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The environmental and physicochemical characteristics and fungal communities of two batches of Chinese Luzhou-flavored Daqu were investigated during the fermentation stage and storage period. The D...

BACKGROUND: Natamycin is an antibiotic which shows strong inhibition and wide spectrum against most fungi. It is produced mainly through batch and fed‐batch fermentations, which are characterized by long culture time, low productivity and enormous discharge of waste biomass. In the present study, a new strategy using immobilized cells was proposed for continuous natamycin production via repeated batch culture to address these shortcomings. RESULTS: A combination of cell immobilization and repeated batch culture was employed to continuously produce natamycin in both flasks and a 5‐L fermenter. The immobilized cells served as seeds and producing strains, and exhibited high vitality of cell growth and natamycin biosynthesis during six cycles of repeated batch culture. The application of the new strategy led to remarkable decrease of lag phase and removal of time intervals among traditional multiple batch cultures, resulting in a 32.10% reduction of total culture time. In addition, the new strategy showed 1.8‐fold higher natamycin titre and 195.24% productivity improvement relative to traditional strategies, and decreased waste biomass discharge, thus consituting a high‐efficiency, environmentally friendly strategy for natamycin production. CONCLUSION: This study proposes a new approach to continuous natamycin production, which not only promoted natamycin productivity, but also reduced the fermentation time and the biomass residue discharge. Moreover, it provides reference points for the continuous production of other biochemicals by filamentous bacteria or funguses, which could be of great significance in industrial antibiotics production. © 2019 Society of Chemical Industry

Bacteriocins have attracted increasing interest because of their potential as natural preservatives. Recent studies showed that the Bacillus cereus group is a prominent producer of bacteriocins. Using a laboratory-based screening strategy, we identified a strain in the B. cereus group, Bacillus toyonensis XIN-YC13, with antimicrobial activity against B. cereus. A novel, 70-amino-acid-long leaderless bacteriocin, toyoncin, was purified from the culture supernatant of strain XIN-YC13, and its molecular mass was found to be 7,817.1012 Da. Toyoncin shares no similarity with any other known bacteriocins, and its N-terminal amino acid is formylmethionine rather than methionine. Toyoncin shows good pH and heat stability and exhibits specific antimicrobial activity against two important foodborne pathogens, B. cereus and Listeria monocytogenes. Additionally, toyoncin exerts bactericidal activity and induces cell membrane damage. Toyoncin can also inhibit the outgrowth of B. cereus spores. Preservation assays showed that toyoncin effectively suppressed or eradicated B. cereus and L. monocytogenes in pasteurized skim milk. These results suggest that toyoncin can be used as a new biopreservative against B. cereus and L. monocytogenes in the food industry. IMPORTANCE We identified a novel leaderless bacteriocin, toyoncin, produced by B. toyonensis XIN-YC13. Toyoncin shows good pH and heat stability, and it has specific antimicrobial activity against B. cereus and L. monocytogenes (two important foodborne pathogens), likely by destroying their cell membrane integrity. Toyoncin inhibited the outgrowth of B. cereus spores and effectively inhibited or eliminated B. cereus and L. monocytogenes in a milk model system. These results indicate the potential of toyoncin as a food preservative.

More and more frequently, genomics and comparative genomics have been used as routine methods for general microbiological research. However, using several tools or even writing some scripts are required for completing a simple analysis, which is complicated for most biological researchers. To simplify the operation process, particularly for the convenience of microbiologists, here we have developed PGCGAP, a comprehensive, malleable, and easily installed prokaryotic genomic and comparative genomic analysis pipeline. PGCGAP implements genome assembly, gene prediction and annotation, genome and metagenome distance estimation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variant calling and annotation, and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformaticians to master it. Therefore, a protocol was created to help microbiologists without any experience in bioinformatics to establish their bioinformatics platform and perform routine analyses. This protocol shows how to choose the equipment to install a Linux subsystem on a laptop with a Windows 10 system, to install the PGCGAP and perform all analyses with an example dataset (This protocol applies to PGCGAP version 1.0.34 and later). The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (https://github.com/liaochenlanruo/pgcgap/wiki/Learning-bioinformatics or http://bcam.hzau.edu.cn/linuxwgs.php).

