Abstract:Microbes are the most important commensal organisms in humans, animals and plants, and are the major habitants in soil, sediment, water, air and other habitats. The analysis of microbiome in these habitats has become a basic research technique. As a fast developing technology in recent years, microbiome sequencing and analysis have been widely used in human health, environmental pollution control, food industry, agriculture and animal husbandry and other fields. In order to sort out and summarize the current status, development and application prospects of microbiome sequencing and analysis technologies, this special issue has prepared a collection of 16 papers in this field, that comprise sample preservation and processing, single microbe genome sequencing and analysis, and microbiome feature analysis in special habitats, microbiome related databases and algorithms, and microbiome sequencing and analysis expert consensus. It also introduced in detail the development trend of the microbiome sequencing and analysis, in order to promote the rapid development of the microbiome sequencing and analysis industry and scientific research in China, and provide necessary reference for the healthy development of related industries.

Abstract:In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company’s interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.

Abstract:Gut microbiota is closely related to human health, and its composition can give us health information. The large-scale population sampling is required on gut microbiome research; however, fresh feces samples are not easy to obtain, and rapid low-temperature freezing is difficult to achieve. With the development of technology, preservation solutions are widely used for sample collection, storage, and transport under normal temperature conditions. Preservation solutions can be used in large scale sample collection, wide geographical distribution, diverse on-site sampling conditions, heavy workload, and poor transportation conditions. In this study, five healthy volunteers were recruited. After collecting their fresh stool samples, effect of 5 different commercial preservation solutions was evaluated at room temperature. Samples in different preservation solutions after placing fresh stool samples at the 0, 1, 3, 7, 15, and 30 days were collected. All samples were tested by 16S rRNA V3–V4 high-throughput sequencing to analyze the influence of microbiome composition in different preservation solutions. The results show that different preservation solutions had distinct effects on the gut microbiome composition. Compared with the control, different preservation solutions had little effect on the amount of OUTs; preservation solutions A, B and C were closer to the control in the composition of the gut microbiota, but preservation solution D significantly changed the composition by increasing Actinobacteria and Firmicutes abundance. With the time, all solutions tended to reduce the diversity of the microbiota. Preservation solution E significantly reduced the diversity of the flora; on the 30th day, all five solutions changed the composition; the individual differences in the composition of the gut microbiome were the main factors affecting the similarity of each sample, and were derived from different stools donors. The same samples, no matter which storage solution and storage time, were directly closer to each other. Different storage solutions had different effects on the content of Gram-positive bacilli, Gram-positive cocci and Gram-negative bacteria. Storage solutions C and E reduced the abundance of Bifidobacterium, whereas storage solution D increased; except that preservation solution E relatively reduced the abundance of Lactobacillus, but the preservation solution A, B, C, and D were all closer to the control. Except for the greater difference in preservation solution D, preservation solution C was the closest to the control group on Streptococcus; preservation solution D reduced Ruminococcaceae UCG 003 than the control group. However, other preservation solutions were not much different from the control group; different preservation solutions increased the abundance of Escherichia-Shigella than the control group, and preservation solutions A and B increased the abundance of Klebsiella, but preservation solution C, D, and E were closer to the control group. Overall, preservation solution C performed better in stabilizing the composition of the gut microbiota. This study provides reference for standardized microbiome projects. Subsequent research can choose a targeted preservation solution and preservation time based on this study.

Abstract:Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.

Abstract:In recent years, 16S rRNA amplicon sequencing technology has been widely used to study human gut microbiota and to detect unknown pathogens in clinical samples. However, its resolution to bacterial population can only reach the relative abundance of genus level, and different factors affect the final bacterial profile, such as sample concentrations, PCR cycle numbers and amplification primers. In order to solve these problems, we developed a quantitative 16S rRNA amplicon sequencing method by combining random tag and internal marker method. The new methods improved the accuracy of human gut microbiota, reduced the impact of experimental operation on the results, and improved the comparability between sequencing and other molecular biological methods.

