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*

With the current accumulation of metagenome data, it is possible to build an integrated platform for processing of rigorously selected metagenomic samples (also referred as "metagenomic communities" here) of interests. Any metagenomic samples could then be searched against this database to find the most similar sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories but not well annotated database, and only offer few functions for analysis. On the other hand, the few available methods to measure the similarity of metagenomic data could only compare a few pre-defined set of metagenome. It has long been intriguing scientists to effectively calculate similarities between microbial communities in a large repository, to examine how similar these samples are and to find the correlation of the meta-information of these samples. In this work we propose a novel system, Meta-Mesh, which includes a metagenomic database and its companion analysis platform that could systematically and efficiently analyze, compare and search similar metagenomic samples. In the database part, we have collected more than 7 000 high quality and well annotated metagenomic samples from the public domain and in-house facilities. The analysis platform supplies a list of online tools which could accept metagenomic samples, build taxonomical annotations, compare sample in multiple angle, and then search for similar samples against its database by a fast indexing strategy and scoring function. We also used case studies of "database search for identification" and "samples clustering based on similarity matrix" using human-associated habitat samples to demonstrate the performance of Meta-Mesh in metagenomic analysis. Therefore, Meta-Mesh would serve as a database and data analysis system to quickly parse and identify similar
Cluster Analysis ; Computational Biology ; methods ; Databases, Genetic ; Humans ; Metagenome ; Metagenomics ; methods

Infectious diseases are commonly seen in clinical practice, and pathogen diagnosis is the key link in diagnosis and treatment; however, conventional pathogen detection methods cannot meet clinical needs due to time-consuming operation and low positive rate. As a new pathogen detection method, metagenomic next-generation sequencing (mNGS) has a wide detection range and can detect bacteria, viruses, fungi, parasites, rare pathogens, and even unknown pathogens. The technique of mNGS is unbiased and can rapidly, efficiently, and accurately obtain all nucleic acid information in test samples, analyze pathogens, and guide clinical diagnosis and treatment, thereby playing an important role in complicated infectious diseases. This article reviews the diagnostic advantages and clinical value of mNGS in bacterial, fungal, viral, and parasitic infections.
Bacteria ; Communicable Diseases/diagnosis* ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Metagenomics/methods* ; Sensitivity and Specificity

OBJECTIVES: To study the application value of metagenomic next-generation sequencing (mNGS) in children with severe infectious diseases. METHODS: An analysis was performed on the clinical data and laboratory test results of 29 children with severe infection who were admitted to the Second Affiliated Hospital of Wenzhou Medical University from June 2018 to December 2020. Conventional pathogen culture was performed for the 29 specimens (27 peripheral blood specimens and 2 pleural effusion specimens) from the 29 children, and mNGS pathogen detection was performed at the same time. RESULTS: Among the 29 children, 2 tested positive by conventional pathogen culture with 2 strains of pathogen, and the detection rate was 7% (2/29); however, 20 children tested positive by mNGS with 38 strains of pathogen, and the detection rate was 69% (20/29). The pathogen detection rate of mNGS was significantly higher than that of conventional pathogen culture (P<0.05), and mNGS could detect the viruses, fungi, and other special pathogens that conventional pathogen culture failed to detect, such as Orientia tsutsugamushi. The univariate analysis showed that gender, routine blood test results, C-reactive protein, procalcitonin, D-dimer, radiological findings, and whether antibiotics were used before admission did not affect the results of mNGS (P>0.05). CONCLUSIONS Compared with conventional pathogen culture, mNGS is more sensitive for pathogen detection, with fewer interference factors. Therefore, it is a better pathogenic diagnosis method for severe infectious diseases in children.
Anti-Bacterial Agents ; Child ; Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Metagenomics/methods* ; Sensitivity and Specificity

