Abstract:Interferon (IFN) is a kind of glycoprotein with multifunctional biological activity, and contains three families (type I, type II and type III). Type III interferon (IFN-III) is a novel interferon discovered in the last 16 years. The induction process and biological functions of IFN-III are similar to those of type I interferon (IFN-I). IFN-III plays an important role in antiviral, immunomodulatory, antitumor, suppression of autoimmune diseases, allergic asthma, as well as antibacterial and antifungal. We elaborate here IFN-I and IFN-III in terms of classification, sequence homology and signal transduction. Combining with the achievements of IFN-III in the treatment of diseases in recent years, we try to summarize the related biological functions of IFN-III, to provide a reference for further study of IFN-III.

Abstract:Actinomycetes are a class of Gram-positive bacteria that can produce primary metabolites such as amino acids and secondary metabolites such as antibiotics. Actinomycetes are widely used in food, pharmaceutical, additive and cosmetic industries. In addition, a few actinomycetes, such as Mycobacterium, are pathogen that can cause human, animal and plant diseases. Leucine-responsive regulatory protein (Lrp) is a category of global transcriptional regulator involved in amino acid metabolism and its relevant metabolic processes. They are capable of responding to a variety of amino acids and participating in the regulation of multiple physiological processes in microbial cells, such as amino acid metabolism and transport, central metabolism, bacterial persistence and virulence, etc. This paper summarizes the biological functions of Lrp in actinomycetes, and reviews the research advance of regulatory mechanism of Lrp from different actinomycetes, especially Lrp from Streptomyces coelicolor and Saccharopolyspora erythraea studied.

Abstract:Vibrio parahaemolyticus, a Gram-negative halophilic bacterium, is the main pathogen in marine vertebrates and invertebrates, and can cause acute gastroenteritis, sepsis and necrotizing fasciitis via consumption of raw or poorly cooked, contaminated seafood by human beings. As a globally transmitted pathogen, the pathogenicity of V. parahaemolyticus is closely related to a variety of virulence factors, including the adhesion factors, lipopolysaccharide, hemolysin, type III secretion system (T3SS), type VI secretion system (T6SS), iron uptake system, protease and some other virulence factors. All these virulence factors are only expressed under specific circumstance, indicating that the expression of these virulence factors is tightly regulated by the environmental factors as well as those signals from the host. In this review, we discuss the regulatory mechanisms used by V. parahaemolyticus to control its virulence gene expression, summarize the regulatory pathways that play important roles in V. parahaemolyticus pathogenesis, and highlight key regulatory factors in these regulatory networks. To better understand the pathogenic mechanism of V. parahaemolyticus will definitely help us to develop new strategies to treat and prevent diseases caused by V. parahaemolyticus infections.

Abstract:[Objective] To understand the structure and dynamics of fungal community during raw vinegar brewing. [Methods] In total 51 samples including raw materials, starter, fermenting samples in urns, smoking cupei and leaching cupei were collected from a raw vinegar making enterprise in Shanxi Province, and fungal diversity was analyzed by high throughput sequencing of ITS1 regions. [Results] Except 5 samples having failure amplifications, 489 fungal OTUs were detected in the remaining 46 samples, dominated by Ascomycetes (88.3%). There were significant fungal community differences among groups. The species richness was the lowest in raw materials and starter, the highest in fermenting samples, and medium in smoking and leaching cupei. The dominant fungi from raw materials and starter were Saccharomyces cerevisiae and Aspergillus niger, respectively, which were important inocula for fermentation. There were also obvious fungal community variations during fermentation in urns, which were further divided into early (F2 to F13) and late (F17 to F46) fermentation stages. The abundance of S. cerevisiae and Aspergillus candidus was significantly higher in the early fermentation stage, whereas that of A. niger and Davidiellaceae sp. was significantly higher in the late fermentation stage. [Conclusion] There are significant fungal community variations among different brewing steps and among different fermentation stages in urns. S. cerevisiae and A. niger represent the main fungi contributing to raw vinegar fermentation. This study provides a theoretical basis for the optimization of raw vinegar brewing process.

