Anaerobic growth of a "strict aerobe" (Bacillus subtilis)

Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis

Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.

Development of a Microbioreactor for Bacillus subtilis Biofilm Cultivation

To improve our understanding of Bacillus subtilis growth and biofilm formation under different environmental conditions, two versions of a microfluidic reactor with two channels separated by a polydimethylsiloxane (PDMS) membrane were developed. The gas phase was introduced into the channel above the membrane, and oxygen transfer from the gas phase through the membrane was assessed by measuring the dissolved oxygen concentration in the liquid phase using a miniaturized optical sensor and oxygen-sensitive nanoparticles. B. subtilis biofilm formation was monitored in the growth channels of the microbioreactors, which were designed in two shapes: one with circular extensions and one without. The volumes of these microbioreactors were (17 ± 4) μL for the reactors without extensions and (28 ± 4) μL for those with extensions. The effect of microbioreactor geometry and aeration on B. subtilis biofilm growth was evaluated by digital image analysis. In both microbioreactor geometries, stable B. subtilis biofilm formation was achieved after 72 h of incubation at a growth medium flow rate of 1 μL/min. The amount of oxygen significantly influenced biofilm formation. When the culture was cultivated with a continuous air supply, biofilm surface coverage and biomass concentration were higher than in cultivations without aeration or with a 100% oxygen supply. The channel geometry with circular extensions did not lead to a higher total biomass in the microbioreactor compared to the geometry without extensions.

Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts

Thermophilic acetogenic bacteria have attracted attention as promising candidates for biotechnological applications such as syngas fermentation, microbial electrosynthesis, and methanol conversion. Here, we aimed to isolate and characterize novel thermophilic acetogens from diverse environments. Enrichment of heterotrophic and autotrophic acetogens was monitored by 16S rRNA gene-based bacterial community analysis. Seven novel Moorella strains were isolated and characterized by genomic and physiological analyses. Two Moorella humiferrea isolates showed considerable differences during autotrophic growth. The M. humiferrea LNE isolate (DSM 117358) fermented carbon monoxide (CO) to acetate, while the M. humiferrea OCP isolate (DSM 117359) transformed CO to hydrogen and carbon dioxide (H2 + CO2), employing the water-gas shift reaction. Another carboxydotrophic hydrogenogenic Moorella strain was isolated from the covering soil of an active charcoal burning pile and proposed as the type strain (ACPsT) of the novel species Moorella carbonis (DSM 116161T and CCOS 2103T). The remaining four novel strains were affiliated with Moorella thermoacetica and showed, together with the type strain DSM 2955T, the production of small amounts of ethanol from H2 + CO2 in addition to acetate. The physiological analyses of the novel Moorella strains revealed isolate-specific differences that considerably increase the knowledge base on thermophilic acetogens for future applications.

Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution

The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.

Membrane depolarization kills dormant Bacillus subtilis cells by generating a lethal dose of ROS

The bactericidal activity of several antibiotics partially relies on the production of reactive oxygen species (ROS), which is generally linked to enhanced respiration and requires the Fenton reaction. Bacterial persister cells, an important cause of recurring infections, are tolerant to these antibiotics because they are in a dormant state. Here, we use Bacillus subtilis cells in stationary phase, as a model system of dormant cells, to show that pharmacological induction of membrane depolarization enhances the antibiotics' bactericidal activity and also leads to ROS production. However, in contrast to previous studies, this results primarily in production of superoxide radicals and does not require the Fenton reaction. Genetic analyzes indicate that Rieske factor QcrA, the iron-sulfur subunit of respiratory complex III, seems to be a primary source of superoxide radicals. Interestingly, the membrane distribution of QcrA changes upon membrane depolarization, suggesting a dissociation of complex III. Thus, our data reveal an alternative mechanism by which antibiotics can cause lethal ROS levels, and may partially explain why membrane-targeting antibiotics are effective in eliminating persisters.

Bacillus spp. as potential probiotics: promoting piglet growth by improving intestinal health

The application of Bacillus spp. as probiotics in the swine industry, particularly for piglet production, has garnered significant attention in recent years. This review aimed to summarized the role and mechanisms of Bacillus spp. in promoting growth and maintaining gut health in piglets. Bacillus spp. can enhance intestinal barrier function by promoting the proliferation and repair of intestinal epithelial cells and increasing mucosal barrier integrity, thereby reducing the risk of pathogenic microbial invasion. Additionally, Bacillus spp. can activate the intestinal immune system of piglets, thereby enhancing the body's resistance to diseases. Moreover, Bacillus spp. can optimize the gut microbial community structure, enhance the activity of beneficial bacteria such as Lactobacillus, and inhibit the growth of harmful bacteria such as Escherichia coli, ultimately promoting piglet growth performance and improving feed efficiency. Bacillus spp. has advantages as well as challenges as an animal probiotic, and safety evaluation should be conducted when using the newly isolated Bacillus spp. This review provides a scientific basis for the application of Bacillus spp. in modern piglet production, highlighting their potential in improving the efficiency of livestock production and animal welfare.

BacteSign: Building a Findable, Accessible, Interoperable, and Reusable (FAIR) Database for Universal Bacterial Identification

With the increasing incidence of diverse global bacterial outbreaks, it is important to build an immutable decentralized database that can capture regional changes in bacterial resistance with time. Herein, we investigate the use of a rapid 3D printed µbiochamber with a laser-ablated interdigitated electrode developed for biofilm analysis of Pseudomonas aeruginosa, Acinetobacter baumannii and Bacillus subtilis using electrochemical biological impedance spectroscopy (EBIS) across a 48 h spectrum, along with novel ladder-based minimum inhibitory concentration (MIC) stencil tests against oxytetracycline, kanamycin, penicillin G and streptomycin. Furthermore, in this investigation, a search query database has been built demonstrating the deterministic nature of the bacterial strains with real and imaginary impedance, phase, and capacitance, showing increased bacterial specification selectivity in the 9772.37 Hz range.

Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring

In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.

Collibacillus ludicampi gen. nov., sp. nov., a new soil bacterium of the family Alicyclobacillaceae

A novel moderately thermophilic aerobic bacterium, strain TP075T, was isolated from soil collected from an athletic field in Japan. Strain TP075T is a rod-shaped, aerobic bacterium that forms terminal endospores. The KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH and temperature were 4.0–5.0 and 47–50 °C, respectively. Draft genome sequencing showed that the G+C content of genomic DNA was 46.5 mol%. Branched-chain fatty acids (iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0) were the major components of the cellular fatty acid profile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain TP075T belongs to the family Alicyclobacillaceae , with the highest similarity to Effusibacillus consociatus CCUG53762T (92.6%) and Tumebacillus soil CAU11108T (92.5%). Genome-based analyses indicated that strain TP075T and the most closely related strain, Effusibacillus pohliae DSM 22757T, share an average amino acid identity value of 62.57% and an average nucleotide identity value of 70.86 %. The results obtained in this study suggest that strain TP075T represents a novel species of a novel genus, for which we propose the name Collibacillus ludicampi gen. nov., sp. nov. with type strain TP075T (= JCM 34430T=TBRC 15189T).

Anode-assisted electro-fermentation with Bacillus subtilis under oxygen-limited conditions

BACKGROUND

Bacillus subtilis is generally regarded as a ubiquitous facultative anaerobe. Oxygen is the major electron acceptor of B. subtilis, and when oxygen is absent, B. subtilis can donate electrons to nitrate or perform fermentation. An anode electrode can also be used by microorganisms as the electron sink in systems called anodic electro-fermentation. The facultative anaerobic character of B. subtilis makes it an excellent candidate to explore with different electron acceptors, such as an anode. This study aimed to optimise industrial aerobic bioprocesses using alternative electron acceptors. In particular, different end product spectrum of B. subtilis with various electron acceptors, including anode from the electro-fermentation system, was investigated.

RESULTS

B. subtilis was grown using three electron acceptors, i.e. oxygen, nitrate and anode (poised at a potential of 0.7 V vs. standard hydrogen electrode). The results showed oxygen had a crucial role for cells to remain metabolically active. When nitrate or anode was applied as the sole electron acceptor anaerobically, immediate cell lysis and limited glucose consumption were observed. In anode-assisted electro-fermentation with a limited aeration rate, acetoin, as the main end product showed the highest yield of 0.78 ± 0.04 mol_product/mol_glucose, two-fold higher than without poised potential (0.39 ± 0.08 mol_product/mol_glucose).

CONCLUSIONS

Oxygen controls B. subtilis biomass growth, alternative electron acceptors utilisation and metabolites formation. Limited oxygen/air supply enabled the bacteria to donate excess electrons to nitrate or anode, leading to steered product spectrum. The anode-assisted electro-fermentation showed its potential to boost acetoin production for future industrial biotechnology applications.

The effects of multiwalled carbon nanotubes and Bacillus subtilis treatments on the salt tolerance of maize seedlings

Nanomaterials, including multiwalled carbon nanotubes (MWCNTs), have been recently applied in agriculture to improve stress resistance, leading to contradictory findings for antioxidant responses and mineral nutrient uptake. A pot experiment involving maize in low-salinity sandy loam soils was conducted with the application of different concentrations (0, 20, 50 mg/L) of MWCNTs and the growth-promoting rhizobacterium Bacillus subtilis (B. subtilis). The dose-dependent effects of MWCNTs were confirmed: 20 mg/L MWCNTs significantly promoted the accumulation of osmolytes in maize, particularly K⁺ in the leaves and roots, increased the leaf indoleacetic acid content, decreased the leaf abscisic acid content; but the above-mentioned promoting effects decreased significantly in 50 mg/L MWCNTs-treated plants. We observed a synergistic effect of the combined application of MWCNTs and B. subtilis on plant salt tolerance. The increased lipid peroxidation and antioxidant-like proline, peroxidase (POD), and catalase (CAT) activities suggested that MWCNTs induced oxidative stress in maize growing in low-salinity soils. B. subtilis reduced the oxidative stress caused by MWCNTs, as indicated by a lower content of malondialdehyde (MDA). The MWCNTs significantly increased the leaf Na⁺ content and leaf Na⁺/K⁺ ratio; however, when applied in combination with B. subtilis, the leaf Na⁺/K⁺ ratio decreased sharply to 69% and 44%, respectively, compared to those of the control (CK) group, the contents of which were partially regulated by abscisic acid and nitrate, according to the results of the structural equation model (SEM). Overall, the increased osmolytes and well-regulated Na⁺/K⁺ balance and transport in plants after the combined application of MWCNTs and B. subtilis reveal great potential for their use in combating abiotic stress.

Effect of Spore-Forming Probiotics on the Poultry Production: A Review

Due to the bad aspects associated with the use of antibiotics, the pressure on poultry production prompted the efforts to find out suitable growth-promoting and disease-preventing alternatives. Although many cost-effective alternatives have been developed, currently, one of the most auspicious alternatives for poultry feed is spore-forming probiotics, which can exert more beneficial effects as compared to normal probiotics, because of their ability to withstand the harsh external and internal conditions which result in increased viability. Many studies have already used spore-forming probiotics to improve different parameters of poultry production. Our laboratory has recently isolated a spore-forming bacterial strain, which has the potential to be used as a probiotic. So, to provide a detailed understanding, the current review aimed to collect valuable references to describe the mechanism of action of spore-forming probiotics and their effect on all the key aspects of poultry production.