Abstract:The important role of intestinal microorganisms in human health has been widely confirmed. At present, most of the studies on intestinal microorganisms are based on amplification of the V3-V4 region of bacterial 16S rRNA gene, and little attention has been paid to archaea. In this study, a primer set which can amplify 16S rRNA gene of both bacteria and archaea at the same time was used. By comparing the community changes before and after probiotics intake, it showed that this primer set is suitable for analyzing the changes of human intestinal bacteria and archaea communities. The fecal samples of volunteers were collected, and the amplification and high-throughput sequencing were carried out by using bacterial primer set (B primer) and bacterial and archaeal universal primer (AB primer); several commonly used rRNA databases were used to determine the amplification ability of the primer set to bacteria and archaea. The results showed that AB primer could display the bacterial community amplified by B primer, and could obtain the sequence of common methanogenic archaea in intestinal tract. AB primer set can analyze the bacteria and archaea in the intestinal tract at the same time by only one amplification and sequencing, which can show the structure of intestinal microbial community more comprehensively, which is suitable for the research of intestinal microorganisms.

Abstract:Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.

Abstract:The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of antibiotics, many pathogens have developed resistance, and even “Super Bacteria” resistance to multiple drugs have evolved. In the arms race between humans and pathogens, humans are about to face a situation where no medicine is available. Research on microbial antibiotic resistance genes, resistance mechanisms, and the spread of resistance has attracted the attention of many scientific researchers, and various antibiotic resistance gene databases and analysis tools have emerged. In this review, we collect the current databases that focus on antibiotics resistance genes, and discuss these databases in terms of database types, data characteristics, antibiotics resistance gene prediction models and the types of analyzable sequences. In addition, a few gene databases of anti-metal ions and anti-biocides are also involved. It is believed that this summary will provide a reference for how to select and use antibiotic resistance gene databases.

Abstract:Metagenomic next-generation sequencing (mNGS) could be used for pathogen detection from nearly all types of clinical samples. Especially, the unique diagnostic capability of pathogen mNGS detecting unknown causative agent of infectious diseases makes this method become an importation complement and irreplaceable component for conventional routine laboratory test. However, the complexity of the testing process, the rapid product update, and the insufficiency in quality control and evaluation methods that all make clinical transformation, industry development, and regulation of this technology full of challenge and uncertainty. This review briefly introduces the technical advantages and challenges, and describes the general workflow and quality control steps in details. Finally, it focuses on current considerations regarding quality evaluation methods and standards for pathogen mNGS.

Abstract: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.

Abstract:Freshwater snail is an important biological group in aquatic ecosystem and an intermediate host of many parasites. Intestinal flora plays an important role in animal energy metabolism and resistance to pathogens. We analyzed the intestinal microbiota diversity of Radix auricularia (RA) and Planorbella trivolvis (PL) by 16S rRNA high-throughput sequencing. At the phylum level, RA had 23 phyla, including Proteobacteria (33.63%), Cyanobacteria (15.33%), Chloroflexi (13.95%), and Actinomycetes (12.99%). PL had 13 phyla, including Proteobacteria (54.88%), Bacteroidetes (28.49%), and Actinomycetes (7.65%). At the genus level, there were 445 genera in RA, including Pleurocapsa, Thiodictyon, Leptotrichia, and Nocardioides. There were 238 genera in PL, including Cloacibacterium, OM60NOR5_clade, Pseudomonas, and Rhodobacter. Ninety-three genera were the common core flora of the two snail species (all the samples were present), and 27 genera had an abundance greater than 0.5%. The structure of intestinal microbiota was significantly different between the two groups (P=0.027). We performed the functional prediction of intestinal microbiota using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and the results show that the KEGG functional composition of the intestinal flora of the two snails was similar, and the abundance of the amino acid metabolism, carbohydrate metabolism and membrane transport were large. In summary, the intestinal microbiota of the two snails was high in diversity and significantly different, but there were a large number of common core flora.

Abstract:Multi-species solid-state fermentation in a mud pit is one of the typical features of strong-flavor baijiu, in which archaea plays important roles, however, the archaeal community distribution and diversity during fermentation are still lack of research. The biomass, composition and succession of archaea communities in fermented grains and pit mud were analyzed by high throughput sequencing. The potential interaction between archaea and bacteria was analyzed by co-occurrence network. Results demonstrate that the average biomass of archaea in pit mud was about 200 times higher than that of fermented grains. There was no significant difference in archaeal community structure between fermented grains and pit mud (r=0.017, P=0.074), but succession patterns between them showed significant correlation (r=0.30, P=0.03). Methanobacterium was the most abundant archaea in fermented grains and pit mud, and other dominant groups included Methanosarcina, Methanocorpusculum, Methanoculleus, and Methanobrevibacter. The co-occurrence network analysis showed that Methanobacterium was positively correlated with most bacteria in fermented grains and pit mud, especially with Hydrogenispora and Caproiciproducens, the dominant bacteria in pit mud. Our results revealed the temporal and spatial distribution characteristics and potential functions of the archaeal community in the mud pit of strong-flavor baijiu.

