Emerging Trends for Microbiome Analysis： From Single-Cell Functional Imaging to Microbiome Big Data

Method development has always been and will continue to be a core driving force of microbiome science.In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms:(1) a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging;(2) a shift from interrogating a consortium or population of cells to probing individual cells;and(3) a shift from microbiome data analysis to microbiome data science. Some of the recent methoddevelopment efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding 'Made-in-China' tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.

The Oral Microbiome Bank of China

The human microbiome project（HMP） promoted further understanding of human oral microbes. However, research on the human oral microbiota has not made as much progress as research on the gut microbiota. Currently, the causal relationship between the oral microbiota and oral diseases remains unclear, and little is known about the link between the oral microbiota and human systemic diseases. To further understand the contribution of the oral microbiota in oral diseases and systemic diseases, a Human Oral Microbiome Database（HOMD） was established in the US. The HOMD includes 619 taxa in 13 phyla, and most of the microorganisms are from American populations. Due to individual differences in the microbiome, the HOMD does not reflect the Chinese oral microbial status. Herein, we established a new oral microbiome database—the Oral Microbiome Bank of China（OMBC,http：//www.sklod.org/ombc）. Currently, the OMBC includes information on 289 bacterial strains and 720 clinical samples from the Chinese population, along with lab and clinical information. The OMBC is the first curated description of a Chinese-associated microbiome; it provides tools for use in investigating the role of the oral microbiome in health and diseases, and will give the community abundant data and strain information for future oral microbial studies.

DNA Extraction Protocol for Biological Ingredient Analysis of Liuwei Dihuang Wan

Traditional Chinese medicine （TCM） clinical practice. So far, the methods commonly preparations are widely used for healthcare and used for quality evaluation of TCM preparations mainly focused on chemical ingredients. The biological ingredient analysis of TCM preparations is also important because TCM preparations usually contain both plant and animal ingredients, which often include some mis-identified herbal materials, adulterants or even some biological contaminants. For biological ingredient analysis, the efficiency of DNA extraction is an important factor which might affect the accuracy and reliability of identification. The component complexity in TCM preparations is high, and DNA might be destroyed or degraded in different degrees after a series of processing procedures. Therefore, it is necessary to establish an effective protocol for DNA extraction from TCM preparations. In this study, we chose a classical TCM preparation, Liuwei Dihuang Wan （LDW）, as an example to develop a TCM-specific DNA extraction method. An optimized cetyl trimethyl ammonium bromide （CTAB） method （TCM-CTAB） and three commonly-used extraction kits were tested for extraction of DNA from LDW samples. Experimental results indicated that DNA with the highest purity and concentration was obtained by using TCM-CTAB. To further evaluate the different extraction methods, amplification of the second internal transcribed spacer （ITS2） and the chloroplast genome trnL intron was carried out.

Meta-QC-Chain:Comprehensive and Fast Quality Control Method for Metagenomic Data

Next-generation sequencing （NGS） technology has revolutionized and significantly impacted metagenomic research.However,the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating reads,which will significantly compromise downstream analysis.Many quality control （QC） tools have been proposed,however,few of them have been verified to be suitable or efficient for metagenomic data,which are composed of multiple genomes and are more complex than other kinds of NGS data.Here we present a metagenomic data QC method named Meta-QC-Chain.Meta-QC-Chain combines multiple QC functions： technical tests describe input data status and identify potential errors,quality trimming filters poor sequencing-quality bases and reads,and contamination screening identifies higher eukaryotic species,which are considered as contamination for metagenomic data.Most computing processes are optimized based on parallel programming.Testing on an 8-GB real dataset showed that Meta-QC-Chain trimmed low sequencing-quality reads and contaminating reads,and the whole quality control procedure was completed within 20 min.Therefore,Meta-QC-Chain provides a comprehensive,useful and high-performance QC tool for metagenomic data.Meta-QC-Chain is publicly available for free at： http：//computationalbioenergy.org/meta-qc-chain.html.

Comprehensive understanding to the public health risk of environmental microbes via a microbiome-based index

Bacteria are ubiquitous in built environments(BE)and different human body sites.Among the myriad of microbes,the pathogenic bacteria are of great interest to public health and safety,which were the cause of many public health emergency outbreak.