The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.

Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.

Oxidative stress resistance prompts pyrroloquinoline quinone biosynthesis in Hyphomicrobium denitrificans H4-45.

Pyrroloquinoline quinone (PQQ) is a natural antioxidant with diverse applications in food and pharmaceutical industries. A lot of effort has been devoted toward the discovery of PQQ high-producing microbial species and characterization of biosynthesis, but it is still challenging to achieve a high PQQ yield. In this study, a combined strategy of random mutagenesis and adaptive laboratory evolution (ALE) with fermentation optimization was applied to improve PQQ production in Hyphomicrobium denitrificans H4-45. A mutant strain AE-9 was obtained after nearly 400 generations of UV-LiCl mutagenesis, followed by an ALE process, which was conducted with a consecutive increase of oxidative stress generated by kanamycin, sodium sulfide, and potassium tellurite. In the flask culture condition, the PQQ production in mutant strain AE-9 had an 80.4% increase, and the cell density increased by 14.9% when compared with that of the initial strain H4-45. Moreover, batch and fed-batch fermentation processes were optimized to further improve PQQ production by pH control strategy, methanol and H2O2 feed flow, and segmented fermentation process. Finally, the highest PQQ production and productivity of the mutant strain AE-9 reached 307 mg/L and 4.26 mg/L/h in a 3.7-L bioreactor, respectively. Whole genome sequencing analysis showed that genetic mutations in the ftfL gene and thiC gene might contribute to improving PQQ production by enhancing methanol consumption and cell growth in the AE-9 strain. Our study provided a systematic strategy to obtain a PQQ high-producing mutant strain and achieve high production of PQQ in fermentation. These practical methods could be applicable to improve the production of other antioxidant compounds with uncleared regulation mechanisms. KEY POINTS: • Improvement of PQQ production by UV-LiCl mutagenesis combined with adaptive laboratory evolution (ALE) and fermentation optimization. • A consecutive increase of oxidative stress could be used as the antagonistic factor for ALE to enhance PQQ production. • Mutations in the ftfL gene and thiC gene indicated that PQQ production might be increased by enhancing methanol consumption and cell growth.

Identification of animal species of origin in meat based on glycopeptide analysis by UPLC-QTOF-MS.

Adulteration of meat and meat products causes a concerning threat for consumers. It is necessary to develop novel robust and sensitive methods which can authenticate the origin of meat species to compensate for the drawbacks of existing methods. In the present study, the sarcoplasmic proteins of six meat species, namely, pork, beef, mutton, chicken, duck and turkey, were analyzed by one-dimensional gel electrophoresis. It was found that enolase could be used as a potential biomarker protein to distinguish between livestock and poultry meats. The glycosylation sites and glycans of enolase were analyzed by UPLC-QTOF-MS and a total of 41 glycopeptides were identified, indicating that the enolase N-glycopeptide profiles of different meats were species-specific. The identification models of livestock meat, poultry and mixed animal were established based on the glycopeptide contents, and the explanation degree of the three models was higher than 90%. The model prediction performance and feasibility results showed that the average prediction accuracy of the three models was 75.43%, with the animal-derived meat identification model showing superiority in identifying more closely related species. The obtained results indicated that the developed strategy was promising for application in animal-derived meat species monitoring and the quality supervision of animal-derived food.

Characterization of antifungal cyclic dipeptides of Lacticaseibacillus paracasei ZX1231 and active packaging film prepared with its cell-free supernatant and bacterial nanocellulose.

Fungal infection and/or spoilage are major concerns of crop and food security worldwide, prompting the developments and application of various antimicrobial agents. In this study, nine strains of lactic acid bacteria (LAB) with antifungal activities were isolated from the traditional Chinese fermented wort of Meigui rice vinegar, where fungi coexist. The cell-free supernatant (CFS) of Lacticaseibacillus paracasei ZX1231 exhibited significant inhibitory activities against Aspergillus niger, Penicillium citrinum, Penicillium polonicum, Zygosaccharomyces rouxii, Talaromyces rubrifaciens, and Candida albicans. Among the four cyclic dipeptides (CDPs) uncovered from the CFS, cyclo(Phe-Leu) and cyclo(Anthranily-Pro) were found in the family Lactobacillaceae for the first time, which inhibited the C. albicans filamentation by targeting upon RAS1-cAMP-PKA pathway. CFS antifungal activities were optimally combined with a bacterial nanocellulose (BNC) matrix to prepare the active quality packaging CFS-BNC films. The challenge tests confirmed that CFS-BNC films significantly inhibited the fungi growth and thus prolonged the shelf life of bread, beef, cheese and soy sauce. L. paracasei ZX1231, its CFS, and the CFS-BNC film may have extensive applications in food preservation and food packaging.

Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin-antitoxin system, and linkage with CRISPR-Cas system.

Acetobacter is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with Acetobacter, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in Acetobacter. Here, prophage prediction analysis using 148 available genomes from 34 Acetobacter species was carried out. In addition, the type II toxin-antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order Caudovirales dominated by the families Siphoviridae and Myroviridae prophages (71.4%). Notably, Acetobacter strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. Acetobacter prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in Acetobacter aceti, while the other Acetobacter species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of Acetobacter.

Dermatan sulfate and chondroitin sulfate from Lophius litulon alleviate the allergy sensitized by major royal jelly protein 1.

The objective of the present study was to explore the desensitization effect of dermatan sulfate (DS) and chondroitin sulfate (CS) from Lophius litulon (Ll) on mice sensitized by major royal jelly protein 1 (MRJP1). First, the affinity between six glycosaminoglycans and the MRJP1 polyclonal antibody was measured by the ELISA method. Lophius litulon dermatan sulfate (Ll DS) and Lophius litulon chondroitin sulfate (Ll CS) were selected due to their highest binding affinity. Second, the molecular docking method was used to explore the interaction between Ll DS and MRJP1 and Ll CS and MRJP1. The results showed that Ll DS and Ll CS combined with MRJP1 successfully, which meant a potential function of relieving the MRJP1-caused allergy. Finally, the MRJP1-sensitized mice model was established and confirmed that Ll DS and Ll CS had the desensitization ability to relieve MRJP1-induced allergic symptoms. To validate the conclusion, the relief of allergic symptoms in mice was observed. The production of total IgE, MRJP1-specific IgE and histamine was measured. The desensitization mechanism was further studied by measuring cytokines (IL-4 and IFN-γ) from splenocytes stimulated with MRJP1 in vitro. Based on in vivo and in vitro experiments, it was confirmed that Ll DS and Ll CS have the ability to alleviate MRJP1-induced allergic symptoms, which proposes a potential candidate material against IgE-mediated food allergy.

Genetic Regulation of Mycotoxin Biosynthesis.

Mycotoxin contamination in food poses health hazards to humans. Current methods of controlling mycotoxins still have limitations and more effective approaches are needed. During the past decades of years, variable environmental factors have been tested for their influence on mycotoxin production leading to elucidation of a complex regulatory network involved in mycotoxin biosynthesis. These regulators are putative targets for screening molecules that could inhibit mycotoxin synthesis. Here, we summarize the regulatory mechanisms of hierarchical regulators, including pathway-specific regulators, global regulators and epigenetic regulators, on the production of the most critical mycotoxins (aflatoxins, patulin, citrinin, trichothecenes and fumonisins). Future studies on regulation of mycotoxins will provide valuable knowledge for exploring novel methods to inhibit mycotoxin biosynthesis in a more efficient way.

Structural Property, Immunoreactivity and Gastric Digestion Characteristics of Glycated Parvalbumin from Mandarin Fish (Siniperca chuaisi) during Microwave-Assisted Maillard Reaction.

This study was aimed to investigate the structural and immunological properties of parvalbumin from mandarin fish during the Maillard reaction. The microwave-assisted the Maillard reaction was optimized by orthogonal designed experiments. The results showed that the type of sugar and heating time had a significant effect on the Maillard reaction (p < 0.05). The SDS-PAGE analysis displayed that the molecular weight of parvalbumin in mandarin fish changed after being glycated with the Maillard reaction. The glycated parvalbumin was analyzed by Nano-LC-MS/MS and eleven glycation sites as well as five glycation groups were identified. By using the indirect competitive ELISA method, it was found that microwave heating gave a higher desensitization ability of mandarin fish parvalbumin than induction cooker did. In vitro gastric digestion experiments showed that microwave-heated parvalbumin was proved to be digested more easily than that cooked by induction cookers. The microwave-assisted Maillard reaction modified the structure of parvalbumin and reduced the immunoreactivity of parvalbumin of mandarin fish.