Abstract:[Objective] Phosphorus-soluble bacteria were screened from the soil around the roots of tomato plants to provide phosphorus-soluble bacteria resources for the development of biofertilizers for increasing production and saving fertilizer, and their growth-promoting mechanism was preliminarily explored. [Methods] Inorganic phosphorus medium was used to isolate and screen the growth-promoting strains from soil by serial dilution plating method. The excellent growth-promoting strains were identified by morphological characteristics, 16S rRNA gene sequence and gyrB gene sequence analysis, and the effects of environmental factors and nutrient factors on phosphorus solubility were studied by orthogonal and single factor test. Organic acids produced by excellent growth-promoting strains were identified by HPLC-MS, according to the standard substances of corresponding organic acids, and the growth-promoting effect of strains on tomato was determined by pot experiment. [Results] A good growth-promoting strain named PHODB35 was isolated. It was identified as Bacillus amyloliquefaciens. The orthogonal test of environmental factors shows that the optimum conditions for dissolving phosphorus of strain PHODB35 were pH 7.0, temperature at 30℃ and 5% inoculation. The results of single-factor experiments on nutrient factors show that strain PHODB35 had the best phosphorus dissolution effect with glucose as carbon source, ammonium sulfate as nitrogen source, calcium phosphate as phosphorous source, initial pH 7.0 and temperature at 30℃. The effective phosphorus concentration was 88.77 mg/L. Gluconic acid was produced by strain PHODB35. Pot experiment showed that the application of strain PHODB35 had obvious growth-promoting effect on tomato seedlings. Compared with the control, the plant height, above-ground fresh weight, under-ground fresh weight, substrate and plant available phosphorus content were increased by 28.21%, 22.59%, 113.06%, 45.08% and 16.24%, respectively, after inoculating strain PHODB35, indicating that strain PHODB35 had certain fertilizer effect and could be used for the development of growth-promoting agents. [Conclusion] Phosphorus solubilizing bacteria were screened to provide resources for further development of tomato specific growth-promoting agent or special microbial organic fertilizer, and to provide theoretical and experimental basis for the application of strain PHODB35 in agricultural production.

Abstract:[Objective] To investigate DNA lesions and repair response caused by the DNA double strand break (DSB) generated by the genome editing tools including CRISPR/Cas9 and CRISPR/Cpf1 in Saccharomyces cerevisiae, we used the damage and repair of S. cerevisiae genomic DNA caused by a chemical substance methyl methane sulfonate (MMS) as a comparison and elucidated the changes of edited cells at the cellular and transcriptional levels. [Methods] Initial cells were divided into two situations, including unsynchronized cell cycle and synchronized cell cycle to G0/G1 phase by α-factor. We measured the growth profiles of CRISPR/Cas9-and CRISPR/Cpf1-mediated edited cells. We employed flow cytometry to detect the arrested cell cycle of edited cells. We used Real-time PCR to quantify the transcriptional expression changes of key genes involved in DNA damage response in edited cells and MMS-treated cells. [Results] Growth of initial cells, which were either unsynchronized or synchronized cell cycle by α-factor, were inhibited by genome editing. Cell viabilities of edited cells decreased, and the cell cycles were arrested at the G2/M phase. Furthermore, along with the prolongation of editing time, mutation efficiency of edited cells increased while cell viabilities decreased. The mutation efficiency and viabilities of CRISPR/Cpf1 edited cells were lower than those of CRISPR/Cas9, and thus the damage induced by CRISPR/Cpf1 was stronger than that of CRISPR/Cas9. Both these two editing tools induced significantly up-regulated transcriptional expressions of RNR3 and HUG1, which are key genes involved in DNA damage response in yeast. Additionally, the extent of CRISPR/Cpf1-mediated up-regulation was higher than that of CRISPR/Cas9, but both were lower than MMS treatment. [Conclusion] This study analyzed DNA lesions and repair response caused by CRISPR/Cas9-and CRISPR/Cpf1-mediated genome editing at the cellular and transcriptional levels, and preliminarily revealed the divergent extents of S. cerevisiae in response to different DSBs, thus providing an important guidance for improving the editing capacity and estimating the safety of genome editing.

