The human resident microorganisms constitute the second genome of human body. Oral microbiome is closely related to the oral and systemic health and diseases. Implementation of high-throughput gene chip and second-generation sequencing has gained in-depth characterization of the oral microbiome, changing our view on host-microbe interactions. In this review, we summarized the latest progress in oral microbial metagenomics and addressed its potential value in the prevention and treatment of oral diseases and other systemic disorders.
Humans ; Metagenome ; Metagenomics ; Mouth ; microbiology

The microbial diversity in soil ecosystems is higher than in any other microbial ecosystem. The majority of soil microorganisms has not been characterized, because the dominant members have not been readily culturable on standard cultivation media; therefore, the soil ecosystem is a great reservoir for the discovery of novel microbial enzymes and bioactivities. The soil metagenome, the collective microbial genome, could be cloned and sequenced directly from soils to search for novel microbial resources. This review summarizes the microbial diversity in soils and the efforts to search for microbial resources from the soil metagenome, with more emphasis on the potential of bioprospecting metagenomics and recent discoveries.
Clone Cells ; Ecosystem ; Genome ; Metagenome ; Metagenomics ; Soil

Genetic admixture in human, the result of inter-marriage among people from different well-differentiated populations, has been extensively studied in the New World, where European colonization brought contact between peoples of Europe, Africa, and Asia and the Amerindian populations. In Asia, genetic admixing has been also prevalent among previously separated human populations. However, studies on admixed populations in Asia have been largely underrepresented in similar efforts in the New World. Here, I will provide an overview of population genomic studies that have been published to date on human admixture in Asia, focusing on population structure and population history.
Africa ; Asia ; Colon ; Europe ; Humans ; Metagenomics

In the present day, bioinformatics becomes the modern science with several advantages. Several new "omics" sciences have been introduced for a few years and those sciences can be applied in biomedical work. Here, the author will summarize and discuss on important applications of omics studies in microbiology focusing on microbial pathogeny. It can be seen that genomics and proteinomics can be well used in this area of biomedical studies.
Computational Biology ; Humans ; Metagenome ; Metagenomics ; Microbiology ; Proteomics

Microorganisms contain a large number of biocatalysts, which are of great potential in industrial applications. However, the traditional cultural approaches can obtain only less than 1% of microorganisms. As a culture-independent method, metagenomics is an advanced solution by means of extracting all microbial genomic DNAs in certain environmental habitat, constructing and screening metagenomic libraries to seek novel functional genes. It serves as an effective tool for studying these uncultured microorganisms. Therefore, mining novel biocatalysts from metagenome has drawn the attention of researchers in the world. In this paper, environment sample category, genomic DNA extraction, library construction and screening strategies were reviewed. Recent examples of isolated biocatalysts from metagenomic libraries were presented. Future research directions of metagenomics were also discussed.
Biocatalysis ; DNA ; Genomic Library ; Metagenomics ; trends

Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.
Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Soil Microbiology ; Wetlands

Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.
Algorithms ; Computational Biology ; Metagenome ; Metagenomics ; Microbiota/genetics*

The application of metagenomic second-generation sequencing (mNGS) is shifting from research to clinical laboratories due to rapid technological advances and significant cost reductions. Although many studies and case reports have confirmed that the success of mNGS in improving the prevention, diagnosis, treatment and tracking of infectious diseases, there are still some obstacles that must be overcome. The results of mNGS show all the possible pathogens in the sample, however, in the face of thousands of microbes that can infect humans, it remains challenging to accurately identify the key pathogens. So far, there is no unified interpretation standard for mNGS in clinical practice. This article reviews the interpretation of mNGS results for pathogen infection in different systems, the clinical interpretation and application regulations of mNGS results, and the challenges of mNGS interpretation in pathogen diagnosis.
Humans ; Communicable Diseases ; Metagenomics ; Sensitivity and Specificity

In recent years, many studies have found that vaginal microbiota is closely related to female reproductive tract diseases. However, traditional microbial culture technology has the defects of long culture cycle and most microorganisms cannot be cultured. The development of metagenomics technique has broken the limitations of culture technology, and has been gradually applied to the study of vaginal microorganisms with the characteristics of high throughput, short time, identification of microbial population structure and gene function. It also provides technical support for elucidating the relationship between vaginal microbiota and female reproductive tract diseases. This article mainly introduces the metagenomics techniques and their applications in prevention, screening and diagnosis of common female reproductive tract diseases, and discusses their promising development and limitations to be overcome.
Female ; Humans ; Microbiota/genetics* ; Vagina ; Metagenomics/methods*

Uncultured microorganisms comprise the majority of the planet's biological diversity. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Recently, new techniques for studying microbial communities, collectively called metagenomics, have been developed to overcome the limitations of culturing. This review assesses the potential of metagenomic techniques to analyze the relative abundance of microbial species under varying human environmental conditions and to discover infectious causes of unexplained human diseases.
Biodiversity ; Communicable Diseases ; Genetic Variation ; Humans ; Metagenome ; Metagenomics