Surface Display of porcine circovirus type 2 antigen protein cap on the spores of bacillus subtilis 168: An effective mucosal vaccine candidate

The oral mucosal vaccine has great potential in preventing a series of diseases caused by porcine circovirus type 2 (PCV2) infection. This study constructed a recombinant Bacillus subtilis RB with PCV2 Capsid protein (Cap) on its spore surface and cotB as a fusion partner. The immune properties of the recombinant strain were evaluated in a mouse model. IgA in intestinal contents and IgG in serum were detected by enzyme-linked immunosorbent assay (ELISA). The results demonstrated that recombinant spores could activate strong specific mucosal and humoral immune responses. In addition, spores showed good mucosal immune adjuvant function, promoting the proliferation of CD3+, CD4+ and CD8+ T cells and other immune cells. We also found that the relative expression of inflammatory cytokines such as IL-1β, IL-6, IL-10, TNF-α and IFN in the small intestinal mucosa was significantly up-regulated under the stimulation of recombinant bacteriophage. These effects are important for the balance of Th1/Th2-like responses. In summary, our results suggest that recombinant B. subtilis RB as a feed additive provides a new strategy for the development of novel and safe PCV2 mucosal subunit vaccines.

History of fecal transplantation; camel feces contains limited amounts of Bacillus subtilis spores and likely has no traditional role in the treatment of dysentery

Introduction

A widely cited story on the origins of fecal transplantation suggests that German soldiers in North Africa used camel feces containing Bacillus subtilis to treat dysentery in World War 2. We investigated if this story is accurate and if there is sufficient Bacillus subtilis in camel feces to be potentially therapeutic.

Methods and results

A literature analysis shows that all references to the story are based on a single review paper that mentions the use of camel feces in passing and only provides indirect evidence for this claim. An extensive literature search failed to find independent evidence that camel feces has traditionally been used in the treatment of dysentery in North Africa. With 16S sequence analysis we did not detect Bacillus subtilis in feces from two different Egyptian camels. Using a more sensitive culture-based assay we could detect low amounts of Bacillus subtilis spores in these fecal samples, with comparable concentrations to those present in human feces and soil.

Conclusions

Because we could not find evidence for the use of camel feces in the treatment of diarrhea and because we show that only low amounts of Bacillus subtilis spores are present in camel feces, we conclude that the use of camel feces should no longer be mentioned in the context of origins of fecal transplantation.

Comparative evaluation of the microbial diversity and metabolite profiles of Japanese-style and Cantonese-style soy sauce fermentation

Microorganisms play essential roles in flavor formation during soy sauce fermentation. Different soy sauce fermentation types significantly affect flavor formation. However, comparisons of microbial communities and metabolites between different fermentation types have been little studied. Here, we investigated variation in microbial communities, metabolite profiles, and metabolic pathways during Japanese-type (JP) and Cantonese-type (CP) fermentation. Free amino acids and volatile compound profiles varied significantly between fermentation types, with JP samples containing higher contents of esters (39.84%; p < 0.05), alcohols (44.70%; p < 0.05) in the 120 d fermentation samples. Volatile compound profiles varied significantly between fermentation types, with JP samples containing higher contents of esters, alcohols, and free amino acids (p < 0.05). Metagenomic analysis indicated that both JP and CP communities were dominated by Tetragenococcus, Staphylococcus, Weissella (bacteria), and Aspergillus (fungi), but the two communities varied differently over time. Tetragenococcus drastically increased in abundance throughout the fermentation (from 0.02 to 59.2%) in JP fermentation, whereas Tetragenococcus (36.7%) and Staphylococcus (29.7%) dominated at 120 d of fermentation in CP fermentation. Metagenomic functional profiles revealed that the abundances of most genes involved with carbohydrate, amino acid, and lipid metabolism exhibited significant differences between fermentation types (p < 0.05) during the middle to late fermentation stages. Furthermore, predicted metabolic pathways for volatile substance biosynthesis differed between JP and CP fermentation, likely explaining the differences in flavor metabolite profiles. In addition, most of the genes associated with flavor generation were affiliated with Tetragenococcus, Weissella, Staphylococcus, Bacillus, and Aspergillus, suggesting that these microbes play important roles in flavor production during soy sauce fermentation. This study significantly improves our understanding of microbial functions and their metabolic roles in flavor formation during different soy sauce fermentation processes.

Beneficial Effects of Spore-Forming Bacillus Probiotic Bacteria Isolated From Poultry Microbiota on Broilers' Health, Growth Performance, and Immune System

Probiotics are known for their beneficial effects on poultry health and wellbeing. One promising strategy for discovering Bacillus probiotics is selecting strains from the microbiota of healthy chickens and subsequent screening for potential biological activity. In this study, we focused on three probiotic strains isolated from the gastrointestinal tract of chickens bred in different housing types. In addition to the previously reported poultry probiotic Bacillus subtilis KATMIRA1933, three strains with antimutagenic and antioxidant properties Bacillus subtilis KB16, Bacillus subtilis KB41, and Bacillus amyloliquefaciens KB54, were investigated. Their potential effects on broiler health, growth performance, and the immune system were evaluated in vivo. Two hundred newly hatched Cobb500 broiler chickens were randomly divided into five groups (n = 40). Four groups received a standard diet supplemented with the studied bacilli for 42 days, and one group with no supplements was used as a control. Our data showed that all probiotics except Bacillus subtilis KATMIRA1933 colonized the intestines. Treatment with Bacillus subtilis KB54 showed a significant improvement in growth performance compared to other treated groups. When Bacillus subtilis KB41 and Bacillus amyloliquefaciens KB54 were applied, the most significant immune modulation was noticed through the promotion of IL-6 and IL-10. We concluded that Bacillus subtilis KB54 supplementation had the largest positive impact on broilers' health and growth performance.