Abstract:Continuous planting of muskmelon and excessive application of chemical fertilizers have caused a series of problems, such as imbalance of the soil micro-ecological environment, serious soil-borne diseases and yield loss. Application of Bacillus subtilis agent is an important way to improve soil micro-ecological environment, prevent soil-borne diseases, and promote plant growth. In this study, B. subtilis was used as experimental agent to analyze the effects of different application methods on the soil microbial diversity and growth of muskmelon in greenhouse. The number of culturable microorganisms in soil was measured by dilution-plate method. The diversity of soil uncultivated microorganisms was determined by Illumina Miseq sequencing technology. The yield of muskmelon was measured by weighing method. The number of culturable bacteria in the root irrigation, hole application and dipping root application groups was higher than that of the control in different muskmelon growth stages, but there was no significant difference among the three different application methods. The number of soil fungi from B. subtilis agent treatment groups in flowering stage was significantly lower in comparison to the control group. However, B. subtilis agent treatment did not cause significant difference on soil fungi number at the fruiting and pulling stage. Diversity analysis of uncultured microorganisms showed that the Shannon index values of bacteria were higher and Simpson index values were lower respectively in the three B. subtilis treatment groups than that in the control. Moreover, the dipping root treatment produced the lowest Shannon index value and the highest Simpson index value of fungi. NMDS and cluster analysis showed that B. subtilis agents dipping root treatment significantly affected the bacterial and fungal flora, both of which were clustered into one independent branch. The application of B. subtilis agents, especially dipping root treatment, significantly decreased the abundance of Bacteroidetes, increased the abundance of Actinobacteria and Acidobacteria. The B. subtilis agent treatment didn’t produce significant effect on the diversity of fungal flora except Chytridiomycota. The height, stem diameter and leaf area of muskmelon increased by applying B. subtilis agents, and dipping root treatment produced the most significant effect. As a new type of environmental protection fertilizer, B. subtilis agent can increase the number of soil culturable microorganisms, improve soil microbial diversity, and promote growth and yield. This study would provide a scientific basis for the rational application of B. subtilis.

Abstract:To investigate the degradation of polycyclic aromatic hydrocarbons (PAHs) and the changes of rhizosphere microorganisms in the rhizosphere soil of Leymus chinensis during the remediation of PAHs contaminated soil by Comamonas testosteroni (C.t)-assisted Leymus chinensis, we evaluated the removal of PAHs in the rhizosphere of Leymus chinensis using gas chromatography-mass spectrometry (GC-MS), analyzed the bacterial community and the diversity in Leymus chinensis rhizosphere soil by high-throughput sequencing technology, characterized the correlation among PAHs degradation and bacterial community components performing redundancy analysis (RDA) and network analysis, and predicted PAHs degradation potential via PICRUSt software in this paper. The degradation of PAHs in the rhizosphere of Leymus chinensis was promoted, the abundance and diversity of bacteria and the correlation among bacteria and PAHs were changed, and the degradation potential of PAHs in Leymus chinensis rhizosphere soil was enhanced in the later stage of phytoremediation (60–120 d) due to the incorporation of C.t. The accelerated degradation of three PAHs (Nap, Phe, BaP) was accompanied by the differ abundance and correlation of Proteobacteria (Sphingomonas, MND1, Nordella), Actinomycetes (Rubrobacter, Gaiella), Acidobacteria (RB41) and Bacteroides (Flavobacterium) affected by C.t. The results provide new insight into the microorganism choices for microbial assisted plant remediation of soil PAHs and the mechanisms of enhanced PAHs degradation via the combination of Comamonas testosteroni engineering bacteria and plants.