Mechanistic insights into the inhibitory effect of theaflavins on virulence factors production in Streptococcus mutans.

Streptococcus mutans is the primary etiological agent associated with cariogenic process. The present study aimed to investigate the antibacterial and anti-virulence activities of theaflavins (TFs) to Streptococcus mutans UA159 as well as the underlying mechanisms. The results showed that TFs were capable of suppressing the acid production, cell adherence, water-insoluble exopolysaccharides production, and biofilm formation by S. mutans UA159 with a dosage-dependent manner while without influencing the cell growth. By a genome-wide transcriptome analysis (RNA-seq), we found that TFs attenuated the biofilm formation of S. mutans UA159 by inhibiting glucosyltransferases activity and the production of glucan-binding proteins (GbpB and GbpC) instead of directly blocking the expression of genes coding for glucosyltransferases. Further, TFs inhibited the expression of genes implicated in peptidoglycan synthesis, glycolysis, lipid synthesis, two-component system, signaling peptide transport (comA), oxidative stress response, and DNA replication and repair, suggesting that TFs suppressed the virulence factors of S. mutans UA159 by affecting the signal transduction and cell envelope stability, and weakening the ability of cells on oxidative stress resistance. In addition, an upregulated expression of the genes involved in protein biosynthesis, amino acid metabolism, and transport system upon TFs treatment indicated that cells increase the protein synthesis and nutrients uptake as one self-protective mechanism to cope with stress caused by TFs. The results of this study increase our current understanding of the anti-virulence activity of TFs on S. mutans and provide clues for the use of TFs in the prevention of dental caries.

Impacts of type II toxin-antitoxin systems on cell physiology and environmental behavior in acetic acid bacteria.

Acetic acid bacteria (AAB) are a group of Gram-negative and strictly aerobic microorganisms widely used in vinegar industry, especially the species belonging to the genera Acetobacter and Komagataeibacter. The environments inhabited by AAB during the vinegar fermentation, in particular those natural traditional bioprocesses, are complex and dynamically changed, usually accompanied by diverse microorganisms, bacteriophages, and the increasing acetic acid concentration. For this reason, how AAB survive to such harsh niches has always been an interesting research field. Previous omic analyses (e.g., genomics, proteomics, and transcriptomics) have provided abundant clues for the metabolic pathways and bioprocesses indispensable for the acid stress adaptation of AAB. Nevertheless, it is far from fully understanding what factors regulate these modular mechanisms overtly and covertly upon shifting environments. Bacterial toxin-antitoxin systems (TAS), usually consisting of a pair of genes encoding a stable toxin and an unstable antitoxin that is capable of counteracting the toxin, have been uncovered to have a variety of biological functions. Recent studies focusing on the role of TAS in Acetobacter pasteurianus suggest that TAS contribute substantially to the acid stress resistance. In this mini review, we discuss the biological functions of type II TAS in the context of AAB with regard to the acid stress resistance, persister formation and resuscitation, genome stability, and phage immunity. KEY POINTS: • Type II TAS act as regulators in the acid stress resistance of AAB. • Type II TAS are implicated in the formation of acid-tolerant persister cells in AAB. • Type II TAS are potential factors responsible for phage immunity and genome stability.

Tooth brushing using toothpaste containing theaflavins reduces the oral pathogenic bacteria in healthy adults.

Theaflavins (TFs) are the main bioactive component in black tea. At present, little effort has been done to evaluate the influence of TFs when included in the toothpaste on the diversity of oral microbiota. In this study, eighty samples collected from the saliva and supragingival plaque of 20 healthy adults using toothpaste with the absence or presence of TFs for a period of 4 weeks were used for the oral microbiome analysis by 16S rRNA gene sequencing. Alpha and beta diversity analysis showed that tooth brushing using the toothpaste with TFs significantly increased the microbial abundance in the saliva samples, and altered the oral microbiota obtained from the saliva and supragingival plaque. The linear discriminant analysis revealed that the use of toothpaste with TFs significantly reduced the abundance of oral pathogens (e.g., Prevotella, Selenomonas, and Atopobium) while increased the abundance of oral-health associated bacteria (e.g., Streptococcus and Rothia). In addition, using toothpaste with TFs reduced the functional pathways abundance relevance to the extracellular polymeric substance (EPS) synthesis while enriched the functions in transporters, ABC transporters, two-component system, and amino acid metabolism. Collectively, our results provide evidence for the application of toothpaste containing TFs as a promising oral care product. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02699-7.

