Document name: Current Understanding of (recent Survey of macro human proteome) metaproteome association and modulation human
Journal Name: J Proteome Res
Published: ( 2019 Nian 10 months)
IF：3.78
Technology: macro proteomic review
I. Overview: (whole idea of the article and the results of using refined language to describe)
Over the past decade, the macro protein to provide data for a better understanding of the functional characteristics of microbial groups. Although there have been high-throughput data macro proteome, but understanding its function is unclear, most importantly, these protein molecules in the host of the exact result, lack of understanding of the underlying mechanisms. Here, we discuss the latest progress in research of macro proteome, the possible regulatory mechanisms, biometric macro proteome, challenges and future prospects.
II. Background: (brief Progress dynamic, purpose and meaning)
In the past decade, a number of studies provide strong evidence that human gut microbial diversity. Driving data show that the intestinal flora of the host coexisting. Providing a microorganism as a host intestinal immunity induced, metabolic effectors, pathogens are prevented. Instead, these microorganisms disorders related with various diseases, such as inflammatory bowel disease ( of IBD ), . 1 diabetes ( T 1D ). Based on the establishment of a central database of microbial classification and 16S rRNA metagenomic approach. For the analysis of these databases, not only to provide insight into the complexity of the intestinal microflora, but also a clear influence of diversity on the host. Proteomics is the study of protein macro entire microbial community, to obtain function information related to dynamic interactions between the host and microflora. Limited information obtained from metagenomic studies. Consequently, proteomic techniques can use macros to understand the impact on the flora of the host, to help understand the disease.
Third, an overview of the content
- The relationship between the metagenome, macro transcriptome, proteome macro
Metagenome can get all mixed microbial genes, but can not identify bacterial activity situation. Macros can be used as transcriptome gene activity index, but can not fully represent the actual execution of protein function. Protein macro understanding of protein function than the macro and macro genome transcriptome. It can understand the pathophysiology in situ by bacteria, eventually elucidate the function of the operation of the digestive tract. Further, to understand the relationship between the host and microbes. A number of studies show that proteomic macro macro protein associated with some of the core functions of a healthy human intestine. For example, carbohydrates, amino acid metabolism. Studies of cystic fibrosis ( CF2 ) metagenomic patients and healthy controls and macro modeling proteomic studies, found that increasing the number of Bacteroides, and Firmicutes reduced, which is found opposite metagenome. Due to biological factors lead to two omics data discrepancies, still needs further study.
Table 1 metagenome and compared between groups Metaproteomics
- Stability and diversity of the intestinal microbiota
Intestinal microbial species richness, but also by the attention. Several studies have revealed the stability of the intestinal flora. Mehta et al. Study of fecal microbiota of adult men and found metagenomic transcriptome stable than macro. Inter-individual differences metagenomic larger than the intra-individual differences, but instead macro transcriptome differences, differences within individual is bigger than the difference between individuals. Research Metaproteomics newborns after birth stool was found 21 flora day of the complexity of the gut increased significantly, but the identification of the proteins from 96% down to 30% . Metagenomic these changes previously reported and 16 S sequencing similar.
Different ages intestinal flora case
It was reported that adult intestinal flora is relatively stable, a longitudinal study to explore a famous artist 45 of parenteral between years, 45% of microorganisms is stable. Healthy human intestinal flora function relatively conservative, the top 25 limited changes in protein function may be the interaction network shows in disease states.
Healthy macro situation enzyme protein function
- Relationship with the host
More and more evidence of the symbiotic relationship between the host immune system and microbes, and ultimately achieve the goal of maintaining a host homeostasis. Interaction with the host microorganism can be further explained by the microflora balance between the system and the host immune system. Intestinal flora protect the host from pathogens through nutritional competitive way. Further gut microbes induce antimicrobial peptides generated, phenolic compounds involved in the metabolism of foods, either directly or indirectly interact with the host intestinal nervous system.