Abstract:By analyzing the shift of microbial communities under different iron/sulfur ratios, the response of metallurgical microorganisms to energy substrates was investigated based on molecular ecological networks. High-throughput sequencing of microbial samples from different domesticated batches was conducted to analyze the changes in community composition, alpha and beta diversity. Based on the molecular ecological network, the interactions between microorganisms under different iron/sulfur ratios were explored. Keystones were identified to analyze the community response to energy substrates. In the process of domestication based on different energy substrates, the dominant species in the in iron-rich and sulfur-less community were Acidithiobacillus ferrooxidans and A. ferriphilus. A. thiooxidans accounted for up to 90% in the sulfur-rich and iron-less community after 3 domesticating batches. The results of alpha and beta diversity analysis show that the domestication process of sulfur-rich and iron-less substrates reduced the diversity of microbial communities. Molecular ecological network analysis shows that the keystones were all rare species with low abundance. During the domestication by sulfur-rich and iron-less energy substrates, the bacterial species had a closer symbiotic relationship and the community was more stable. Through this domestication experiment, the impact of different energy substrates on microbial aggregation was clarified. Domesticating metallurgical microorganisms by using sulfur-rich and iron-less energy substrates made the microbial colonies to be more stable, which was conducive to the oxidation of iron and sulfur, promoting the dissolution of sulfide minerals. Our findings provide a reference for the directional domestication of metallurgical microorganisms.

Abstract:Streptomyces aureofaciens DM-1 is a high-yielding 6-demethylchlortetracycline producer. The genome sequencing of DM-1 reveals a linear chromosome containing 6 824 334 bps nucleotides with GC content of 72.6%. In this genome, a total of 6 431 open reading frames were predicted by using glimmer 3.02, Genemark and Z-Curve softwares. Twenty-eight secondary metabolite biosynthetic gene clusters were uncovered by using AntiSMASH gene prediction software, including the complete 6-demethylchlortetracycline biosynthetic gene cluster. A frame-shift mutation in methyltransferase coding region was detected, which may result in the demethylation of chlortetracycline. The complete genome sequence of S. aureofaciens DM-1 provides basic information for functional genomics studies and selection of high-yielding strains for 6-demethylchlortetracycline.

Abstract:The marine genus Marinobacterium was first identified in 1997, and a total of 18 species have been characterized so far, 10 of which have published whole-genome sequencing data. This article summarizes the characteristics of Marinobacterium genus and analyzes the genome sequencing data related to the carbon source utilization, polyhydroxyalkanoate metabolism, and aromatic compounds degradation. The Marinobacterium species possess the complete glycolysis pathway and tricarboxylic acid cycle, yet lack genes involved in xylose utilization. All strains of the Marinobacterium genus contain the genes encoding for the typeⅠand type Ⅲ polyhydroxyalkanoate synthases, suggesting that the genus may have ability of polyhydroxyalkanoate accumulation. The Marinobacterium species contain the degradation pathways of aromatic compounds. Benzene, phenol and benzoic acid can be degraded into catechol via different enzymes, subsequently catechol is converted to 3-ketoadipate through the ortho-cleavage pathway. Alternatively, catechol can be degraded into pyruvate and acetyl-CoA. The analysis of genome sequencing data of the Marinobacterium genus provides in-depth understanding of the metabolic characteristics, indicating that the genus may have certain applications in the synthesis of polyhydroxyalkanoate and the removal of marine aromatic compounds.

Abstract:Alzheimer’s disease (AD) and Parkinson’s disease (PD) are common neurodegenerative diseases in human. The pathogenesis of AD and PD is complex, and the current drugs and surgical treatments have not successfully alleviated or terminated the progression of the diseases. The lentiviral vector (LV) is a retroviral vector. In recent years, LV mediated gene therapy has been a hotspot to study the mechanisms of human disease and clinical drug discovery. This review summarizes the recent progresses in the treatment of AD and PD by the application of LV, and offers a prospect for its application.

Abstract:Exoelectrogens are promising for a wide variety of potential applications in the areas of environment and energy, which convert chemical energy from organic matter into electrical energy by extracellular electrons transfer (EET). Microorganisms with different mechanisms and EET efficiencies have been elucidated. However, the practical applications of exoelectrogens are limited by their fundamental features. At present, it is difficult to realize the extensive application of exoelectrogens in complex and diverse environments by means of traditional engineering strategies such as rational design and directed evolution. The exoelectrogens with excellent performance in environments can be screened with efficient strain identification technologies, which promote the widespread applications of exoelectrogens. The aims of this review are to summarize the methods of screening based on different types of exoelectrogens, and to outline future research directions of strain screening.

