The largest and most comprehensive microbiological and human disease research data release to date May 31, 2019 Source: Singularity Network Today, the singularity cake is really nothing to pave the way, just want to take everyone straight to the theme! why? Because the results of the second phase of the Human Microbiome Program (iHMP) have finally been released! Starting with the iHMP in 2014, the full name is called the Integrated Human Microbiome Program, which focuses on the relationship between microbes and three types of diseases: pregnancy and preterm birth, inflammatory bowel disease, and pre-diabetes. Four studies were published today in Nature. · Medicine and Nature. And Nature has opened a column that summarizes all the research results of the two-stage Human Microbiome Project (HMP) and seven editorial/view articles/comment articles that show the importance of HMP. HMP was launched by the National Institutes of Health (NIH) in 2007. The HMP Alliance includes 45 top research institutes around the world. In the first phase, the researchers focused on the nasal, oral, skin, gastrointestinal and genitourinary tracts of healthy people, describing the characteristics of microbial composition from different perspectives, and developing new research techniques and calculations. Analysis tools, built a resource library. These studies have also laid the foundation for iHMP. The reason why it is called the “integrated†human microbiome project is that instead of focusing on “composition†as in the first phase, it explores the mutual interaction between microorganisms and hosts. The role, including immune, metabolic and molecular dynamics, allows us to have a more stereoscopic and comprehensive understanding of the relationship between microbes and diseases. After so much, let’s let the singular cake introduce in detail what the researchers found out. Inflammatory bowel disease Inflammatory bowel disease (IBD) is a type of autoimmune disease that mainly includes Crohn's disease and ulcerative colitis, and millions of people worldwide suffer from IBD. IBD has always been considered a “western disease†and is less common in economically underdeveloped areas. However, in the past 20 years, the incidence and incidence of diseases in Asia, especially in China, have also increased rapidly. It is expected that by 2025, the Western countries will be tied [1]. In iHMP, the researchers conducted a one-year study of 132 patients to collect their feces, tissues, and blood samples. The most frequent frequency was about once every two weeks, and after a year, 2,965 samples were collected. From these samples, the genome, transcriptome, proteome, metabolome, and viral group of the patient's microbes were analyzed, as well as the patient's own exome, epigenome, transcriptome, and serological features [2]. Overall, the metabolite diversity of patients with IBD is not high, similar to observations of gut microbial diversity, possibly due to malabsorption of nutrients, increased water or blood levels in the gut, or food intake by the patient in the gut. The stay time is short. It is particularly noteworthy that pantothenic acid and niacin (vitamins B5 and B3) are very low in the intestinal tract of patients with IBD. They are cofactors involved in lipid metabolism, and niacin has anti-inflammatory and anti-apoptotic functions. Overall, the patient's intestinal microbial disorders are accompanied by a decrease in diversity and a reduction in beneficial metabolites such as short-chain fatty acids. Patients with Crohn's disease have a reduction in obligate anaerobic bacteria including Faecalibacterium prausnitzii and Roseburia hominis, as well as enrichment of facultative anaerobic bacteria represented by E. coli. Clostridium hathewayi, Clostridium bolteae and R. Gnavus has been increased in the intestinal microbiome of patients with IBD disorders. In addition, the researchers also observed some differences that were not previously discovered. For example, acylcarnitine levels have increased significantly in patients with IBD, and many of them are anti-inflammatory substances. For patients with IBD, the stability of the gut microbiome is much lower than that of a healthy person. Sometimes it takes only a few weeks, and the composition of the microbe is “unrecognizableâ€, which is extremely rare among healthy people. At the site of intestinal inflammation, the researchers identified 305-920 genes that are differentially expressed in healthy individuals, and they interact directly with the genes of some microorganisms, affecting the structural integrity of bacteria, bacterial growth, and bacterial life. The microenvironment and nutrient intake of bacteria. These findings can play an important role in elucidating the mechanisms of IBD and the development of drugs. Prediabetes Type 2 diabetes has more than 400 million patients worldwide. Pre-diabetes or hyperglycemia is the "predecessor" of type 2 diabetes, and up to 70% of pre-diabetes patients eventually develop into formal type 2 diabetes. The researchers conducted a four-year study in 106 healthy and pre-diabetic patients, collecting blood samples and nasal, intestinal microbial samples approximately every three months, combining their hemoglobin A1C (HbA1C), fasting blood glucose. Glucose tolerance and insulin resistance were analyzed comprehensively [3]. They found that insulin