Abstract:[Objective] To explore the networked and the topological structure of gut microbiota, we applied network analysis in this study to characterize the gut microbiome co-occurrence networks. [Methods] Gut microbiome data were divided into two groups based on the equol-metaboliting ability of hosts. We constructed the co-occurrence network of gut microbiota with Spearman correlation coefficients with FDR judgment in each group and analyzed the difference between groups. At the same time, the topological structure of random network was used to compare with the real network to uncover the significant differences. Finally, the species taxonomy information was taken into the network and revealed different features.[Results] The networks of two groups retained 45 and 47 different species respectively and show different complexity. From our data, we found the structure of the real network topology is specific and more interaction within different phylum in equol producer group. [Conclusion] By network analysis, we can discover the complexity of the interactions among the different species of gut microbes, and demonstrate the feature of network topology that was rarely reported before. And the method will also provide a new perspective of gut microbiota research in the future.

Abstract:In the last five years, the delicate relationship between microbiota and human health has become a global research focus. In particular, development of metagenomics that is based on next-generation high-throughput sequencing technology has greatly advanced the field. However, bioinformatic analyses are often a great challenge for metagenomic studies. Here we review the common analytic methods for metagenomics.

Abstract:We have entered into post-antibiotic era, phage therapy has been refocused recently, bacteriophages are different from the normal antibiotics. It is unsuitable to use the established safety assessment system for classical antimicrobial agents to evaluate the safety of bacteriophages for therapy. So, it is necessary to establish the safety assessment system of phage therapy involved in the whole procedures of choosing bacteriophages, including phage production, the choice of bacteriophage products, phage's administration routes, and the bacterial infection patients that enrolled for phage therapy. In this study, we systematically analyzed the safety problem involved in phage therapy and established the safety assessment system of phage therapy. It can provide basis for phages to enter into clinical therapy in the future.

Abstract:Antibiotic resistance has caused major damages to public health and social economy, and effective control has become a stressing need. This review summarizes recent changes in the scope and methods of antibiotic resistance investigation, and discusses the contributions of foodborne bacteria, gut, fecal and waste water microbiota, drug administration routes, and biofilm to the mega antibiotic resistance problem seen today. We also present new directions for mitigation of antibiotic resistance and diseases.

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Abstract:[Objective] Heterologous expression of some human genes in yeast cells leads a severe growth defect. This phenomenon can occur when intrinsic yeast regulatory mechanisms are perturbed by the physiological function of the ectopically expressed human protein. Yeast cells are amenable to genetic studies and used as a platform for high-throughput screening. Thus, yeast cells harboring such growth inhibitory human proteins may be useful to analyze physiological function of the human protein and applied to find its inhibitor. In the present study, we constructed a collection of yeast expression plasmid harboring human protein-coding genes. Using the human gene library, we established a screening system to identify genes whose expression cause a growth defect in yeast cells. [Methods] Using the Gateway recombination technology, human protein-cording genes were cloned into a yeast expression plasmid. The resulting plasmids were individually transformed into yeast cells and analyzed whether their expression effects on yeast growth. Furthermore, identified inhibitory genes were expressed as GFP fusion proteins and their localization in yeast cells were analyzed. [Results and Conclusion] Among 2991 human protein-cording genes, we identified 29 genes whose expression caused a sever growth defect in yeast cells. Some of them are causative genes to develop human disorders. For example, PDLIM4 is involved in development of osteoporosis and prostate cancer. Physiological function of PDLIM4 has not been understand very well. Our study may provide another option to investigate human proteins.

Abstract:Virus, as a strict intracellular parasitic organism, needs to use a variety of host proteins to complete their life cycle. To prevent and control viral diseases, it is necessary to provide useful data for understanding the replication and pathogenesis of viruses. Compared with the traditional RNA interference screening, CRISPR/Cas9 technology, as an emerging approach in recent years, exhibits more specific and faster characterization to achieve gene knockout or other genome editing. Therefore, it has wide applications in the study of functional genes. Based on the CRISPR/Cas9 system, we can construct a host genome-wide sgRNA library and further screen and identify the key host factors involved in multiple biological processes of pathogen invasion or replication. Lastly, we hope that the virus life cycle will be completely revealed in terms of virus-host interaction network, and high-throughput screening platform based on CRISPR/Cas9 technology will provide a powerful tool for researching virology and immunology. This review aims to introduce the screening steps of CRISPR/Cas9-based high-throughput screening platform, and summarize the applications and outlooks of this platform in screening host factors involved in viral replication.

Abstract:The relationship between gut microbiota and mitochondria is very close. On the one hand, intestinal microorganisms can directly or indirectly through the digestion of nutrients in food to produce metabolites such as short-chain fatty acids, hydrogen sulfide and nitric oxide, affect the energy metabolism process associated with mitochondria, regulate mitochondrial reactive oxygen species production, and regulate mitochondria and even the entire body's immune response. On the other hand, intestinal cell mitochondrial dysfunction and mitochondrial genome genetic variation also affect the composition and function of the gut microbiota. In this paper, we summarized recent advances in the relationship between gut microbiota and mitochondria. It provides a theoretical basis for targeting the intestinal flora and mitochondria to regulate intestinal health.