Abstract:Dihydroorotate dehydrogenase is a flavin-dependent mitochondrial enzyme to catalyze the fourth step of the de novo synthesis of pyrimidine and to oxidize dihydroorotate to orotate. By selectively inhibiting dihydroorotate dehydrogenase, thereby inhibiting pyrimidine synthesis, the enzyme has been developed for the treatment of cancer, autoimmune diseases, bacterial or viral infections, parasitic diseases and so on. The development of inhibitory drugs requires a detailed understanding of the structural characteristics and catalytic cycle mechanism of dihydroorotate dehydrogenase. Therefore, this paper reviews these two aspects, and indicates perspectives of these inhibitors in clinical application.

Abstract:Metastasis is the leading cause of mortality for cancer patients, and lymphatic metastasis is one of the main ways of tumor metastasis. The role of CCL21 and its receptor CCR7 in lymphatic metastasis has been increasingly concerned in recent years. CCR7 is mainly expressed by both dendritic cells and T cells for immune responses. CCL21, the chemokine ligand for CCR7, secreted from lymphatic endothelial cells binds CCR7 and recruits immune cells toward lymphatic vessels and lymphatic nodes. CCR7 expressed tumor cells can also metastasize to lymphatic system by the similar way as immune cells. Targeting CCL21/CCR7 axis to inhibit lymphatic metastasis but remain potent anti-tumor immune response has increasingly become a spot light of tumor immunotherapy. In this review, we summarize the role of CCL21/CCR7 axis in lymphatic metastasis, as well as preclinical trials and clinical trials in targeting CCL21/CCR7 axis for tumor metastasis therapy, hoping to accelerate the progress on tumor metastasis therapy by targeting CCL21/CCR7 axis.

Abstract:Consolidated bioprocessing (CBP) is a multi-step process in a bioreactor, which completes hydrolase production, enzymatic hydrolysis, and microbial fermentation. It is considered to be the most promising process for the production of second-generation biofuels because of its simple steps and low cost. Due to the complexity of lignocellulose degradation and the butanol synthesis pathway, few wild microorganisms can directly utilize lignocellulose to synthesize butanol. With the development of synthetic biology, single-bacterium directly synthesizes butanol using lignocellulose by introducing a butanol synthesis pathway in the cellulolytic Clostridium. However, there are still some problems such as heavy metabolic load of single bacterium and low butanol yield. Co-culture can relieve the metabolic burden of single bacterium through the division of labor in different strains and can further improve the efficiency of butanol synthesis. This review analyzes the recent research progress in the synthesis of biobutanol using lignocellulose by consolidated bioprocessing from both the single-bacterium strategy and co-culture strategy, to provide a reference for the research of butanol and other biofuels.

Abstract:Human milk oligosaccharides (HMO) are important immunoactive components found in breast milk. Scientific research proves that HMOs are significantly beneficial for infant health. 2’-fucosyllactose (2’-FL) is the major component of HMO, which obtained growing attentions from food industry. Besides, 3-fucosyllactose (3-FL) is another important fucosyllactose and it has a similar synthetic route comparing to 2’-FL. Thus, research of the two HMO components has interactive effects for each other. Recently, numerous publications are available for 2’-FL and 3-FL. The microbial cell factory is able to massively produce fucosyllactose via an efficient way, which will show considerable influences in dairy industry. In this paper, we review recent studies on 2’-FL and 3-FL, and discuss their prospects according to published literature and patents.

Abstract:Bile acids facilitate the absorption of lipids, and affect the development of various diseases by regulating intestinal flora structure and modulating immunity and metabolism. It is therefore important to quantitatively detect bile acids. Current analytical methods are still immature due to constituent complexity, structural heterogeneity and bioactive variability of bile acids. Detection of individual bile acids is of significance for pharmacological research, clinical diagnosis and disease prevention. Advances have been made in bile acid analysis from multiple sources including serum, bile, urine and feces, although several limitations still exist for bile acid quantification. Here we review research progress in conventional bile acid assays, including spectrophotometry, thin-layer chromatography, liquid/gas chromatography and liquid/gas chromatography-mass spectrometry. Moreover, we emphasize the development of bile acid biosensors that may have promising prospects.