resistance is associated with higher levels of inflammation and changes in lipid metabolism, with some long-chain and polyunsaturated fatty acids involved. Microorganisms that affect insulin resistance/insulin sensitivity include the genus Blautia, Odoribacter, Oscillibacter, and Pseudoflavonifracter, and the metabolites include guanidine lactic acid and hippuric acid. Respiratory viral infections and changes in body weight can cause changes in thousands of specific molecules and gut microbes, while insulin-resistant patients and healthy, insulin-sensitive people respond differently to this change. For example, during respiratory viral infection, the inflammatory response in patients with insulin resistance is delayed and diminished, but intestinal microbial changes are significant. Correspondingly, the changes in nasal microbes are small, and the abundance and diversity of nasal microbes in insulin-sensitive people are significantly reduced. The researchers identified hundreds of molecules that have changed during the development of pre-diabetes to type 2 diabetes, explain the pathogenesis of type 2 diabetes, and can be used for early screening. Pregnancy and premature birth During pregnancy, the mother's vaginal microbial composition changes, and the four Lactobacillus bacteria are significantly increased (L. crispatus, L. iners, L. gasseri, and L. jensenii). However, changes in vaginal microbial composition are largely influenced by ethnicity. Women of European descent have little difference in composition between pregnant and non-pregnant women, while African women have the most significant differences, but interestingly, vaginal microbial diversity in African women Always higher than other ethnic groups [4]. During pregnancy, the metabolic capacity of the vaginal microbiome is diminished, and 17 metabolic pathways become less active. These changes generally occur during the first 3 months of pregnancy. These changes are mainly for pregnant women who are born in full-term, as for pregnant women who are born prematurely, and L in their vagina. The level of crispatus decreased, bacterial vaginitis-associated bacteria 1 (BVAB1), Sneathia amnii, TM7-H1 bacteria, a group of Prevo and another 9 taxa (taxa) increased bacterial levels [5]. Their elevation is associated with elevated levels of pro-inflammatory factors and is also associated with vitamin D deficiency, suggesting that vaginal microbes may mediate a link between vitamin D deficiency and preterm birth. Premature birth is also a worldwide problem, with about 15 million premature births in less than 37 weeks a year [6], the second leading cause of neonatal deaths worldwide. The causes of preterm birth are complex. These microbial, cytokine and metabolite changes may be key biomarkers. Combined with clinical manifestations, researchers can develop premature risk assessment algorithms for specific ethnic women, predict and conduct appropriate Intervention. According to statistics, over the past 10 years, more than $1.7 billion has been spent on research in the human microbiome. Compared with inputs, currently based on human microbiome research products, including diagnostics, treatment and other purposes, their value is between 275 million and 400 million US dollars, and by 2024 this number is expected to grow to 7.5. Between $100 million and $1.9 billion is a very large market [7]. Although the release of the results of this study is very important, the research of the human microbiome is far from reaching a true climax. We have a long way to go to find out the true relationship between microbes and diseases. Lita Proctor, former coordinator of HMP, presented two fronts for microbial research in the next 10 years in a review article [7]. First, the standardization of data, with the standard, the results of the research can be more reproducible, especially after the multi-omics intervention in microbiology research, the researchers have a large number of reference data, single research on HMP two stages , it produces 42TB of data, how can they better help researchers? Standardization of data is required. The other is international collaboration. The differences in race, geography and life and eating habits will have a significant impact on microbes. With data sharing and comparison, we can understand the relationship between microbes and diseases more accurately and profoundly. . So far, the two phases of the HMP that have lasted for 12 years have ended. However, the microbiome projects in some countries, including China, are still underway. We and the microbes will have more and more wonderful stories. 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Put a screenshot, the singular cake can be said 
Patient sampling process and multi-omics analysis project 
Complex interactions between different components 
The relationship between insulin resistance (IR) and insulin-sensitive (IS) populations and intestinal microbes varies widely 
a: vaginal microbial abundance in pregnant (top) and non-pregnant (bottom) women b: vaginal microbial abundance in all women and pregnant and non-pregnant women of African, European and Spanish origin 
Vaginal microorganisms associated with full-term production (left) and preterm birth (right) 
Image source: pixabay.com
The largest and most comprehensive microbiological and human disease research data release to date