访视次数最多为6次。随访时间为0.96 ~ 5.96年，平均3.08年。我们建议进行宏基因组测序，而不是16 S测序，这是大多数流行病学微生物组项目的标准。宏基因组学的优势在于，全基因组鸟枪测序方法除了捕获原核生物（细菌、古细菌）外，还捕获真核生物（真菌）和病毒。此外，与16 S测序相比，宏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与疾病之间的因果关系，以确定潜在的治疗目标。

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.