Effect of Bacillus subtilis Zeolite Used for Sediment Remediation on Sulfide, Phosphate, and Nitrogen Control in a Microcosm

Eutrophication is an emerging worldwide issue concerning the excessive accumulation of various pollutants in sediments, owing to the release of industrial or household wastewaters to coastal areas. The coastal sediment of Goseong Bay in the Republic of Korea is organically enriched with pollutants, including heavy metals, sulfide, phosphate, and ammonia. Microbial remediation and capping techniques have been suggested as effective routes for sediment remediation. In this study, Bacillus subtilis zeolite (BZ) was used as a sediment capping material, and effective remediation of coastal sediment was observed in a 40-day laboratory microcosm experiment. A significant decrease in the sediment water content and reduced concentration of acid volatile sulfide were observed in the BZ-capped sediment. In the overlying water and pore water, significant decreases in phosphate and dissolved inorganic nitrogen (DIN; NO₂-N + NO₃-N and NH₄-N) concentrations were observed in the BZ-treated experiment. Based on our findings, we conclude that BZ could be an effective capping material for coastal sediment remediation.

Bacillus subtilis PS-216 Antagonistic Activities against Campylobacter jejuni NCTC 11168 Are Modulated by Temperature, Oxygen, and Growth Medium

As the incidence of Campylobacter jejuni and campylobacteriosis grows, so does the need for a better understanding and control of this pathogen. We studied the interactions of C. jejuni NCTC 11168 and a potential probiotic, Bacillus subtilis PS-216, in cocultures at different starting ratios and temperatures (20 °C, 37 °C, 42 °C), under different atmospheres (aerobic, microaerobic), and in different growth media (Mueller–Hinton, chicken litter medium, chicken intestinal-content medium). Under microaerobic conditions, B. subtilis effectively inhibited the growth of C. jejuni at 42 °C (log reduction, 4.19), even when C. jejuni counts surpassed B. subtilis by 1000-fold in the starting inoculum. This inhibition was weaker at 37 °C (log reduction, 1.63), while no impact on CFUs was noted at 20 °C, which is a temperature nonpermissive of C. jejuni growth. Under aerobic conditions, B. subtilis supported C. jejuni survival. B. subtilis PS-216 inhibited the growth of C. jejuni in sterile chicken litter (4.07 log reduction) and in sterile intestinal content (2.26 log reduction). In nonsterile intestinal content, B. subtilis PS-216 was able to grow, to a lesser extent, compared to Mueller–Hinton media, still showing potential as a chicken probiotic that could be integrated into the chicken intestinal microbiota. This study showed the strong influence of environmental parameters on the variability of C. jejuni and B. subtilis interactions. Furthermore, B. subtilis PS-216 antagonism was strongest against C. jejuni NCTC 11168 under conditions that might represent conditions in the chicken environment (42 °C, microaerobic atmosphere, chicken litter medium).

The coordinated population redistribution between Bacillus subtilis submerged biofilm and liquid-air pellicle

Bacillus subtilis is a widely used bacterial model to decipher biofilm formation, genetic determinants and their regulation. For several years, studies were conducted on colonies or pellicles formed at the interface with air, but more recent works showed that non-domesticated strains were able to form thick and structured biofilms on submerged surfaces. Taking advantage of time-lapse confocal laser scanning microscopy, we monitored bacterial colonization on the surface and observed an unexpected biphasic submerged biofilm development. Cells adhering to the surface firstly form elongated chains before being suddenly fragmented and released as free motile cells in the medium. This switching coincided with an oxygen depletion in the well which preceded the formation of the pellicle at the liquid-air interface. Residual bacteria still associated with the solid surface at the bottom of the well started to express matrix genes under anaerobic metabolism to build the typical biofilm protruding structures.

Nutrient L-Alanine-Induced Germination of Bacillus Improves Proliferation of Spores and Exerts Probiotic Effects in vitro and in vivo

As alternatives to antibiotics in feed, probiotic Bacillus carries multiple advantages in animal production. Spores undergo strain-related germination in the gastrointestinal tract, but it is still unknown whether the probiotic function of the Bacillus depends on the germination of spores in vivo. In this study, based on 14 potential probiotic Bacillus strains from fermented food and feed, we detected the germination response of these Bacillus spores in relation to different germinating agents. The results showed the germination response was strain-specific and germinant-related, and nutrient germinant L-alanine significantly promoted the growth of strains with germination potential. Two strains of Bacillus subtilis, S-2 and 312, with or without a high spore germination response to L-alanine, were selected to study their morphological and genic differences induced by L-alanine through transmission electron microscopy and comparative transcriptomics analysis. Consequently, after L-alanine treatment, the gray phase was largely increased under microscopy, and the expression of the germination response genes was significantly up-regulated in the B. subtilis S-2 spores compared to the B. subtilis 312 spores (p < 0.05). The protective effect of L-alanine-induced spore germination of the two strains was comparatively investigated both in the IPEC-J2 cell model and a Sprague–Dawley (SD) rat model challenged by enterotoxigenic Escherichia coli K99. The result indicated that L-alanine helped B. subtilis S-2 spores, but not 312 spores, to decrease inflammatory factors (IL-6, IL-8, IL-1 β, TNF-α; p < 0.05) and promote the expression of occludin in IPEC-J2 cells. Besides, supplement with L-alanine-treated B. subtilis S-2 spores significantly improved the growth of the SD rats, alleviated histopathological GIT lesions, and improved the ratio of jejunal villus length to crypt depth in comparison to the B. subtilis S-2 spores alone (p < 0.05). Improved species diversity and abundance of fecal microbiota were only observed in the group with L-alanine-treated S-2 spores (p < 0.05). The study demonstrates L-alanine works well as a probiotic Bacillus adjuvant in improving intestinal health, and it also provides a solution for the practical and accurate regulation of their use as antibiotic alternatives in animal production.