- Post-translational modification of proteins macro group
Studies have shown that using a variety of mechanisms to interfere with the pathogen after host translational modifications, affecting key features of their infection. PTM host - potential function microbe interactions are still unclear. There is no macro protein P conduct genomics research TM, but to explore the response of these bacteria help to understand the relationship between the intestinal microflora and the host response system.
- Research Metaproteomics group dysbiosis
Drugs and diseases can cause macro protein levels in patients with dysbiosis. Long-term consumption of high-fat diet can trigger inflammation. Macro protein by the impact of antibiotic treatment greatly. Pressure will induce microbial change.
Disease-related changes in gut microbes
5.1 dysbiosis and inflammatory bowel disease ( the I BD)
Two children for IBD discovery research Metaproteomics carbohydrate group, amino acids and lipid metabolism, as well as enhance the defense capabilities of microorganisms and DNA repair-related changes in protein differences.
5.2 Cystic Fibrosis ( C F)
CF patients exhibit butyrate related carbohydrate, and protein levels decrease flagellin. Host protein analysis showed elevated levels of acute phase reactants.
5.3 ecological imbalance and cirrhosis
Metagenomic the ecological imbalance linked to cirrhosis of the liver. There is a macro protein and liver cirrhosis, and the results showed that patients with cirrhosis of the enzyme glucose and energy production significantly increased. Protein production increased metabolic activity of microorganisms to adapt to changes in the liver cirrhosis. Such mechanisms help to increase the energy supply to compensate for disease-related malnutrition.
5.4 ecological imbalance and 1 diabetes
Recently there are some with the macro proteomic 1 study of diabetes, studies have shown that these patients macros protein and amino acid transport, metabolism, transcription, P TM, a protein related to the life cycle partner.
5.5 associated with obesity
Most obese patients is to change the energy-generating-related proteins, such as increased yield butyrate, formed specific pilin protein, flagellin increase. Bacteroides higher activity in obese individuals
5.6 gut and major depression
Intestinal and central nervous system disorders, such as depression, autism, have been reported.
- Challenging macro proteomic experiments
Microbial sample complexity, microorganism enrichment from a stool specimen comprising a dual filter, differential centrifugation. The double-filtered microorganism ( 0.2-2um ) and human ( 10-100um magnitude of the difference) cells enriched cell, this approach is likely to lose adhesion to the surface of the food on the microorganism or host cell proteins. Different extraction effect is not the same cracking process, which uses the method and ultrasound SDS, cover more proteins. Overall, the need to establish a standard macro Proteome Extraction method before the experiment.
- Macro proteomic challenge for computing resources
There on Earth 1 Wanyi microbial gene sequences redundant search results in a long time and is difficult to get a clear result, so choosing the right database for challenging macro Proteome Research. Public databases, such as U niprot , NCBI , RefSeq and Ensemble , a multi-sequence will be extended search time, FDR higher. Generating parallel database sequencing sample more suitable for subsequent proteomic analysis. Two-step search can overcome the large search space. Another MetaPro-IQ iteratively search. And different proteomic analysis, most of the macro protein species lacks the overall classification and functional information, need to improve functional annotation.
- Macro quantitative proteome Policy
The most common use of the spectrum counting, peak area method. Quantification of the label is also used, such as SILAC , Silam , SILAMi . Heavy isotope labeling method and the like are also used.
Fourth, outlook
Since many kinds of microorganisms, such that the presence of non-microbial protein sample complexity increases, and foods such as host proteins have some influence on the macro proteome research. But with the macro proteomic technology development, will develop a macro protein tag group in the future. Macro protein computing needs more resources, cloud computing effective way to solve this problem so. DIA technology helps to improve the stability of the macro protein research. And we will need multiple sets of research collaboration to clarify the effect of the intestinal flora of the disease.
Article highlights (and product integration point ) :
Summary of macro protein research
Read by: Charms