Abstract:High-throughput sequencing technology has enhanced our understanding of gut microbiome and epigenetic modification, establishing the potential links between gut microbiome and epigenetic modification of host. It illuminates the development of a lot of diseases such as immune-related, metabolic, cardiovascular diseases and even cancer. Intestinal microbiome that is inseparable from human body interacts with host cells. Dysbiosis of gut microbiome may influence the status of epigenome from host. Indeed, the relationship between epigenetic regulation of host and variation of gut microbiome and its metabolites was reported responding for many diseases. Therefore, the gut microbiome could function as a diagnostic marker for certain diseases. The transplantation of healthy intestinal microbiome would re-balance dysbiosis and serve as an effective treatment strategy. Here, we gave a comprehensive introduction about how gut microbiome played direct roles in epigenetic modulation of host cells, and its indirect impact on epigenetic modification mainly through metabolites like bioactive low-molecular-weight substances and other enzymatic cofactors. Additionally, we talked about the great potentials and applied value of gut microbiome in diagnosis and treatment of related diseases.

Abstract:[Objective] We studied the roles of 14-3-3 protein Bmh1 of Candida albicans in its cell growth and hyphal development by using a Tet-off promoter. [Methods] Based on the URA3⁺ strain SN152 of C. albicans, we deleted one BMH1 allele and replaced the promoter of the other allele with the Tet-off promoter, generating a strain in which Bmh1 expression was controlled by Doxycycline. Then we explored the phenotypes of cell growth and hyphal development via spot analysis and morphological observations. Further, we preliminarily studied the position of Bmh1 in the network of hyphal development regulation via overexpression of Bmh1 in the mutants of ras1, flo8, efg1, cph1 and tec1, which were very important hyphal development regulators. Finally, we constructed some Bmh1 mutants with different C-terminals and detected their effects on cell growth and hyphal development of Candida albicans. [Results] Doxycycline-induced knockdown of Bmh1 inhibited cell growth severely. Highly-expressed Bmh1 improved hyphal development significantly without Doxycycline induction. This improvement bypassed the effects of ras1, efg1, cph1 and tec1 gene deletions and was blocked by flo8 deficiency. All Bmh1 mutants with C-terminal deletion or heterologous C-terminals grew normally with Doxycycline induction and the hyphal development was not improved obviously. [Conclusion] We validated that the 14-3-3 protein Bmh1 of Candida albicans is essential for cell growth, proving the tight controlling of the Tet-off promoter on Bmh1 expression. Bmh1 functions as a positive regulator of hyphal development and plays roles in the downstream of Ras1, Efg1, Cph1 and Tec1, and in the upstream of Flo8. The conserved domain of Bmh1 is required for cell growth while the C-terminal is not.

Abstract:Alterations of intestinal microbiota, intestinal barrier dysfunction and bacterial translocation are the common pathogenetic characteristics in cirrhosis, which is an end-stage of liver disease resulting from different causal agents. Alterations of intestinal microbiota play an important role in induction and promotion of liver disease progression. Probiotics have been shown to exhibit limited efficacy in targeting gut barrier dysfunction caused by liver cirrhosis, while a vast studies attests to the beneficial effects of probiotics in the gut. Recently, more and more evidences suggests that certain probiotics components or metabolites (defined as "postbiotics") have beneficial properties as same as the viability status of probiotics. Postbiotics exert a variety of beneficial effects, including modulation of the microbiota composition, regulation of the epithelial barrier function and intestinal immune responses. The merits of probiotics include clear chemical structures and safety dose parameters. In this review, we introduced the effects of gut dysbiosis on complications and disease progression of cirrhosis. Specifically, discussion is focused on the prospect of postbiotics in modulation of the gut dysbiosis in cirrhosis and its potential role in improve the disease progression.

Abstract:A plaque biofilm is an aggregate of complex microbial communities attached to the enamel surface. The formation and growth of plaque biofilms have a direct or indirect impact on oral health. Many studies have confirmed that oral diseases such as dental caries and periodontal diseases are related to the accumulation of bacteria and the formation of plaque. During the formation of plaque biofilms, the initial colonization of bacteria on the surface of the tooth is crucial for the biofilm composition and structure of the microorganisms. These primary colonization bacteria determine the type and numbert of microorganisms with which subsequent symbionts are formed. Different microbial constituents may play different roles in oral pathological conditions associated with biofilm formation. Therefore, in this paper, the growth and control of dental plaque biofilm in human oral cavities were reviewed, and the early colonization and maturation process of the biofilm and the control of dental plaque biofilm through physical and chemical methods were introduced. These contents may provide valuable information to study the formation mechanism of plaque biofilm and related oral diseases prevention and treatment.

