Genomic analysis of Bacillus subtilis lytic bacteriophage ϕNIT1 capable of obstructing natto fermentation carrying genes for the capsule-lytic soluble enzymes poly-γ-glutamate hydrolase and levanase

Genome, biology and stability of the Thurquoise phage – A new virus from the Bastillevirinae subfamily

Bacteriophages from the Bastillevirinae subfamily (Herelleviridae family) have proven to be effective against bacteria from the Bacillus genus including organisms from the B. cereus group, which cause food poisoning and persistent contamination of industrial installations. However, successful application of these phages in biocontrol depends on understanding of their biology and stability in different environments. In this study, we isolated a novel virus from garden soil in Wrocław (Poland) and named it ‘Thurquoise’. The genome of that phage was sequenced and assembled into a single continuous contig with 226 predicted protein-coding genes and 18 tRNAs. The cryo-electron microscopy revealed that Thurquoise has complex virion structure typical for the Bastillevirinae family. Confirmed hosts include selected bacteria from the Bacillus cereus group–specifically B. thuringiensis (isolation host) and B. mycoides, but susceptible strains display different efficiency of plating (EOP). The eclipse and latent periods of Thurquoise in the isolation host last ~ 50 min and ~ 70 min, respectively. The phage remains viable for more than 8 weeks in variants of the SM buffer with magnesium, calcium, caesium, manganese or potassium and can withstand numerous freeze–thaw cycles if protected by the addition of 15% glycerol or, to a lesser extent, 2% gelatine. Thus, with proper buffer formulation, this virus can be safely stored in common freezers and refrigerators for a considerable time. The Thurquoise phage is the exemplar of a new candidate species within the Caeruleovirus genus in the Bastillevirinae subfamily of the Herelleviridae family with a genome, morphology and biology typical for these taxa.

Co-production of levan with other high-value bioproducts: A review

Levan is a homopolysaccharide of fructose that has both scientific and industrial importance, with various applications in health, pharmaceutical, cosmetic and food industries. Despite its broad spectrum of uses, there are only a limited number of commercial levan sources due to the high costs related to its production. To make production economically viable, efforts have been concentrated on the selection of levan-producing microorganisms, the genetic manipulation of new strains, and the use of inexpensive agro-industrial byproducts as substrates. Another efficient strategy involves the concomitant synthesis of other products with high market value and as such, the successful co-production of levan was demonstrated with fructooligosaccharides, ethanol, sorbitol, poly-ε-lysine, poly-γ-glutamic acid and polyhydroxyalkanoates. This paper offers a systematic review of important aspects regarding recent strategies involving the simultaneous synthesis of levan and other bioproducts of aggregate value reported to date and discusses the challenges and opportunities for its large-scale production and applications.

Phage Adsorption to Gram-Positive Bacteria

The phage life cycle is a multi-stage process initiated by the recognition and attachment of the virus to its bacterial host. This adsorption step depends on the specific interaction between bacterial structures acting as receptors and viral proteins called Receptor Binding Proteins (RBP). The adsorption process is essential as it is the first determinant of phage host range and a sine qua non condition for the subsequent conduct of the life cycle. In phages belonging to the Caudoviricetes class, the capsid is attached to a tail, which is the central player in the adsorption as it comprises the RBP and accessory proteins facilitating phage binding and cell wall penetration prior to genome injection. The nature of the viral proteins involved in host adhesion not only depends on the phage morphology (i.e., myovirus, siphovirus, or podovirus) but also the targeted host. Here, we give an overview of the adsorption process and compile the available information on the type of receptors that can be recognized and the viral proteins taking part in the process, with the primary focus on phages infecting Gram-positive bacteria.

The role of virome in the gastrointestinal tract and beyond

The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.