The quality of traditional Chinese medicines (TCMs) has been mainly evaluated based on chemical ingredients, yet recently more attentions have been paid on biological ingredients, especially for pill-based preparations. It is a key approach to establish a fast, accurate and systematic method of biological ingredient analysis for realization of modernization, industrialization and internationalization of TCMs. The biological ingredient analysis of TCM preparations could be abstracted as the identification of multiple species from a biological mixture. The metagenomic approach based on high-throughput-sequencing (HTS) and big-data-mining has been considered as one of the most effective methods for multiple species analysis of a biological mixture, which would also be helpful for the analysis of biological ingredients in TCMs. Simultaneous identification of diverse species, including the prescribed species, adulterants, toxic species, protected species and even the biological impurities introduced through production process, could be achieved by selecting appropriate DNA biomarkers, as well as applying large-scale sequence comparison and data mining. By this approach, it is prospective to offer an evaluation basis for the effectiveness, safety and legality of TCM preparations.
Biological Products ; chemistry ; Data Mining ; High-Throughput Nucleotide Sequencing ; Medicine, Chinese Traditional ; Metagenomics ; methods

With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
Animals ; Bacteria ; genetics ; Computational Biology ; methods ; High-Throughput Nucleotide Sequencing ; methods ; Humans ; Metagenomics ; Single-Cell Analysis ; methods

Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
Animals ; Bacteria ; enzymology ; Enzymes ; genetics ; Gene Library ; High-Throughput Screening Assays ; methods ; Metagenome ; genetics ; Metagenomics ; methods ; Plants ; enzymology

OBJECTIVES: To study the application value of metagenomic next-generation sequencing (mNGS) for pathogen detection in childhood agranulocytosis with fever. METHODS: A retrospective analysis was performed on the mNGS results of pathogen detection of 116 children with agranulocytosis with fever who were treated from January 2020 to December 2021. Among these children, 38 children with negative mNGS results were enrolled as the negative group, and 78 children with positive results were divided into a bacteria group (n=22), a fungal group (n=23), and a viral group (n=31). Clinical data were compared between groups. RESULTS: For the 116 children with agranulocytosis and fever, the median age was 8 years at diagnosis, the median turnaround time of mNGS results was 2 days, and the positive rate of mNGS testing was 67.2% (78/116). Compared with the negative group, the bacterial group had a higher procalcitonin level (P<0.05), the fungal group had higher level of C-reactive protein and positive rate of (1,3)-β-D glucan test/galactomannan test (P<0.05), and the fungal group had a longer duration of fever (P<0.05). Among the 22 positive microbial culture specimens, 9 (41%) were consistent with the mNGS results. Among the 17 positive blood culture specimens, 8 (47%) were consistent with the mNGS results. Treatment was adjusted for 28 children (36%) with the mNGS results, among whom 26 were cured and discharged. CONCLUSIONS The mNGS technique has a shorter turnaround time and a higher sensitivity for pathogen detection and can provide evidence for the pathogenic diagnosis of children with agranulocytosis and fever.
Agranulocytosis/diagnosis* ; Bacteria ; Child ; Fever/diagnosis* ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Metagenomics/methods* ; Retrospective Studies ; Sensitivity and Specificity

Animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. The gut microbial community of humans and animals has received significant attention from researchers because of its association with health and disease. The application of metagenomics technology enables researchers to study not only the microbial composition but also the function of microbes in the gastrointestinal tract. In this paper, combined with our own findings, we summarized advances in studying gastrointestinal tract microorganism with metagenomics and the bioinformatics technology.
Animals ; Gastrointestinal Tract ; microbiology ; Humans ; Hyperglycemia ; etiology ; Inflammatory Bowel Diseases ; etiology ; Metagenome ; physiology ; Metagenomics ; methods ; Obesity ; etiology

DNA stable-isotope probing (DNA-SIP) is a recently developed method with which the incorporation of stable isotope from a labeled substrate is used to identify the function of microorganisms in the environment. The technique has now been used in conjunction with metagenomics to establish links between microbial identity and particular metabolic functions. The combination of DNA-SIP and metagenomics not only permits the detection of rare low-abundance species from metagenomic libraries but also facilitates the detection of novel enzymes and bioactive compounds. We summarize recent progress in SIP-metagenomic techniques and applications and discuss prospects for this combined approach in environmental microbiology and biotechnology.
Animals ; DNA ; genetics ; DNA Probes ; chemistry ; genetics ; metabolism ; DNA, Bacterial ; chemistry ; genetics ; metabolism ; Humans ; Isotope Labeling ; methods ; Metagenomics ; methods ; Molecular Probe Techniques ; Sequence Analysis, DNA ; methods