Three -generation sequencing technology: Let you "see" "skeleton" of microbial genes

A large number of microorganisms live in our human intestine. These microorganisms continue to reproduce in the intestine and coexist with human beings. They together form an indispensable and important component of the human intestine. We are collectively referred to as the intestinal microorganisms.

So, do you know what special points are the human intestinal microorganisms that coexist with you? What are the methods of studying intestinal microorganisms?

What are the characteristics of human intestine microbes?

First of all, the most significant feature of the intestinal microorganism is the huge number. According to scientists, the number of microorganisms in human intestines is 3-10 times higher than the number of human cells.

However, their volume is small, and the diameter is less than one tenth of human cells, or even smaller. Therefore, even if a large number of microorganisms live in the intestine, the human intestine will not burst.

(Picture source: veer)

Secondly, there are many species included in the human intestine microorganisms. In addition to the bacteria we often mention, the human intestine also includes fungi, viruses and native animals, but the content of bacteria is the most, accounting for more than 90%.

Therefore, the name "intestinal microorganisms" we often mention, in most cases, represent intestinal bacteria. At present, there are more than 4,600 types of bacteria found in the human intestine, and more than 70%of these bacterial species have not been cultivated, and they do not know specific activity and functions.

(Picture source: veer)

Finally, the human intestine microbial group and the mutual benefit of the human body. Bacteria often act as the role of "decomposition" in the biosphere, and the bacteria in the human intestine also play similar functions. In life, when the food we eat cannot be completely digested in the stomach, we will eventually be used and degraded into small molecular substances in the intestine, and then absorbed by our human body.

(Picture source: veer)

At the same time, when we are sick and taking medicine, some drugs will be decomposed into effective drug molecules by microbial metabolism in the intestine, and then absorb the effect of treatment by the intestine. In addition, microorganisms in the intestine have also evolved with human beings to form a natural barrier to resist foreign microorganisms, and play a function of anti -infection.

Therefore, if the ecosystem of the intestinal microorganisms is unbalanced, it may cause metabolic function disorders in the intestinal tract, and even cause intestinal diseases.

(Picture source: veer)

What are the methods of studying intestinal microorganisms?

The method of studying microorganisms mainly depends on "cultivation". The so -called cultivation is to allow microorganisms to grow in a medium containing carbon and nitrogen substances, grow under the appropriate temperature and oxygen concentration, and then observe its physiological state and biological creatures active.

(Picture source: veer)

However, this method is time -consuming and laborious, and the "high -throughput" is to study intestinal bacteria on a large scale, and most of the intestinal bacteria cannot be cultivated.

However, with the development of sequencing technology, we can understand the intestinal microorganisms in a high volume without cultivation, especially the genome of the intestinal microorganisms. At present, most of the related research uses the method of second -generation sequencing to perform functional analysis of the intestinal microbial species, but there are certain limitations and deficiencies.

However, the rapid development of the three -generation sequencing technology in recent years has made up for some of the shortcomings in the second -generation sequencing technology. At the same time, the combination of the two also provides better methods for exploring the intestinal microorganisms.

In what aspects of the three -generation sequencing?

Before the improvement of the third -generation sequencing technology, let's first understand the method of second -generation sequencing technology to analyze the intestinal microorganisms:

First of all, extract the DNA of the intestinal microorganisms through experimental methods, and then randomly interrupt them into small fragments of about 150bp or 250pb, and then use second -generation technologies to sequenize DNA small fragments. (Contigs), the so -called Contigs is a longer genetic fragment formed by short fragment splicing extension, and then the contigs that mixed with different microorganisms are separated by species.

Among them, the last step is also called Binning, which is a very complicated process. The conventional second -generation sequencing technology is different from the sizes of the splicing genes. Like a thousand pieces of small pieces of puzzles, if these small pieces cannot be classified, it will be difficult for us to spell a complete map.

(Picture source: Jian Shu)

In addition, the sequences obtained by the second -generation sequencing technology are shorter, and there are certain limitations for complex genomic regions (such as gene duplicate areas) and large structural variation (loss or insertion of large gene fragments).

Compared with the second -generation sequencing technology, the biggest improvement of the third -generation sequencing technology is that it can obtain ultra -long DNA fragments and help researchers in deep sequencing genes or regions that are interested in. Moreover Save a lot of time. The most important point, the three -generation sequencing can also directly detect the "methylation modification" of DNA, and the methylation modification is like a genetic switch. It can control the expression of genes, so it also provides convenient conditions for scientists to study the expression of genes of genes. Essence

Finally, by combining the combination of second -generation sequencing and third -generation sequencing, you can get high -quality single bacteria genomes in complex environments, and improve the detection ability of structural variation [3].

The long sequence sequence of the third -generation sequencing is like a "skeleton", and then this skeleton is used as a reference to infer the corresponding relationship between the short -sequence fragments of the second -generation sequencing, so as to stitch it and finally get a high -quality bacterial genome. (Picture source: Cao Jiabao)

Seeing this, do you have a deeper understanding of these friends who get along with yourself? If you want to know, you can discuss with you in the comment area ~

Produced: Popular Science China

Author: Cao Jiabao (Institute of Microbiology, Chinese Academy of Sciences)

Producer: China Science Popularization Expo

references

1. The research progress of Lin Yan, Ancestor Peng, Xie Haisheng, etc. The intestinal flora and human disease pathogenesis [J]. Journal of Pharmaceuticals, 2016, 51 (6): 843-852.

2. The research progress of Lin Hua, Ou Minglin, Chen Jiejing, etc. The intestinal microorganisms and human diseases [J]. International biomedical engineering magazine, 2019,42 (3): 258-262.

3. Chen, L., Zhao, N., Cao, J. Et Al. Short-and Long-Read Metagenomics Expand Individualized Structural Variations in Gut Microbiomes. Nat Commun 13, 3175 (2022).

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