Abstract:Three-dimensional (3D) genomics is an emerging discipline that studies the 3D spatial structure and function of genomes, focusing on the 3D spatial conformation of genome sequences in the nucleus and its biological effects on biological processes such as DNA replication, DNA recombination and gene expression regulation. The invention of chromosome conformation capture (3C) technology speeds up the research on 3D genomics and its related fields. Furthermore, the development of 3C-based technologies, such as the genome-wide chromosome conformation capture (Hi-C) and chromatin interaction analysis using paired-end tag sequencing (ChIA-PET), help scientists get insight into the 3D genomes of various species. Aims of 3D genomics are to reveal the spatial genome organization, chromosomal interaction patterns, mechanisms underlying the transcriptional regulation and formation of biological traits of microorganism, plant, animal. Additionally, the identification of key genes and signaling pathways associated with biological processes and disease via chromosome 3C technology boosts the rapid development of agricultural science, life science and medical science. This paper reviews the research progress of 3D genomics, mainly in the concept of 3D genomics, the development of chromosome 3C technologies and their applications in agricultural science, life science and medical science, specifically in the field of tumor.

Abstract:Human epidermal growth factor (hEGF) is a typical member of the growth factor family that activates epidermal growth factor receptors. It is synthesized and secreted by multiple tissues and organs of the human body, regulating the cell proliferation, differentiation and migration via binding to receptors and activating a series of signaling pathways. In recent years, the research on hEGF has been extended to its role in human physiology and pathology, especially in tissue regeneration and wound healing. This paper reviews the research progress of hEGF, briefly describes its gene and protein structure and characteristics, mechanisms and biological effects, with the emphasis on the roles and influences in the healing of gastrointestinal ulcers, skin wound repair and tumor pathology.

Abstract:In order to explore the microbial communities and functions of activated sludge in an Anaerobic-anoxic-oxic (A2/O) process under the start-up of Actinic reaction enzyme system (ARES) system and to understand the impact of the ARES system in domestic sewage treatment process, the activated sludge microbial community structure in the A2/O process system before and after ARES system start-up was analyzed by Illumina-HiSeq 2000 high-throughput sequencing platform. By combining with the main parameters related to the effect of sewage treatment, we analyzed the environmental functions of the microbial communities. The microbial community structure of activated sludge was significantly different before and after the ARES system start-up. There were 9 main bacterial phyla in the system (average relative abundance ≥1%), accounting for 96%–98% of the total bacteria sequenced. After the ARES system was started, the relative abundance of Betaproteobacteria and Chlorobi increased by 3.45%–3.85% and 0.45%–2.61%, respectively. In the anaerobic unit, the relative abundance of Bacteroidetes increased by 12.97%, while the Actinobacteria and Firmicutes decreased by 9.60% and 1.45%, respectively. At the genus level of bacteria, the relative abundance of Denitratisoma increased by 0.80%–3.27%, while the Haliangium and Arcobacter decreased by 3.36%–4.52% and 1.48%–3.45%, respectively. The relative abundance of bacteria was significantly different before and after the ARES system start-up. There were 7 abundant fungi phyla (average relative abundance ≥1%) in the system. After the ARES system was started, the relative abundance of Rozellomycota decreased by 42.71%–46.77%. In the anaerobic unit, the relative abundance of Ascomycota decreased by 13.39%, while the relative abundance of Glomeromycota increased by 13.86%. At the genus level of fungi. The relative abundance of Entomophthoraceae sp. and Glomcromycota sp. increased by 31.35%–36.50% and 6.27%–13.84%, respectively, while the Rozellomycota sp. and Xylochrysis lucida decreased by 42.71%–46.77% and 3.67%–5.54%, respectively. Our results showed that the application of ARES system caused the response of the microbial community to environmental changes, especially for the fungi communities, in the meanwhile, improved the effluent quality, especially the removal rate of total nitrogen.

Abstract:(2S)-taxifolin is an important flavonoid that has anti-inflammatory and anti-oxidation effects. It is widely used in pharmaceutical and nutraceutical industries. Flavone 3-hydroxylase (F3H) can catalyze the synthesis of (2S)-taxifolin and other 3-hydroxylated flavonoids from (2S)-eriodictyol. Due to the low catalytic efficiency of F3H, the titer of many 3-hydroxyflavones, such as taxifolin, synthesized by microbial method is relatively low. In this study, a SmF3H was identified from the transcriptome of Silybum marianum (L.) Gaertn. The results of fermentation showed that SmF3H can catalyze the flavone 3-hydroxylation reaction, and its catalytic efficiency was significantly higher than that of commonly used SlF3H from Solanum lycopersicum. Six promoters with different transcription strength were selected to optimize the synthesis pathway from the flavonoid precursor (2S)-naringenin to (2S)-taxifolin. The results showed that the highest titer of (2S)-taxifolin (695.90 mg/L in shake flask) could be obtained when the PGAL7 promoter was used to control the expression of SmF3H. The titer of (2S)-taxifolin was further improved to 3.54 g/L in a 5-L fermenter, which is the highest titer according to current available literatures.