Consumer demand for “fresh food” with no chemical preservatives has prompted researchers to pay more attention to natural antimicrobial peptides such as bacteriocins. Nisin is currently the most widely used food biopreservative among the bacteriocins; however, its applications are restricted due to its low stability at neutral and alkaline pH values. Circular bacteriocins have potent antimicrobial activity against foodborne pathogens, show exceptional stability, and have great potential to be developed as biopreservatives. Here, we take advantage of the precursor peptides of 15 reported circular bacteriocins to devise an in silico approach to identify potential circular bacteriocins in sequenced microbial genomes. A total of nearly 7,000 putative precursor peptides were identified from 86 species of bacteria and further classified into 28 groups based on their amino acid similarity. Among the groups, 19 showed low similarity (less than 50%) to any known precursor peptide of circular bacteriocins. One novel circular bacteriocin in group 11, cerecyclin, showed the highest identity (34%) to the known circular bacteriocin enterocin NKR-5-3B and was selected for verification. Cerecyclin showed antimicrobial activity against several Gram-positive bacteria, inhibited the outgrowth of Bacillus cereus spores, and did not exhibit hemolysis activity. Moreover, it showed 4-fold- to 8-fold-higher antimicrobial activity against B. cereus and Listeria monocytogenes than nisin A. Cerecyclin also had increased stability compared to nisin A under neutral or alkaline conditions. This work not only identified a promising food biopreservative but also provided a rich source for novel circular bacteriocins. IMPORTANCE Circular bacteriocins are promising biopreservatives, and it is important to identify more novel circular bacteriocins to enhance the current arsenal of antimicrobials. In this study, we used an in silico approach to identify a large number of novel circular bacteriocins and classified these bacteriocins into 28 groups rather than the 2 groups that were described in previous studies. Nineteen groups were novel and had low similarity (less than 50%) to any known precursor peptides of circular bacteriocins; this finding greatly expands the awareness of the novelty and diversity of circular bacteriocins. A novel circular bacteriocin which we named cerecyclin was identified in the B. cereus group; this circular bacteriocin had great antimicrobial activity against some foodborne pathogens and showed extreme stability. This study not only identified a promising food biopreservative but also provided a rich source for the identification of novel circular bacteriocins and the development of new biopreservatives.

In recent years, bacteriocins have attracted considerable interest for use as natural food preservatives against spoilage and pathogenic microorganisms. Recent studies have shown that the strains of Bacillus cereus group produce a range of highly diverse bacteriocins. In this study, we screened a large number of Bacillus cereus group strains and isolated one strain, Bacillus sp. Xin1, with antimicrobial activity against several food-borne pathogens. A novel circular bacteriocin, bacicyclicin XIN-1 (MW: 5848.1719 Da), was purified from the culture supernatant of Bacillus sp. Xin1. This bacteriocin exhibited high thermal stability, wide pH tolerance, and a wide range of antimicrobial activities against Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus, three important foodborne pathogens, as well as other pathogens. Bacicyclicin XIN-1 also inhibited the outgrowth of Bacillus cereus spores and did not show hemolysis activity. Bacicyclicin XIN-1 effectively inhibited or eliminated B. cereus ATTCC14579, S. aureus ATCC6538, and L. monocytogenes LM201 in skim milk. Our findings indicate that bacicyclicin XIN-1 has a remarkable potential for use as a natural food preservative in the food industry.

Glucose, xylose, and fructose from biomass are renewable sources for glycerol production. Here, a TPI1 gene encoding triose phosphate isomerase (TPI) was identified in Kluyveromyces marxianus NBRC1777. The TPI1 gene was deleted in the KU70 defective K. marxianus, resulting in YZB115. YZB115 could grow with glucose, fructose, and xylose as sole carbon sources, which is contrary to the Saccharomyces cerevisiae TPI1 deletion strain. Under aerobic conditions, YZB115 fermented 80 g/L glucose, fructose, and xylose, producing 40.32, 41.84, and 18.64 g/L glycerol with productivities of 0.84, 0.50, and 0.22 g/L/h at 42 °C without by-product, respectively. The yields were about 0.5 g/g when hexoses were used, which is 98 % of the theoretical maximum. The yield decreased to 0.22 g/g when xylose was used. In summary, our study showed the potential of K. marxianus to produce glycerol and glycerol derivatives from cellulose, lignocellulosic, and inulin biomass at high temperature.