Distinct Interaction Mechanism of RNAP and ResD and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilisψ

The ResD-ResE signal transduction system plays a pivotal role in anaerobic nitrate respiration in Bacillus subtilis. The nasD operon encoding nitrite reductase is essential for nitrate respiration and is tightly controlled by the ResD response regulator. To understand the mechanism of ResD-dependent transcription activation of the nasD operon, we explored ResD-RNA polymerase (RNAP), ResD-DNA, and RNAP-DNA interactions required for nasD transcription. Full transcriptional activation requires the upstream promoter region where five molecules of ResD bind. The distal ResD-binding subsite at -87 to -84 partially overlaps a sequence similar to the consensus distal subsite of the upstream (UP) element with which the Escherichia coli C-terminal domain of the α subunit (αCTD) of RNAP interacts to stimulate transcription. We propose that interaction between αCTD and ResD at the promoter-distal site is essential for stimulating nasD transcription. Although nasD has an extended -10 promoter, it lacks a reasonable -35 element. Genetic analysis and structural simulations predicted that the absence of the -35 element might be compensated by interactions between σ^A and αCTD, and between αCTD and ResD at the promoter-proximal ResD-binding subsite. Thus, our work suggested that ResD likely participates in nasD transcription activation by binding to two αCTD subunits at the proximal and distal promoter sites, representing a unique configuration for transcription activation. IMPORTANCE A significant number of ResD-controlled genes have been identified and transcription regulatory pathways in which ResD participates have emerged. Nevertheless, the mechanism of how ResD activates transcription of different genes in a nucleotide sequence-specific manner has been less explored. This study suggested that among the five ResD-binding subsites in the promoter of the nasD operon, the promoter-proximal and -distal ResD-binding subsites play important roles in nasD activation by adapting different modes of protein-protein and protein-DNA interactions. The finding of a new-type of protein-promoter architecture provides insight into the understanding of transcription activation mechanisms controlled by transcription factors including the ubiquitous response regulators of two-component regulatory systems particularly in Gram-positive bacteria.

Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism

Background

Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment.

Methods

Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria.

Results

16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch.

Conclusions

The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02346-4.

Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions

The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.

Anaerobic Solid-State Fermentation of Soybean Meal With Bacillus sp. to Improve Nutritional Quality

The study evaluated the impact of fermentation with Bacillus sp. on the nutritional quality of soybean meal (SBM) and the changes of bacterial community structure during fermentation. High protease-producing strains were screened to degrade SBM macromolecular protein and anti-nutritional factors (ANFs). Unsterilized SBM then underwent an anaerobic solid-state fermentation method to evaluate the effects of fermentation. Results showed that for the nine high-producing protease strains that were screened, acid-soluble protein (ASP) contents in fermented SBM increased, with the highest value found to be 13.48%, which was fermented using strain N-11. N-11 was identified as Bacillus subtilis. N-11 fermentation reduced ANFs such as glycinin and β-conglycinin by 82.38 and 88.32%, respectively. During N-11 fermentation, the bacterial richness and diversity in SBM increased but not significantly. The high-yield protease strain B. subtilis N-11 selected in this experiment improved the nutritional quality of SBM through fermentation, and it can be used for industrial large-scale production.

A Review of the Effects and Production of Spore-Forming Probiotics for Poultry

Simple Summary

Spore-forming probiotics are widely used in the poultry industry for their beneficial impact on host health. The main feature that separates spore-forming probiotics from the more common lactic acid probiotics is their high resistance to external and internal factors, resulting in higher viability in the host and correspondingly, greater efficiency. Their most important effect is the ability to confront pathogens, which makes them a perfect substitute for antibiotics. In this review, we cover and discuss the interactions of spore-forming probiotic bacteria with poultry as the host, their health promotion effects and mechanisms of action, impact on poultry productivity parameters, and ways to manufacture the probiotic formulation. The key focus of this review is the lack of reproducibility in poultry research studies on the evaluation of probiotics’ effects, which should be solved by developing and publishing a set of standard protocols in the professional community for conducting probiotic trials in poultry.

Abstract

One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing.

Performance of microbial community dominated by Bacillus spp. in acid mine drainage remediation systems: A focus on the high removal efficiency of SO4 2-, Al3+, Cd2+, Cu2+, Mn2+, Pb2+, and Sr2

A consortium of microbial community was used for the treatment of acid mine drainage wastewater laden with sulphate and heavy metals. The wastewater was treated in an anaerobic continuously stirred tank bioreactor. The microbial community activity increased the pH from 5.6 to 6.5, and improved sulphate removal up to 85% from an initial sulphate concentration of 8080 mg SO42−/L in a continuous mode, following enrichment for 21 d. The maximum heavy metal removal percentage was observed for Cd (98%), Al (97%), Mn (95%), Pb (94%), Sr (94%) and Cu (91%). The microbial community showed synergy between strictly anaerobic and facultative Firmicutes sp., which were responsible for the bioreactor performance. The biochemical reaction indicated the microbial community has a wider range of substrates dominated by metallo-aminopeptidases.

Anaerobic Oxidation of Methane Coupled with Dissimilatory Nitrate Reduction to Ammonium Fuels Anaerobic Ammonium Oxidation

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is critical for mitigating methane emission and returning reactive nitrogen to the atmosphere. The genomes of n-DAMO archaea show that they have the potential to couple anaerobic oxidation of methane to dissimilatory nitrate reduction to ammonium (DNRA). However, physiological details of DNRA for n-DAMO archaea were not reported yet. This work demonstrated n-DAMO archaea coupling the anaerobic oxidation of methane to DNRA, which fueled Anammox in a methane-fed membrane biofilm reactor with nitrate as only electron acceptor. Microelectrode analysis revealed that ammonium accumulated where nitrite built up in the biofilm. Ammonium production and significant upregulation of gene expression for DNRA were detected in suspended n-DAMO culture with nitrite exposure, indicating that nitrite triggered DNRA by n-DAMO archaea. ¹⁵N-labeling batch experiments revealed that n-DAMO archaea produced ammonium from nitrate rather than from external nitrite. Localized gradients of nitrite produced by n-DAMO archaea in biofilms induced ammonium production via the DNRA process, which promoted nitrite consumption by Anammox bacteria and in turn helped n-DAMO archaea resist stress from nitrite. As biofilms predominate in various ecosystems, anaerobic oxidation of methane coupled with DNRA could be an important link between the global carbon and nitrogen cycles that should be investigated in future research.

