Microorganisms and their environment constitute a complex ecosystem, which is an important part of the biodiversity on earth. The microbiome refers to the collection of all microorganisms and their genetic information in a specific environment or ecosystem, and its connotation includes the interaction of microorganisms with their environment and host. Microbiomics is the study of the microbiome, which explores their structure, function, and relationship with the environment or the host.
Microbiome research can be broadly divided into three stages:
1) The first stage: Before the 1970s, strains were obtained mainly by traditional microbial isolation and culture techniques, followed by a series of complicated physiological and biochemical analyses. The understanding of microorganisms remains at the stage of morphological observation, description, classification, and physiology.
2) The second stage: Beginning in the 1980s, the development of molecular biology technologies such as BIOLOG technology, phospholipid fatty acid method, DNA fingerprinting, gene chip, etc., realized the direct analysis of environmental microbial communities without relying on microbial culture, inaugurating a new era of microbial molecular ecology research.
a) It is worth noting that during the development of technologies such as DNA fingerprinting, the first generation of sequencing technology, namely Sanger sequencing, has also emerged. Handelsman et al. (1998) from the University of Wisconsin proposed the concept of metagenomics for the first time, whose research object is total DNA in a specific environment. The metatranscriptome emerged after metagenomics. It uses all RNA in a specific environment as its research object to explore the transcription level of all genomes. Leininger et al. (2006) first used 454 pyrosequencing technology to conduct a macrotranscriptome study on complex microbial communities.
3) The third stage: Beginning in 2006, revolutionary breakthroughs in high-throughput sequencing and mass spectrometry technologies, as well as the rapid development of bioinformatics, have greatly promoted microbiome research.
The interactions among microorganisms and between microorganisms and their environment are extremely complex. By combining metagenomics with macrotranscriptomics, macroproteomics, and metametabolomics initiated by a new generation of mass spectrometry technology, the structure and function of the microbiome can be analyzed more comprehensively and systematically.
Microbial metagenomics: The study of community composition, genetic information and co-evolutionary relationships with the environment by extracting all DNA from the microorganisms in the environment.
Microbial metatranscriptomics: The study of the transcriptome information of all microorganisms in the environment, revealing the expression level of relevant genes on the spatiotemporal scale, so as to study the related functions of microbial communities.
Microbial metaproteomics: Qualitative and quantitative analysis of all protein components of environmental microorganisms under specific environmental conditions and at specific times.
Microbial metabolomics: Qualitative and quantitative analysis of all low-molecular-weight metabolites (including metabolic intermediates, hormones, signal molecules and secondary metabolites, etc.) of microorganisms during a specific physiological period. Their interaction with the environment can also be studied.