Abstract:[Objective] To explore the electroactive microorganism in the intestinal tract of marine annelids represented by Urechis unicinctus and characterizing its physiological and electrochemical properties.[Methods] The strain was isolated using plate scribing and identified by 16S rRNA gene sequencing. The morphology of the isolate was depicted by scanning electron microscope. High performance liquid chromatography (HPLC) was used to analyze the metabolites. The quantifications of Fe(Ⅱ) and Mn(Ⅱ) reduction were carried out by ferrozine and formaldoxime assays, respectively. Single-chamber microbial fuel cells (SCMFC) were used to test the electrochemical activity by cyclic voltammetry. [Results] A facultative anaerobic bacterium, Shewanella marisflavi UU-3-2 (with the similarity of 99.93%), was successfully isolated which was a rod bacterium with the length about 2 μm and width about 0.5 μm. The metabolic analysis showed that this strain could use sodium lactate as an electron donor, fumarate as an electron acceptor for anaerobic respiration with acetate and succinate production. Ferrozine and formaldoxime assays illustrated that Fe(Ⅲ)/Mn(Ⅳ) in the Fe₂O₃/MnO₂ were reduced. The maximum current density was 146 mA/m², and the results of cyclic voltammetry revealed that the oxidation peak and reduction peak happened at 0.14 V and -0.51 V, respectively. [Conclusion] An electrochemical activity microbe, Shewanella marisflavi UU-3-2, was successfully isolated from marine animals represented by Urechis unicinctus, indicating the widespread existence of electrochemical activity microorganisms in marine annelids' intestine.

Abstract:[Objective] To successfully establish the C57BL/6 mice experimental infection model for foot-and-mouth disease virus. [Methods] The foot-and-mouth disease virus O/HK/CHA/99 MF4 strain, which is insensitive to C57BL/6 mice, was selected and continuously passaged in C57BL/6 mice (in vivo) and fetal pig kidney cells (in vitro). [Results] We successfully obtained a foot-and-mouth disease virus mutant (O/HK/CHA/99 MF4C5), which was sensitive to C57BL/6 mouse. [Conclusion] This study successfully established C57BL/6 mice model for a foot-and-mouth disease virus mutant strain, which lays a foundation for the evaluation of the efficacy of foot-and-mouth disease vaccine and the study on pathogenicity in the future.

Abstract:[Objective] To reveal the metabolic pathways of n-propanol synthesis and corresponding microorganisms during Luzhou-flavor liquor fermentation.[Methods] The microorganisms and metabolic pathways related to the synthesis of n-propanol were analyzed by metatranscriptome analysis, and the capability of corresponding microorganisms to synthesize n-propanol was investigated.[Results] Three possible n-propanol synthetic pathways were discovered during Luzhou-flavor liquor fermentation. All of them contributed to the synthesis of n-propanol based on the transcriptome analysis. However, the time and capability of microorganisms to synthesize n-propanol through these pathways were different. Fungi synthesized n-propanol mainly through citramalate pathway and threonine metabolic pathway, whereas bacteria synthesized n-propanol through propanoate pathway and partial threonine metabolic pathway. Moreover, yeast strains and lactic acid bacteria isolated from fermented grains were confirmed to be corresponding to the synthesis of n-propanol during Luzhou-flavor liquor fermentation.[Conclusion] Discovery of metabolic pathways of n-propanol synthesis and corresponding microorganisms during Luzhou-flavor liquor fermentation help to understand the formation mechanism of n-propanol in the process of Chinese liquor fermentation.

Abstract:[Objective] To investigate the effects of long-chain inulin supplementation on the gut microbiota recovery after antibiotics treatment induced dysbiosis. [Methods] Fifty healthy 10-week-old BALB/c mice were randomly divided into 2 groups, 15 mice were used as controls (the Ctrl group), and the remaining 35 mice were provided water containing 4 antibiotics (the ABx group) ad libitum for 7 days. On the 8th day, the antibiotic-induced dysbiosis mice were randomly divided into 2 groups. One group was provided drinking water containing 5% inulin as the inulin recovery group (the Ire group), and the other group received normal drinking water as the spontaneous recovery group (the Sre group). The treatment continued for 21 continuous days. On the 7th day after ABx treatment and on the 7th, 14th and 21th day of the recovery treatment, the colon samples were collected and subjected to histological analysis; the feacal samples were collected and subjected to 16S rRNA V3-V4 region sequencing and analyzed with bioinformatic softwares. [Results] The antibiotics treatment induced slight colonic inflammation but serious gut microbiota dysbiosis. Histological analysis showed that the colonic inflammation gradually decreased after 21 days of either long chain inulin supplementation or spontaneous recovery. However long-chain inulin intervention delayed the recovery of colon tissue compared to spontaneous recovery. Neither inulin supplementation nor spontaneous recovery could restore gut microbiota composition at the genus level. In particular, long-chain inulin supplementation might result in selective expansion of some opportunistic pathogens and elevated the pathways associated with diseases linked to gut microbiota function. [Conclusion] Long-chain inulin supplementation, after antibiotic-induced severe gut microbiota dysbiosis, delayed the reconstruction of the gut microbiota and might led to potential adverse effects.