Biotin, a universal and essential cofactor: Synthesis, ligation and regulation

Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.

Investigating the Modes of Action of the Antimicrobial Chalcones BC1 and T9A

Xanthomonas citri subsp. citri (X. citri) is an important phytopathogen and causes Asiatic Citrus Canker (ACC). To control ACC, copper sprays are commonly used. As copper is an environmentally damaging heavy metal, new antimicrobials are needed to combat citrus canker. Here, we explored the antimicrobial activity of chalcones, specifically the methoxychalcone BC1 and the hydroxychalcone T9A, against X. citri and the model organism Bacillus subtilis. BC1 and T9A prevented growth of X. citri and B. subtilis in concentrations varying from 20 µg/mL to 40 µg/mL. BC1 and T9A decreased incorporation of radiolabeled precursors of DNA, RNA, protein, and peptidoglycan in X. citri and B. subtilis. Both compounds mildly affected respiratory activity in X. citri, but T9A strongly decreased respiratory activity in B. subtilis. In line with that finding, intracellular ATP decreased strongly in B. subtilis upon T9A treatment, whereas BC1 increased intracellular ATP. In X. citri, both compounds resulted in a decrease in intracellular ATP. Cell division seems not to be affected in X. citri, and, although in B. subtilis the formation of FtsZ-rings is affected, a FtsZ GTPase activity assay suggests that this is an indirect effect. The chalcones studied here represent a sustainable alternative to copper for the control of ACC, and further studies are ongoing to elucidate their precise modes of action.

Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions

Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.

The Role of Fnr Paralogs in Controlling Anaerobic Metabolism in the Diazotroph Paenibacillus polymyxa WLY78

Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5, and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Both the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to a 50% reduction in nitrogenase activity, and double deletion of fnr1 and fnr3 resulted to a 90% reduction in activity. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic conditions. Fnr1 and Fnr3 inhibited expression of the genes involved in the aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes.IMPORTANCE The members of the nitrogen-fixing Paenibacillus spp. have great potential to be used as a bacterial fertilizer in agriculture. However, the functions of the fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we found that in P. polymyxa WLY78, Fnr1 and Fnr3 were responsible for regulation of numerous genes in response to changes in oxygen levels, but Fnr5 and Fnr7 exhibited little effect. Fnr1 and Fnr3 indirectly or directly regulated many types of important metabolism, such as nitrogen fixation, Fe uptake, respiration, and electron transport. This study not only reveals the function of the fnr genes of P. polymyxa WLY78 in nitrogen fixation and other metabolisms but also will provide insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.

Biosurfactant-Mediated Membrane Depolarization Maintains Viability during Oxygen Depletion in Bacillus subtilis

The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how populations adapt to shifts in oxygen availability. Here, we find that when oxygen was depleted from stationary phase B. subtilis cultures, ∼90% of cells died while the remaining cells maintained colony-forming ability. We discover that production of the antimicrobial surfactin confers two oxygen-related fitness benefits: it increases aerobic growth yield by increasing oxygen diffusion, and it maintains viability during oxygen depletion by depolarizing the membrane. Strains unable to produce surfactin exhibited an ∼50-fold reduction in viability after oxygen depletion. Surfactin treatment of these cells led to membrane depolarization and reduced ATP production. Chemical and genetic perturbations that alter oxygen consumption or redox state support a model in which surfactin-mediated membrane depolarization maintains viability through slower oxygen consumption and/or a shift to a more reduced metabolic profile. These findings highlight the importance of membrane potential in regulating cell physiology and growth, and demonstrate that antimicrobials that depolarize cell membranes can benefit cells when the terminal electron acceptor in respiration is limiting. This foundational knowledge has deep implications for environmental microbiology, clinical anti-bacterial therapy, and industrial biotechnology.

Oral administration of transgenic biosafe microorganism containing antimicrobial peptide enhances the survival of tilapia fry infected bacterial pathogen

To develop an alternative to conventional antibiotics used in the aquaculture and livestock industries, we employed Bacillus subtilis, considered a biosafe microorganism, to express the degradable antimicrobial peptide lactoferricin. An expression plasmid pP43-6LFBII-GFP, in which reporter GFP cDNA was fused downstream of lactoferricin cDNA driven by an endogenous constitutive P43 promoter was electroporated into B. subtilis, followed by regeneration and cultivation. The putative colonies harboring plasmids were primarily screened by PCR-amplification of lactoferricin cDNA. Four transformants which were stable inheritance of plasmid containing lactoferricin cDNA included strains T1, T4, T7 and T13. Based on Western blot and Southern blot analyses, we found that transgenic strains T1 and T13 not only highly expressed exogenous recombinant lactoferricin, but also exhibited more stable inheritance of plasmids with 931 and 647 copies per cell, respectively. In the antibacterial in vitro experiment, the bactericidal activity of each microliter of cell lysate from transgenic strains T1 and T13 (5 × 10⁸ CFU) for Escherichia coli was equivalent to 56 and 53 ng of Ampicillin dosage, respectively, while for Staphylococcus epidermidis, the equivalency T1 and T13 was 154 and 130 ng of Ampicillin dosage, respectively. Equivalencies of bacterial activity for Vibrio parahaemolyticus and Edwardsiella tarda followed suit. In the antibacterial in vivo experiment, we oral-in-tube fed tilapia fry (Oreochromis mossambicus X O. niloticus) with cell lysate from transgenic strain T1 and T13 individually. After 1-h of incubation, we immersed these treated fish fry in a water tank containing E. tarda (5 × 10¹¹ CFU) for a 5-hr bacterial challenge. After one month cultivation, an average survival rate of 63 and 67% was observed after having fed the fish fry with transgenic strains T1 and T13, respectively. However, the average survival rate of fish fry fed with B. subtilis WT strain and transgenic strain T19 without expressing recombinant lactoferricin reached only 5 and 9%, respectively. These data indicate that the survival of fish fry infected by the intestinal pathogen tested could be significantly enhanced by feeding transgenic B. subtilis containing antibacterial peptide. Therefore, we suggest that this strategy could be applied to both aquaculture and livestock industries to (i) reduce the dependency on conventional antibiotics during seasonal outbreaks and (ii) eliminate the problem of antibiotic resistance.