Bacteriophage-Mediated Control of Biofilm: A Promising New Dawn for the Future

Biofilms are complex microbial microcolonies consisting of planktonic and dormant bacteria bound to a surface. The bacterial cells within the biofilm are embedded within the extracellular polymeric substance (EPS) consisting mainly of exopolysaccharides, secreted proteins, lipids, and extracellular DNA. This structural matrix poses a major challenge against common treatment options due to its extensive antibiotic-resistant properties. Because biofilms are so recalcitrant to antibiotics, they pose a unique challenge to patients in a nosocomial setting, mainly linked to lower respiratory, urinary tract, and surgical wound infections as well as the medical devices used during treatment. Another unique property of biofilm is its ability to adhere to both biological and man-made surfaces, allowing growth on human tissues and organs, hospital tools, and medical devices, etc. Based on prior understanding of bacteriophage structure, mechanisms, and its effects on bacteria eradication, leading research has been conducted on the effects of phages and its individual proteins on biofilm and its role in overall biofilm removal while also revealing the obstacles this form of treatment currently have. The expansion in the phage host-species range is one that urges for improvement and is the focus for future studies. This review aims to demonstrate the advantages and challenges of bacteriophage and its components on biofilm removal, as well as potential usage of phage cocktail, combination therapy, and genetically modified phages in a clinical setting.

Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

Diversity and Function of Phage Encoded Depolymerases

Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.

The Novel Enterococcus Phage vB_EfaS_HEf13 Has Broad Lytic Activity Against Clinical Isolates of Enterococcus faecalis

Enterococcus faecalis is a Gram-positive, facultative anaerobic bacterium frequently found in the gastrointestinal tract, oral cavity, and periodontal tissue. Although it is considered a commensal, it can cause bacteremia, endocarditis, endodontic infections, and urinary tract infections. Because antibiotics are cytotoxic not only to pathogens, but also to health-beneficial commensals, phage therapy has emerged as an alternative strategy to specifically control pathogenic bacteria with minimal damage to the normal flora. In this study, we isolated a novel phage, Enterococcus phage vB_EfaS_HEf13 (phage HEf13), with broad lytic activity against 12 strains of E. faecalis among the three laboratory strains and 14 clinical isolates of E. faecalis evaluated. Transmission electron microscopy showed that phage HEf13 has morphological characteristics of the family Siphoviridae. Phage HEf13 was stable at a wide range of temperature (4–60°C) and showed tolerance to acid or alkaline (pH 3–12) growth conditions. Phage HEf13 had a short latent period (25 min) with a large burst size (approximately 352 virions per infected cell). The lytic activity of phage HEf13 at various multiplicities of infection consistently inhibited the growth of diverse clinical isolates of E. faecalis without any lysogenic process. Moreover, phage HEf13 showed an effective lytic activity against E. faecalis on human dentin ex vivo infection model. Whole genome analysis demonstrated that the phage HEf13 genome contains 57,811 bp of double-stranded DNA with a GC content of 40.1% and 95 predicted open reading frames (ORFs). Annotated functional ORFs were mainly classified into four groups: DNA replication/packaging/regulation, phage structure, host cell lysis, and additional functions such as RNA transcription. Comparative genomic analysis demonstrated that phage HEf13 is a novel phage that belongs to the Sap6virus lineage. Furthermore, the results of multiple sequence alignment showed that polymorphism of phage infection protein of E. faecalis (PIP_EF) contributes to determine the host specificity of phage HEf13 against various E. faecalis strains. Collectively, these results suggest that phage HEf13 has characteristics of a lytic phage, and is a potential therapeutic agent for treatment or prevention of E. faecalis-associated infectious diseases.

Application of γ-PGA as the primary carbon source to bioremediate a TCE-polluted aquifer: A pilot-scale study

The effectiveness of using gamma poly-glutamic acid (γ-PGA) as the primary carbon and nitrogen sources to bioremediate trichloroethene (TCE)-contaminated groundwater was studied in this pilot-scale study. γ-PGA (40 L) solution was injected into the aquifer via the injection well (IW) for substrate supplement. Groundwater samples were collected from monitor wells and IW and analyzed for TCE and its byproducts, geochemical indicators, dechlorinating bacteria, and microbial diversity periodically. Injected γ-PGA resulted in an increase in total organic carbon (TOC) (up to 9820 mg/L in IW), and the TOC biodegradation caused the formation of anaerobic conditions. Increased ammonia concentration (because of amine release from γ-PGA) resulted in the neutral condition in groundwater, which benefited the growth of Dehalococcoides. The negative zeta potential and micro-scale diameter of γ-PGA allowed its globule to distribute evenly within soil pores. Up to 93% of TCE removal was observed (TCE dropped from 0.14 to 0.01 mg/L) after 59 days of γ-PGA injection, and TCE dechlorination byproducts were also biodegraded subsequently. Next generation sequence (NGS) analyses were applied to determine the dominant bacterial communities. γ-PGA supplement developed reductive dechlorinating conditions and caused variations in microbial diversity and dominant bacterial species. The dominant four groups of bacterial communities including dechlorinating bacteria, vinyl chloride degrading bacteria, hydrogen producing bacteria, and carbon biodegrading bacteria.