New insights into the antibacterial and quorum sensing inhibition mechanism of Artemisia argyi leaf extracts towards Pseudomonas aeruginosa PAO1.

This study aimed to investigate the anti-quorum sensing (QS) activity of Artemisia argyi leaf extracts (AALE) towards Pseudomonas aeruginosa PAO1 as well as the underlying molecular mechanisms. Using a biosensor Chromobacterium violaceum CV026, AALE were found to have anti-QS activity as AALE treatment significantly inhibited the violacein production of C. violaceum CV026 while produced little effect on the cell growth. Beyond that a higher dosage of AALE inhibited cell growth, sub-MIC of AALE significantly reduced the production of QS-regulated virulence factors (pyocyanin, elastase, and rhamnolipid), biofilm formation, and the swarming and swimming motility in P. aeruginosa PAO1 with a dosage-dependent manner. Quantitative real-time PCR (qRT-PCR) analysis did not detect the direct inhibitory effect of AALE on the expression of QS genes (lasI, lasR, rhlI, and rhlR). By iTRAQ-based quantitative proteomic analysis, 129 proteins were found to be differentially expressed upon AALE treatment, with 85 upregulated and 44 downregulated proteins, respectively. Functional enrichment analysis of the differential proteins revealed that AALE exerted anti-QS activity towards P. aeruginosa PAO1 by upregulating the expression of the global regulator CsrA, inducing oxidative stress, and perturbing protein homeostasis. Moreover, the inhibitory effect of AALE on the virulence of P. aeruginosa PAO1 was likely to be achieved by attenuating the expression of QS-regulated genes instead of QS genes. Collectively, the results of this study provide a basis for the future use of AALE as a preservative in controlling food spoilage caused by P. aeruginosa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02663-5.

Toxin-antitoxin HicAB regulates the formation of persister cells responsible for the acid stress resistance in Acetobacter pasteurianus.

Elucidation of the acetic acid resistance (AAR) mechanisms is of great significance to the development of industrial microbial species, specifically to the acetic acid bacteria (AAB) in vinegar industry. Currently, the role of population heterogeneity in the AAR of AAB is still unclear. In this study, we investigated the persister formation in AAB and the physiological role of HicAB in Acetobacter pasteurianus Ab3. We found that AAB were able to produce a high level of persister cells (10-2 to 100 in frequency) in the exponential-phase cultures. Initial addition of acetic acid and ethanol reduced the ratio of persister cells in A. pasteurianus by promoting the intracellular ATP level. Further, we demonstrated that HicAB was an important regulator of AAR in A. pasteurianus Ab3. Strains lacking hicAB showed a decreased survival under acetic acid exposure. Deletion of hicAB significantly diminished the acetic acid production, acetification rate, and persister formation in A. pasteurianus Ab3, underscoring the correlation between hicAB, persister formation, and acid stress resistance. By transcriptomic analysis (RNA-seq), we revealed that HicAB contributed to the survival of A. pasteurianus Ab3 under high acid stress by upregulating the expression of genes involved in the acetic acid over-oxidation and transport, 2-methylcitrate cycle, and oxidative phosphorylation. Collectively, the results of this study refresh our current understanding of the AAR mechanisms in A. pasteurianus, which may facilitate the development of novel ways for improving its industrial performance and direct the scaled-up vinegar production. KEY POINTS: • AAB strains form persister cells with different frequencies. • A. pasteurianus are able to form acid-tolerant persister cells. • HicAB contributes to the AAR and persister formation in A. pasteurianus Ab3.

Transcriptome response of Acetobacter pasteurianus Ab3 to high acetic acid stress during vinegar production.