Abstract:[Objective] Now, there is no reports on colonization of intestinal bacteria in insects. Exploration for difference of intestinal bacterial structure and composition between two key time points (The starting point is 0-days and the steady point is 7-days after pupation) of intestinal bacterial colonization in Apis mellifera, deepening understanding of intestinal flora colonization in bees and even insects.[Methods] After pupation, five worker individuals were collected from each of the two time points. Samples of workers were dissected and then DNA of intestinal flora was extracted. High-throughput sequencing for the highly variable region of 16S rDNA of intestinal flora was implemented using illumine platform, and then diversity of intestinal flora was analyzed by bioinformatics. Intestinal flora showing the highest relative abundance at the two time points was statistically analyzed, as well as the relative abundance and composition of intestinal flora were compared. [Results] A total of 515156 quality sequences were obtained, with a total length of 227904953 bp and an average length of 442 bp. According to OTUs-based classification, intestinal bacteria of workers were classified into 34 phylum, 82 classes, 221 orders, 405 families and 799 genera, respectively. In addition, there was a significant difference between Alpha diversity index from the starting point and that from the end point of intestinal flora colonization in workers (ACE, P=0.0014; Chao, P=0.0013; Shannon, P=0.0003; Simpson, P=0.0028). It is found that the relative abundance of Lactobacillus, Gilliamella, Bifidobacterium and Snodgrassella increased significantly, and the relative abundance of Acinetobacter, escherichia-shigella, Sphingomonas, Bacteroides, Nesterenkonia and Thermus decreased significantly (P<0.05) in 7-days workers by comparing to 0-days workers. [Conclusion] Intestinal bacterial diversity of the newly emerged (0-day) adult A. mellifera was significantly higher than that of fully colonized (7-day) workers. The relative abundance of several intestinal bacteria in adult worker bees changed significantly after colonizing. Results of the study not only increase our understanding for colonization rules of intestinal bacteria in bee, and also provide important references for studying colonization rules of intestinal bacteria in other insects.

Abstract:[Objective] To reveal the mechanism underlying immune responses of Apis mellifera ligustica to Nosema ceranae stress at small RNA transcriptome level based on deep sequencing and omics analysis. [Methods] A. m. ligustica workers' midguts at 7 and 10 days post N. ceranae stress (Am7T, Am10T) and corresponding normal midguts (Am7CK, Am10CK) were sequenced using small RNA-seq. Related bioinformatic softwares were used to perform quality control of sequencing data, identification of known miRNAs and novel miRNAs and analysis of structural features of miRNAs. The expression of novel miRNAs was verified by Stem-loop RT-PCR. Differentially expressed miRNAs (DEmiRNAs) in Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups were screened out following the standards of|log₂(Fold change)| ≥ 1 and P ≤ 0.05. Target mRNAs of DEmiRNAs were predicted followed by annotation in GO and KEGG databases using softwares, based on annotation information, summary and investigation of cellular and humoral immune-associated pathways and enriched target mRNAs were conducted. Regulatory networks of DEmiRNAs and differentially expressed mRNAs (DEmRNAs) related to immune pathways were constructed according to target binding relationship. RT-qPCR was performed to validate the sequencing data and differential expression of DEmiRNAs. [Results] Here, 165895574 raw reads and 132028990 clean tags were yielded, and average Pearson correlation coefficients among different biological replicas in every group were above 87.92%. 928 known miRNAs and 56 novel miRNAs were identified. The length of these miRNAs was among 18-28 nt, with the most abundant length 18 nt and 22 nt; the first base of most miRNAs had a U bias. The true expression of 12 novel miRNAs was verified. 48 up-regulated miRNAs and 36 down-regulated miRNAs were identified in Am7CK vs. Am7T, while 56 up-regulated miRNAs and 51 down-regulated miRNAs were identified in Am10CK vs. Am10T. These DEmiRNAs can respectively target 9827 and 10720 mRNAs, involving in 50 and 47 functional terms and 138 and 135 pathways. Analysis of regulatory networks of DEmiRNAs and target mRNAs related to immune pathways showed 26 DEmiRNAs in Am7CK vs. Am7T could target 10 DEmRNAs such as endocytosis, whereas 15 DEmiRNAs in Am10CK vs. Am10T can target 10 immune-associated pathways including MAPK signaling pathway. The reliability of sequencing data and differential expression trend of four DEmiRNA was validated. [Conclusion] Host DEmiRNAs may response to N. ceranae through regulating material and energy metabolisms, as well as cellular and humoral immune, but might not regulate the expression of antimicrobial peptide-encoded genes; miR-1-z was likely to participate in cell proliferation, apoptosis and immune processes; oxidative phosphorylation pathway may play a special role in host immune response and host-pathogen interaction.