Energetic funnel facilitates facilitated diffusion

Transcription factors (TFs) are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism-dubbed facilitated diffusion. By studying a collection of TF binding sites of Escherichia coli from the RegulonDB database and of Bacillus subtilis from DBTBS, we reveal a funnel in the binding energy landscape around the target sequences. We show that such a funnel is linked to the presence of gradients of AT in the base composition of the DNA region around the binding sites. An extensive computational study of the stochastic sliding process along the energetic landscapes obtained from the database shows that the funnel can significantly enhance the probability of TFs to find their target sequences when sliding in their proximity. We demonstrate that this enhancement leads to a speed-up of the association process.

Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies

Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. Therefore, the prediction of the promoters for a particular sigma factor is essential for interpreting functional genomic data and observation. This paper develops a new method to predict sigma-54 promoters in bacterial genomes. The new method organically integrates motif finding and machine learning strategies to capture the intrinsic features of sigma-54 promoters. The experiments on E. coli benchmark test set show that our method has good capability to distinguish sigma-54 promoters from surrounding or randomly selected DNA sequences. The applications of the other three bacterial genomes indicate the potential robustness and applicative power of our method on a large number of bacterial genomes. The source code of our method can be freely downloaded at https://github.com/maqin2001/PromotePredictor.

Porphyrinoid photosensitizers mediated photodynamic inactivation against bacteria

The multi-drug resistant bacteria have become a serious problem complicating therapies to such a degree that often the term "post-antibiotic era" is applied to describe the situation. The infections with methicillin-resistant S. aureus, vancomycin-resistant E. faecium, third generation cephalosporin-resistant E. coli, third generation cephalosporin-resistant K. pneumoniae and carbapenem-resistant P. aeruginosa have become commonplace. Thus, the new strategies of infection treatment have been searched for, and one of the approaches is based on photodynamic antimicrobial chemotherapy. Photodynamic protocols require the interaction of photosensitizer, molecular oxygen and light. The aim of this review is to provide a comprehensive overview of photodynamic antimicrobial chemotherapy by porphyrinoid photosensitizers. In the first part of the review information on the mechanism of photodynamic action and the mechanism of the bacteria resistance to the photodynamic technique were described. In the second one, it was described porphyrinoids photosensitizers like: porphyrins, chlorins and phthalocyanines useable in photodynamic bacteria inactivation.

Genomic comparison of facultatively anaerobic and obligatory aerobic Caldibacillus debilis strains GB1 and Tf helps explain physiological differences

Caldibacillus debilis strains GB1 and Tf display distinct phenotypes. Caldibacillus debilis GB1 is capable of anaerobic growth and can synthesize ethanol while C. debilis Tf cannot. Comparison of the GB1 and Tf genome sequences revealed that the genomes were highly similar in gene content and showed a high level of synteny. At the genome scale, there were several large sections of DNA that appeared to be from lateral gene transfer into the GB1 genome. Tf did have unique genetic content but at a much smaller scale: 300 genes in Tf verses 857 genes in GB1 that matched at ≤90% sequence similarity. Gene complement and copy number of genes for the glycolysis, tricarboxylic acid cycle, and electron transport chain pathways were identical in both strains. While Tf is an obligate aerobe, it possesses the gene complement for an anaerobic lifestyle (ldh, ak, pta, adhE, pfl). As a species, other strains of C. debilis should be expected to have the potential for anaerobic growth. Assaying the whole cell lysate for alcohol dehydrogenase activity revealed an approximately 2-fold increase in the enzymatic activity in GB1 when compared with Tf.

The role of the NADH-dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification

Nitrate and nitrite reduction are of paramount importance for nitrogen assimilation and anaerobic metabolism, and understanding the specific roles of each participating reductase is necessary to describe the biochemical balance that dictates cellular responses to their environments. The soluble, cytoplasmic siroheme NADH-nitrite reductase (Nir) in Escherichia coli is necessary for nitrate/nitrite assimilation but has also been reported to either "detoxify" nitrite, or to carry out fermentative ammonification in support of anaerobic catabolism. Theoretically, nitrite detoxification would be important for anaerobic growth on nitrate, during which excess nitrite would be reduced to ammonium. Fermentative ammonification by Nir would be important for maximization of non-respiratory ATP production during anaerobic growth in the presence of nitrite. Experiments reported here were designed to test the potential role of Nir in fermentative ammonification directly by growing E. coli along with mutant strains lacking Nir or the respiratory nitrite reductase (Nrf) under anaerobic conditions in defined media while monitoring nitrogen utilization and fermentation metabolites. To focus on the role of Nir in fermentative ammonification, pH control was used in most experiments to eliminate nitrite toxicity due to nitric acid formation. Our results demonstrate that Nir confers a significant benefit during fermentative growth that reflects fermentative ammonification rather than detoxification. We conclude that fermentative ammonification by Nir allows for the energetically favorable fermentation of glucose to formate and acetate. These results and conclusions are discussed in light of the roles of Nir in other bacteria and in plants.