Acetic acid accumulation is a universal limiting factor to the vinegar manufacture because of the toxic effect of acetic acid on the acid producing strain, such as Acetobacter pasteurianus. In this study, we aimed to investigate the genome-wide transcriptional response of A. pasteurianus Ab3 to high acid stress during vinegar production. By comparing the transcriptional landscape of cells harvested from a long-term cultivation with high acidity (70 ± 3 g/L) to that of low acidity (10 ± 2 g/L), we demonstrated that 1005 genes were differentially expressed. By functional enrichment analysis, we found that the expression of genes related to the two-component systems (TCS) and toxin-antitoxin systems (TAS) was significantly regulated under high acid stress. Cells increased the genome stability to withstand the intracellular toxicity caused by the acetic acid accumulation by repressing the expression of transposases and integrases. Moreover, high acid stress induced the expression of genes involved in the pathways of peptidoglycan, ceramide, and phosphatidylcholine biosynthesis as well as the Tol-Pal and TonB-ExbB systems. In addition, we observed that cells increased and diversified the ATP production to resist high acid stress. Transcriptional upregulation in the pathways of pyrroloquinoline quinone (PQQ) synthesis and thiamine metabolism suggested that cells may increase the production of prosthetic groups to ensure the enzyme activity upon high acid stress. Collectively, the results of this study increase our current understanding of the acetic acid resistance (AAR) mechanisms in A. pasteurianus and provide opportunities for strain improvement and scaled-up vinegar production.Key Points• TCS and TAS are responsive to the acid stress and constitute the regulating networks.• Adaptive expression changes of cell envelope elements help cell resist acid stress.• Cells promote genome stability and diversify ATP production to withstand acid stress.

Investigation of lipid profile in Acetobacter pasteurianus Ab3 against acetic acid stress during vinegar production.

Elucidation of the acetic acid resistance (AAR) mechanisms of Acetobacter pasteurianus is significant for vinegar production. In this study, cell membrane lipid profile of A. pasteurianus Ab3 was investigated by gas chromatography-mass spectrometer (GC-MS) and high performance liquid chromatography-electrospray ionization (HPLC-ESI) combined with high resolution accurate mass/mass spectrometry (HRAM/MS). We observed that cell remodeled the membrane physical state by decreasing the ratio of saturated fatty acids (SFAs)/unsaturated fatty acids (UFAs), and increasing the chain length of fatty acids (FAs) and the content of cyclopropane FAs in response to extreme acid stress. Noticeably, the content of octadecadienoic acid (C18:2) elevated remarkably. Moreover, a continuous reduction in cell membrane fluidity and a "V-type" variance in permeability were discovered. The content of glycerophospholipid and ceramide increased significantly in cells harvested from culture with acidity of 75 g/L and 95 g/L compared to that with acidity of 30 g/L. Among the identified lipid species, the content of phosphatidylcholine (e.g. PC 19:0/18:2 and 19:1/18:0), ceramide (e.g. Cer d18:0/16:1 and d18:0/16:1 + O), and dimethylphosphatidylethanolamine (e.g. dMePE 19:1/16:1) increased notably with increasing acidity. Collectively, these findings refresh our current understanding of the AAR mechanisms in A. pasteurianus Ab3, and should direct future strain breeding and vinegar fermentation.

Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917.

Toxin-antitoxin systems (TASs) have attracted much attention due to their important physiological functions. These small genetic factors have been widely studied mostly in commensal Escherichia coli strains, whereas the role of TASs in the probiotic E. coli Nissle 1917 (EcN) is still elusive. Here, the physiological role of chromosomally encoded type II TASs in EcN was examined. We showed that gene pair ECOLIN_00240-ECOLIN_00245 and ECOLIN_08365-ECOLIN_08370 were two functional TASs encoding CcdAB and HipAB, respectively. The homologs of CcdAB and HipAB were more conserved in E. coli species belonging to pathogenic groups, suggesting their important roles in EcN. CRISPRi-mediated repression of ccdAB and hipAB significantly reduced the biofilm formation of EcN in the stationary phase. Moreover, ccdAB and hipAB were shown to be responsible for the persister formation in EcN. Biofilm and persister formation of EcN controlled by the ccdAB and hipAB were associated with the expression of genes involved in DNA synthesis, SOS response, and stringent response. Besides, CRISPRi was proposed to be an efficient tool in annotating multiple TASs simultaneously. Collectively, our results advance knowledge and understanding of the role of TASs in EcN, which will enhance the utility of EcN in probiotic therapy.Key points• Two TASs in EcN were identified as hipAB and ccdAB.• Knockdown of HipAB and CcdAB resulted in decreased biofilm formation of EcN.• Transcriptional silencing of hipAB and ccdAB affected the persister formation of EcN.• An attractive link between TASs and stress response was unraveled in EcN.• CRISPRi afforded a fast and in situ annotation of multiple TASs simultaneously.