Abstract:[Objective] To study the effects of lariciresinol-4-beta-D-glucopyranoside on the growth and biofilm formation of Streptococcus mutans.[Methods] MTT[3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay was used to analyze the effects of lariciresinol-4-beta-D-glucopyranoside on the biofilm formation of Streptococcus mutans; oxygen sensitivity test was used to detect the effects of lariciresinol-4-beta-D-glucopyranoside on oxygen sensitivity of S. mutans; Realtime PCR was used to detect gene expression level. The cytotoxic of lariciresinol-4-beta-D-glucopyranoside was analyzed by using human monocytes. [Results] We found that lariciresinol-4-β-D-glucopyranoside could significantly inhibit the growth of S. mutans, and also suppress the biofilm formation of S. mutans in a concentration-dependent manner. And in lariciresinol-4-β-D-glucopyranoside-treated biofilms, we also found that the mRNA expression levels of brpA (transcriptional regulator), recA (recombinase A), nth (endonuclease III), luxS (S-ribosylhomocysteinase), ffh (fifty four homologue), smx (sulfamethoxazole), gtfB (glucosyltransferase-I) and gtfC (glucosyltransferase-SI) were all decreased. We further revealed that lariciresinol-4-β-D-glucopyranoside (50 μg/mL) had no effect on the growth and LDH activity of human monocytes. [Conclusion] Our findings suggested that lariciresinol-4-β-D-glucopyranoside inhibited the biofilm formation of S. mutans, and the decrease of luxS, brpA, ffh, recA, nth, smx, gtfB and gtfC might contribute to the antibacterial effects of lariciresinol-4-β-D-glucopyranoside.

Abstract:[Objective] Vibrio vulnificus is a pathogen with the highest mortality in Vibrio genus. However, currently there is lacking knowledge of virulence-associated factors across the whole genome wide for this species. By using bacterial genome-wide association study (BGWAS), we investigated the genes that are related with different sources (clinical/environment) of V. vulnificus isolates, aiming to provide further understanding on genetic factors that potentially influence its pathogenicity. [Methods] In total 260 V. vulnificus genomes were analyzed, including 139 newly sequenced in this study and 121 published genomes. We identified the genomes variations, including SNPs and accessory genes from the dataset, and then by using software pyseer, we determined the associations between sources of isolates and SNPs, genes, and Kmers, separately. We annotated the function of the statistically significant genes and inferred their possible influence on virulence of the bacteria. [Results] We found that 11 genes to be significantly correlated with clinical isolates of V. vulnificus, among which 9 were newly identified in this study.[Conclusion] By using methods of population genomics and statistical genetics, we screened the potential virulence-associated factors of V. vulnificus across the whole genome. Our findings provided new targets on vaccine designing and drug development, and would help to get further insight on pathogenic mechanism of this pathogen.

Abstract:[Objective] To explore the role of lipopolysaccharide in Avian pathogenic Escherichia coli (APEC). [Methods] By using λ-phage Red recombination system, we generated the lipid A biosynthesis associated genes lpxL and lpxM mutants E516ΔlpxL, E516ΔlpxM, E516ΔlpxLΔlpxM, E522ΔlpxL, E522ΔlpxM and E522ΔlpxLΔlpxM. We conducted a series of in vivo and in vitro assays to investigate their biological characteristics and pathogenicity. [Results] The growth rate of the strains was basically the same. The ability of resistance to serum and killing by chicken macrophages were significantly impaired, E516ΔlpxL, E516ΔlpxLΔlpxM, E522ΔlpxM and E522ΔlpxLΔlpxM were significantly attenuated than those of the wild-type strains, and E516ΔlpxM and E522ΔlpxL had no obvious difference in relation to their parent strains. LD₅₀ results show that the pathogenicity of mutants was significantly attenuated than those of the wild-type strains. The colonization and survival model demonstrated that the loads of mutants were significantly decreased compared with those of the wild-type strains in all bloods and organs tested in chickens. The ability of mutants to enter and survive in chicken macrophage HD-11 is significantly reduced compared with those of the parent strains. [Conclusion] These results indicated that lpxL and lpxM genes are critical to the pathogenicity of APEC E516 and E522, lpxL had a more significant effect on virulence of APEC E516, and lpxM gene on virulence of APEC E522.