Significance of bacteriophages in fermented soybeans: A review

Bacteriophages are ubiquitous and have been reported to have been found in many food products. Their presence is important as they have the ability to interact with their bacterial host in food matrices. Fermented soybean products, one of the most widely consumed ethnic foods among Asian people, are prepared naturally and include Japanese Natto, Indian Kinema, Korean Chongkukjang and Thai Thua Nao. This review highlights bacteriophages which have been isolated from fermented soybean products and also includes an overview of their diversity, occurrence as well as their significance.

High prevalence of Bacillus subtilis-infecting bacteriophages in soybean-based fermented foods and its detrimental effects on the process and quality of Cheonggukjang

While the detrimental effect of bacteriophages on lactic acid bacterial fermentation is well documented, the importance of Bacillus subtilis phages in soybean-based fermented foods is not. In this study, we show for the first time that 100% of Korean soybean-based fermented foods (Doenjang, Gochujang, and Cheonggukjang) and 70% of raw materials (Meju and rice straw) were contaminated with B. subtilis-infecting phages (as high as 3.7 × 10⁴ PFU g^-1). Among 15 isolated B. subtilis-infecting phages, BSP18 was selected for further studies due to its specificity to and relatively broad host infectivity (34%) against B. subtilis. This Myoviridae family phage, BSP18 could infect all of the tested wild-type and commercially-used strains for soybean-based fermented food preparation. Furthermore, artificial contamination of as low as 10² PFU g^-1 of BSP18 significantly inhibited B. subtilis growth during Cheonggukjang fermentation. Moreover, phage-treated samples contained considerably more degraded γ-PGA which could negatively affect the functional property of Cheonggukjang. We also present the data, strongly suggesting BSP18-encoded, not bacterial, γ-PGA hydrolase was responsible for γ-PGA degradation. In conclusion, B. subtilis phages are widespread in Korean soybean-based fermented foods and it should be of great concern as phages may hamper the bacterial growth during fermentation and yield poor quality products.

Complete Nucleotide Sequence Analysis of a Novel Bacillus subtilis-Infecting Bacteriophage BSP10 and Its Effect on Poly-Gamma-Glutamic Acid Degradation

While the harmful effects of lactic acid bacterial bacteriophages in the dairy industry are well-established, the importance of Bacillus subtilis-infecting bacteriophages on soybean fermentation is poorly-studied. In this study, we isolated a B. subtilis-infecting bacteriophage BSP10 from Meju (a brick of dried fermented soybean) and further characterized it. This Myoviridae family bacteriophage exhibited a narrow host range against B. subtilis strains (17/52, 32.7%). The genome of bacteriophage BSP10 is 153,767 bp long with 236 open reading frames and 5 tRNAs. Comparative genomics (using dot plot, progressiveMauve alignment, heat-plot, and BLASTN) and phylogenetic analysis strongly suggest its incorporation as a new species in the Nit1virus genus. Furthermore, bacteriophage BSP10 was efficient in the growth inhibition of B. subtilis ATCC 15245 in liquid culture and in Cheonggukjang (a soybean fermented food) fermentation. Artificial contamination of as low as 10² PFU/g of bacteriophage BSP10 during Cheonggukjang fermentation significantly reduced bacterial numbers by up to 112 fold in comparison to the control (no bacteriophage). Moreover, for the first time, we experimentally proved that B. subtilis-infecting bacteriophage greatly enhanced poly-γ-glutamic acid degradation during soybean fermentation, which is likely to negatively affect the functionalities of Cheonggukjang.