Comparative Genomic Analyses Reveal a Specific Mutation Pattern Between Human Coronavirus SARS-CoV-2 and Bat-CoV RaTG13.

BACKGROUND: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, rapidly grew into a global pandemic. How SARS-CoV-2 evolved remains unclear. METHODS: We performed a comprehensive analysis using the available genomes of SARS-CoV-2 and its closely related coronaviruses. RESULTS: The ratio of nucleotide substitutions to amino acid substitutions of the spike gene (9.07) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was markedly higher than that between other coronaviruses (range, 1.29-4.81); the ratio of non-synonymous to synonymous substitution rates (dN/dS) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was the lowest among all the performed comparisons, suggesting evolution under stringent selective pressure. Notably, the relative proportion of the T:C transition was markedly higher between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 than between other compared coronaviruses. Codon usage is similar across these coronaviruses and is unlikely to explain the increased number of synonymous mutations. Moreover, some sites of the spike protein might be subjected to positive selection. CONCLUSIONS: Our results showed an increased proportion of synonymous substitutions and the T:C transition between SARS-CoV-2 and RaTG13. Further investigation of the mutation pattern mechanism would contribute to understanding viral pathogenicity and its adaptation to hosts.

Characterization and comparative analysis of toxin-antitoxin systems in Acetobacter pasteurianus.

Bacterial toxin-antitoxin (TA) systems play important roles in diverse cellular regulatory processes. Here, we characterize three putative type II TA candidates from Acetobacter pasteurianus and investigate the profile of type II TA systems in the genus Acetobacter. Based on the gene structure and activity detection, two-pairs loci were identified as the canonical hicAB and higAB TA systems, respectively, and DB34_01190-DB34_01195 as a putative new one without a canonical TA architecture. Physiologically, the expression of the three pairs conferred E. coli with additional plasmid maintenance and survival when under acetic acid stress. Chromosomal TA systems can be horizontally transferred within an ecological vinegar microbiota by co-option, and there was a tendency for toxin module loss. The antitoxin retention in the genome is suggested to have a broad role in bacterial physiology. Furthermore, A. pasteurianus strains, universally domesticated and used for industrial vinegar fermentation, showed a higher number of type II TA loci compared to the host-associated ones. The amount of TA loci per genome showed little positive relationship to insertion sequences, although its prevalence was species-associated, to the extent of even being strain-associated. The TA system is a candidate of studying the resistant mechanistic network, the TAs-dependent translatome affords a real-time profile to explore stress adaptation of A. pasteurianus, promoting industrial development.

Chloride-accelerated Cu-Fenton chemistry for biofilm removal.

Biofilms present challenges to numerous industries. Herein, a simple approach was developed based on chloride-accelerated Fenton chemistry, where copper oxide nanoparticles facilitate efficient generation of reactive chlorine species for biofilm removal.

A comparative secretome analysis of industrial Aspergillus oryzae and its spontaneous mutant ZJGS-LZ-21.

Aspergillus oryzae koji plays a crucial role in fermented food products due to the hydrolytic activities of secreted enzymes. In the present study, we performed a comparative secretome analysis of the industrial strain of Aspergillus oryzae 3.042 and its spontaneous mutantZJGS-LZ-21. One hundred and fifty two (152) differential protein spots were excised (p<0.05), and 25 proteins were identified. Of the identified proteins, 91.3% belonged to hydrolytic enzymes acting on carbohydrates or proteins. Consistent with their enzyme activities, the expression of 14 proteins involved in the degradation of cellulose, hemicellulose, starch and proteins, increased in the ZJGS-LZ-21isolate. In particular, increased levels of acid protease (Pep) may favor the degradation of soy proteins in acidic environments and promote the cleavage of allergenic soybean proteins in fermentation, resulting in improvements of product safety and quality. The ZJGS-LZ-21 isolate showed higher protein secretion and increased hydrolytic activities than did strain 3.042, indicating its promising application in soybean paste fermentation.