Genomic and metabolic features of the Bacillus amyloliquefaciens group- B. amyloliquefaciens, B. velezensis, and B. siamensis- revealed by pan-genome analysis

The genomic and metabolic features of the Bacillus amyloliquefaciens group comprising B. amyloliquefaciens, B. velezensis, and B. siamensis were investigated through a pan-genome analysis combined with an experimental verification of some of the functions identified. All B. amyloliquefaciens group genomes were retrieved from GenBank and their phylogenetic relatedness was subsequently investigated. Genome comparisons of B. amyloliquefaciens, B. siamensis, and B. velezensis showed that their genomic and metabolic features were similar; however species-specific features were also identified. Energy metabolism-related genes are more enriched in B. amyloliquefaciens, whereas secondary metabolite biosynthesis-related genes are enriched in B. velezensis. Compared to B. amyloliquefaciens and B. siamensis, B. velezensis harbors more genes in its core-genome which are involved in the biosynthesis of antimicrobial compounds, as well as genes involved in d-galacturonate and d-fructuronate metabolism. B. amyloliquefaciens, B. siamensis, and B. velezensis all harbor a xanthine oxidase gene cluster (xoABCDE) in their core-genomes that is involved in metabolizing xanthine and uric acid to glycine and oxalureate. A reconstruction of B. amyloliquefaciens group metabolic pathways using their individual pan-genomes revealed that the B. amyloliquefaciens group strains have the ability to metabolize diverse carbon sources aerobically, or anaerobically, and can produce various metabolites such as lactate, ethanol, acetate, CO₂, xylitol, diacetyl, acetoin, and 2,3-butanediol. This study therefore provides insights into the genomic and metabolic features of the B. amyloliquefaciens group.

Encapsulation of beneficial probiotic bacteria in extracellular matrix from biofilm-forming Bacillus subtilis

Probiotics, live microbial supplements, are often incorporated into foods and beverages to provide putative health benefits. To ensure their beneficial effects, these organisms must survive processing and storage of food, its passage through the upper gastrointestinal tract (GIT), and subsequent chemical ingestion processes until they reach their target organ. However, there is considerable loss of viability of probiotic bacteria in the acidic conditions of the stomach and the high bile concentration in the small intestine. Bacillus subtilis, a spore-forming non-pathogenic bacterium, recently has gained interest in its probiotic properties; it can effectively maintain a favorable balance of microflora in the GIT. In addition, B. subtilis produces an extracellular matrix that protects it from stressful environments. We suggested that the extracellular matrix produced by B. subtilis could protect other probiotic bacteria and therefore potentially could be used as a vehicle for delivering viable probiotic cells to humans. Therefore, we developed a novel cultivation system that enables co-culturing of B. subtilis along with probiotic lactic acid bacteria (LAB) by increasing production of the extracellular matrix by B. subtilis cells. Moreover, we showed that B. subtilis improved survivability of LAB during food preparation, storage and ingestion. Therefore, we believe that the results of our study will provide a novel technique of using a natural system for preservation and delivery of probiotics to humans.

Novel antibiofilm chemotherapies target nitrogen from glutamate and glutamine

Bacteria in nature often reside in differentiated communities termed biofilms, which are an active interphase between uni-cellular and multicellular life states for bacteria. Here we demonstrate that the development of B. subtilis biofilms is dependent on the use of glutamine or glutamate as a nitrogen source. We show a differential metabolic requirement within the biofilm; while glutamine is necessary for the dividing cells at the edges, the inner cell mass utilizes lactic acid. Our results indicate that biofilm cells preserve a short-term memory of glutamate metabolism. Finally, we establish that drugs that target glutamine and glutamate utilization restrict biofilm development. Overall, our work reveals a spatial regulation of nitrogen and carbon metabolism within the biofilm, which contributes to the fitness of bacterial complex communities. This acquired metabolic division of labor within biofilm can serve as a target for novel anti-biofilm chemotherapies

Mixomics analysis of Bacillus subtilis: effect of oxygen availability on riboflavin production

Background

Riboflavin, an intermediate of primary metabolism, is one kind of important food additive with high economic value. The microbial cell factory Bacillus subtilis has already been proven to possess significant importance for the food industry and have become one of the most widely used riboflavin-producing strains. In the practical fermentation processes, a sharp decrease in riboflavin production is encountered along with a decrease in the dissolved oxygen (DO) tension. Influence of this oxygen availability on riboflavin biosynthesis through carbon central metabolic pathways in B. subtilis is unknown so far. Therefore the unveiled effective metabolic pathways were still an unaccomplished task till present research work.

Results

In this paper, the microscopic regulation mechanisms of B. subtilis grown under different dissolved oxygen tensions were studied by integrating ¹³C metabolic flux analysis, metabolomics and transcriptomics. It was revealed that the glucose metabolic flux through pentose phosphate (PP) pathway was lower as being confirmed by smaller pool sizes of metabolites in PP pathway and lower expression amount of ykgB at transcriptional level. The latter encodes 6-phosphogluconolactonase (6-PGL) under low DO tension. In response to low DO tension in broth, the glucose metabolic flux through Embden–Meyerhof–Parnas (EMP) pathway was higher and the gene, alsS, encoding for acetolactate synthase was significantly activated that may result due to lower ATP concentration and higher NADH/NAD⁺ ratio. Moreover, ResE, a membrane-anchored protein that is capable of oxygen regulated phosphorylase activity, and ResD, a regulatory protein that can be phosphorylated and dephosphorylated by ResE, were considered as DO tension sensor and transcriptional regulator respectively.

Conclusions

This study shows that integration of transcriptomics, ¹³C metabolic flux analysis and metabolomics analysis provides a comprehensive understanding of biosynthesized riboflavin’s regulatory mechanisms in B. subtilis grown under different dissolved oxygen tension conditions. The two-component system, ResD–ResE, was considered as the signal receiver of DO tension and gene regulator that led to differences between biomass and riboflavin production after triggering the shifts in gene expression, metabolic flux distributions and metabolite pool sizes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0764-z) contains supplementary material, which is available to authorized users.

Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang)

Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from traditional Korean food containing soybean (chung-gook-jang). The de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences (CDSs).