Metagenomics Sequencing Technology

Metagenomics Sequencing Technology

Since the last three decades, the study of histology has always been a hot topic of research. The first emerging is genomics, then proteomics, and now the emerging field of hottest application of histology is metagenomics. Metagenomics uses next-generation high-throughput sequencing (NGS) technology to study the genomes of microbial populations in specific environments, and further explores the functional activities, interactions and relationships between microbial populations and their environments to uncover potential biological significance based on the analysis of microbial diversity, population structure and evolutionary relationships. Compared with traditional microbial research methods, metagenomic sequencing technology circumvents the disadvantages that most microorganisms cannot be cultured and trace bacteria cannot be detected, so it has been widely used in environmental microbiology research in recent years.

I. Technical Advantages

Microorganisms include a large group of organisms including bacteria, fungi, and some small protozoa, microscopic algae, and viruses, which are tiny, diverse, and closely related to humans. The traditional methods for microbial diagnosis are culture test and drug sensitivity test, but the positive rate is only about 10%; another is PCR test, which is significantly better than the culture method in terms of sensitivity, specificity and detection time, but because the method is based on the genome sequence of known pathogenic bacteria, the information provided is limited and still cannot solve the problem of low positive rate of clinical diagnosis; in addition, the detection of mixed infections and unknown pathogenic microorganisms is an insurmountable obstacle for traditional detection methods. The limitations of clinical testing methods often lead to incorrect medication and delayed treatment, so it is urgent to develop new testing methods to meet clinical needs as soon as possible.

Metagenomic sequencing (mNGS) can describe all DNA or RNA information present in a sample, allowing analysis of the entire microbiome as well as the human host genome or transcriptome in patient samples, allowing disease-causing microorganisms to be visible. Metagenomic sequencing (mNGS) technology has the following main advantages over traditional microbial detection methods:

1.     No bias detection, able to detect all microorganisms in the environment genetically

2.     Culture-independent, can detect non-culturable species, can detect trace microorganisms

3.     Capable of detecting all sequences of the tested genome

4.     Ability to detect new or rare pathogens

II. Technical Procedures

The whole process of mNGS is divided into dry & wet experiments, and the whole process is under quality-controlled. The wet experiment starts from receiving specimens, processing them specifically for different sample types, extracting nucleic acids for library preparation, and then sequencing them on the machine; the dry experiment includes analysis of the offline data, host removal sequences, comparison with pathogenic microbial databases and drug resistance databases, species identification and drug resistance identification, and finally interpretation of the report, as shown in the figure below:

III. Application

There are many kinds of microorganisms, which are widely involved in many fields such as food, medicine, industry and agriculture, and environmental protection. Therefore, the application fields of mNGS technology are also quite extensive.

1. Medical field: metabolic disease research, tumor cancer research, tumor drug development, etc.

2. Livestock field: gut, rumen (e.g. methanogenic taxa) and animal health/nutritional digestion research, etc.

3. Agricultural field: research on microbial-plant interactions, agricultural tillage, fertilization treatment and soil microbial communities, etc.

4. Environmental field: haze treatment, sewage treatment, oil degradation, acidic mineral water treatment and marine environment research, etc.

5. Bioenergy: research on special functional strains, gene mining, development of engineering bacteria.

6. Special extreme environment: research on microbial taxa under extreme environmental conditions.