Abstract:The large number of gut microbiota (GM) in human body, participating in the material metabolize and energy cycles, regulates the physiological activities of the body. In recent years, many studies demonstrate that the stable state of GM plays an essential role in maintaining the normal function of the brain and nervous system. GM disorder is closely related to some neurological diseases like Parkinson's disease (PD). At present, there are abundant research results on relationship between the pathogenesis of PD and the dysregulation of GM, indicating that GM brings a vital induction effect to the pathogenesis of PD. After reviewing the literature on the correlation of GM with PD and analyzing the change of GM in PD patients, we discuss the relationship between the occurrence of PD and the change of GM. Moreover, we also address the application of faecal transplants treatment in PD treatment in order to provide a reliable theoretical basis for the potential prevention and treatment of PD by regulating GM.

Abstract:The intestine is a complicated microenvironment and hosts a large and complex flora of microorganisms, which plays an important role in host gut health. Quorum sensing is an important mechanism of information transmission among bacteria through chemical signal molecules. This article reviews the composition of quorum sensing system, signal transduction mechanism and the regulation of intestinal biofilm formation by AI-2/LuxS quorum sensing system. This review introduces the lactic acid bacteria AI-2/LuxS quorum sensing system and its role in the regulation of biofilm formation in intestine. The review will evoke new ideas for renovation of intestinal barrier function and intestinal health regulation.

Abstract:Sweeteners are food additives that impart the sweetness to soft drink foods, which can be divided into high-intensity sweeteners and low-calorie sweeteners. At present, the regulatory mechanism of sweeteners on intestinal flora has become one of the hot spots. Sweeteners can affect the ecological balance of the gut microbiota, and then affects the health of the host. More and more data indicates that excessive consumption of sweeteners can cause metabolic dysfunction, and affecting host weight and glucose tolerance. This article reviews the recent research progress of several commonly used sweeteners on intestinal microbial regulation, in order to provide reference for the researchers.

Abstract:[Objective] To evaluate the effect of oral administration of probiotics on the colonization of Escherichia coli K1 and Group B streptococcus (GBS) in the guts and vaginal among pregnant women.[Methods] Vaginal and rectal secretion specimens were collected from 2539 health pregnant women in Guangdong from 2011 to 2017. First, 47 healthy pregnant women involved were randomly divided into the 2 groups. The treatment group received probiotics, while the control group without. Real-time PCR was used to detect the quantitative colonization changes of E. coli K1 in the two groups thereafter. Then, 50 pregnant women subjected to the GBS screening by PCR were randomly divided into 2 groups. Later, real-time PCR was used to detect the quantitative changes of GBS in the two groups. Then, real-time PCR was used to detect GBS in the genital tract and rectal specimens for recording the colonization of GBS. [Results] With no statistical differences between the groups in term of age, multipara proportion and level of education (P>0.05), the colonization of E. coli K1 in the treatment group declined dramatically (F=32.866, P<0.001). Women in the oral probiotics group have lower level of colonization of E. coli K1 (F=41.546, P<0.001). The results suggest that oral administration of probiotics may inhibit the colonization of E. coli K1 in the intestines and vaginas of pregnant women. Meanwhile, the colonization level of GBS in probiotics group declined after taking probiotics. Finally, the GBS carrier rate of the pregnant woman was 8.07% by PCR. [Conclusion] The GBS carrier rate of the screening pregnant women in Guangdong, China was 8.07%. The results suggest that oral administration of probiotics to pregnant women can inhibit the colonization of E. coli K1 in the intestines and vaginas of these women, which may prevent neonatal bacterial meningitis in newborns as a result of hematogenous spread.

Abstract:[Objective] Lactobacillus is closely related to human or animal health, and its presence and content changes can be used as health indicators. Usually, specific primers are the key to successful quantification. Redesigning primers is time-consuming and hard to guarantee its specificity. This study was to screen genus-specific primers for Lactobacillus by theoretical and experimental methods rapidly and effectively, and also to provide a theoretical basis for screening and designing of primers in the future.[Methods] We selected 12 pairs of primers based on the 16S rRNA gene sequence from published literatures and evaluated them using primer design software. Based on the evaluation results, we recombined the primers to obtain the theoretically specific Lactobacillus primers, and test the specificity of the new combination of Lactobacillus primers using the gel electrophoresis and the QX200 droplet digital PCR system. [Results] We screened out a pair of Lactobacillus genus-specific primer named Lab-F1/Lab-R1 by primer-designing software and tests, and its product size was about 300 bp. The ddPCR tests showed that the specificity and sensitivity of the Lab-F1/Lab-R1 were better, and it also could effectively quantify Lactobacillus in fecal samples. [Conclusion] This method can quickly and efficiently screen out the specific primers with better specificity and provide a theoretical basis for the future screening and designing of primers.