Lantibiotics are antimicrobial peptides with potential applications as the next generation of antimicrobials in the food industry and/or the pharmaceutical industry. Nisin has successfully been used as a food preservative for over 40 years, but its major drawback is its limited stability under neutral and alkaline pH conditions. To identify alternatives with better biochemical properties, we screened more than 100 strains of the Bacillus cereus group. Three novel lantibiotics, ticins A1 (4,062.98 Da), A3 (4,048.96 Da), and A4 (4,063.02 Da), which were highly thermostable (121°C for 30 min) and extremely pH tolerant (pH 2.0 to 9.0), were identified in Bacillus thuringiensis BMB3201. They all showed potent antimicrobial activities against all tested Gram-positive bacteria and greater activities than those of nisin A against Bacillus cereus and Listeria monocytogenes , two important foodborne pathogens. These three novel lantibiotics, with their extremely stable properties and potent antimicrobial activities, have the potential for use as biopreservatives.

Due to the rapidly increasing prevalence of multidrug-resistant bacterial strains, the need for new antimicrobial drugs to treat infections has become urgent. Bacteriocins, which are antimicrobial peptides of bacterial origin, are considered potential alternatives to conventional antibiotics and have attracted widespread attention in recent years. Among these bacteriocins, lantibiotics, especially two-component lantibiotics, exhibit potent antimicrobial activity against some clinically relevant Gram-positive pathogens and have potential applications in the pharmaceutical industry. In this study, we characterized a novel two-component lantibiotic termed thusin that consists of Thsα, Thsβ and Thsβ' (mutation of Thsβ, A14G) and that was isolated from a B. thuringiensis strain BGSC 4BT1. Thsα and Thsβ (or Thsβ') exhibit optimal antimicrobial activity at a 1:1 ratio and act sequentially to affect target cells, and they are all highly thermostable (100°C for 30 min) and pH tolerant (pH 2.0 to 9.0). Thusin shows remarkable efficacy against all tested Gram-positive bacteria and greater activities than two known lantibiotics thuricin 4A-4 and ticin A4, and one antibiotic vancomycin against various bacterial pathogens (Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus (MRSA), Staphylococcus sciuri, Enterococcus faecalis, and Streptococcus pneumoniae). Moreover, thusin is also able to inhibit the outgrowth of Bacillus cereus spores. The potent antimicrobial activity of thusin against some Gram-positive pathogens indicates that it has potential for the development of new drugs.

Lantibiotics are ribosomally synthesized peptides that contain multiple posttranslational modifications. Research on lantibiotics has increased recently, mainly due to their broad-spectrum antimicrobial activity, especially against some clinical Gram-positive pathogens. Many reports about various bacteriocins in the Bacillus cereus group have been published, but few were about lantibiotics. In this study, we identified 101 putative lanthipeptide gene clusters from 77 out of 223 strains of this group, and these gene clusters were further classified into 20 types according to their gene organization and the homologies of their functional genes. Among them, 18 types were novel and have not yet been experimentally verified. Two novel lantibiotics (thuricin 4A-4 and its derivative, thuricin 4A-4D) were identified in the type I-1 lanthipeptide gene cluster and showed activity against all tested Gram-positive bacteria. The mode of action of thuricin 4A-4 was studied, and we found that it acted as a bactericidal compound. The transcriptional analysis of four structural genes ( thiA1 , thiA2 , thiA3 , and thiA4 ) in the thuricin 4A gene cluster showed that only one structural gene, thiA4 , showed efficient transcription in the exponential growth phase; the other three structural genes did not. In addition, the putative transmembrane protein ThiI was responsible for thuricin 4A-4 immunity. Genome analysis and functional verification illustrated that B. cereus group strains were a prolific source of novel lantibiotics.