Abstract:Amygdalus pedunculata Pall. is one of the 12 important woody oil crops in China. In this study, we determined the complete chloroplast genome sequence of A. pedunculata Pall. (MG602257) from Mu Us desert in Yulin city, Shaanxi province, China. The plastome was 157 851 bp with 36.8% GC content. Comparisons among the plastomes of MG602257 and other two MG869261 and KY101153 from Genebank of NCBI showed that the total length of these chloroplast genomes was MG602257< MG869261

Abstract:Glypican-3 (GPC3) is a key member of Glypican family and plays an important role in the development, angiogenesis and metastasis of hepatocellular carcinoma (HCC). Most HCC overexpresses GPC3, but GPC3 is hardly detected in normal adult liver and benign liver lesions, so it is regarded as a highly specific diagnostic marker and an ideal therapeutic target for HCC. In this study, we cloned the heavy and light chain variable region gene from the monoclonal antibody targeted to GPC3 screened in the previous stage, and linked it with a segment of flexible peptide (Linker) to obtain the single chain antibody against GPC3. The single chain antibody gene was cloned into vector for prokaryotic expression and purified to obtain high purity protein. Detection shows that the single-chain antibody produced by us has the same binding activity with the full-length antibody, and can accurately target the tumor site of Huh7 tumor-bearing model mice after coupling Cy5.5 fluorescence, suggesting that the single-chain antibody has the potential to realize multi-directional liver cancer precise surgical navigation under the guidance of a probe.

Abstract:Tissue inhibitor of metalloproteinases-2 (TIMP-2) inhibits tumor migration and invasion. Obtaining TIMP-2 protein is conducive to a comprehensive and in-depth study of its function and mechanism in tumorigenesis and development. We collected human TIMP-2 protein through prokaryotic expression in vitro. We expressed, purified and characterized human TIMP-2 protein. First, the human TIMP-2 gene was cloned from the cDNA obtained by reverse transcription of total RNA of human lung cancer A549 cells, and constructed to pET28a vector. The recombinant plasmid pET28a-TIMP-2 was transformed into Escherichia coli BL21(DE3) after restriction endonuclease digestion and sequencing analysis. The expression of TIMP-2 protein was induced by isopropyl-β-D-thiogalactoside (IPTG), and the expression conditions were optimized. After purification by nickel affinity column, the fusion protein His-TIMP-2 was identified by Western blotting method and its biological activity was detected by gelatin zymography. The fusion protein His-TIMP-2 existed in the form of inclusion body in E. coli. In a certain range, the concentration of IPTG had no significant effect on the expression amount of His-TIMP-2. But in this expression system, induction temperature and time were the key parameters, and the expression amount of His-TIMP-2 in E. coli increased with the increase of induction temperature. The purified and refolded fusion protein could effectively inhibit the activity of matrix metalloproteinases expressed by human lung cancer A549 cells. The acquisition of active fusion protein lays a foundation for further study of the function and mechanism of human TIMP-2, and is of great significance for tumor therapy.

Abstract:Studies on the interaction between small organic molecules and DNA are important means to explore drug mechanism and new drugs. Quercetin is a polyhydroxy flavone compound with activities such as anti-cancer, anti-inflammatory, antibacterial, antiviral, hypoglycemic and anti-hypertensive, immunomodulation and cardiovascular protection. Experimental studies aim at confirming if an interaction exists between quercetin and DNA, and determining the type of interaction. The interaction between quercetin and herring DNA can be detected by fluorescence spectrometry and resonance scattering fluorescence spectrometry analysis. The mode of the interaction between quercetin and herring DNA can be detected by UV-Vis spectrophotometry and fluorescence polarization analysis. This review helps understand the in vitro interaction between quercetin and DNA, and assist the development of drugs for corresponding diseases.