Glycerol (Gly) can be dissimilated by two pathways in bacteria. Either this sugar alcohol is first oxidized to dihydroxyacetone (DHA) and then phosphorylated or it is first phosphorylated to glycerol-3-phosphate (GlyP) followed by oxidation. Oxidation of GlyP can be achieved by NAD-dependent dehydrogenases or by a GlyP oxidase. In both cases, dihydroxyacetone phosphate is the product. Genomic analysis showed that Enterococcus faecium harbors numerous genes annotated to encode activities for the two pathways. However, our physiological analyses of growth on glycerol showed that dissimilation is limited to aerobic conditions and that despite the presence of genes encoding presumed GlyP dehydrogenases, the GlyP oxidase is essential in this process. Although E. faecium contains an operon encoding the phosphotransfer protein DhaM and DHA kinase, which are required for DHA phosphorylation, it is unable to grow on DHA. This operon is highly expressed in stationary phase but its physiological role remains unknown. Finally, data obtained from sequencing of a transposon mutant bank of E. faecium grown on BHI revealed that the GlyP dehydrogenases and a major intrinsic family protein have important but hitherto unknown physiological functions.

Streptomyces are efficient chemists with a capacity to generate diverse and potent chemical scaffolds. The secondary metabolism of these soil-dwelling prokaryotes is stimulated upon interaction with other microbes in their complex ecosystem. We observed such an interaction when a Streptomyces isolate was cultivated in a media supplemented with dead yeast cells. Whole-genome analysis revealed that Streptomyces sp. MBK6 harbors the red cluster that is cryptic under normal environmental conditions. An interactive culture of MBK6 with dead yeast triggered the production of the red pigments metacycloprodigiosin and undecylprodigiosin. Streptomyces sp. MBK6 scavenges dead-yeast cells and preferentially grows in aggregates of sequestered yeasts within its mycelial network. We identified that the activation depends on the cluster-situated regulator, mbkZ, which may act as a cross-regulator. Cloning of this master regulator mbkZ in S. coelicolor with a constitutive promoter and promoter-deprived conditions generated different production levels of the red pigments. These surprising results were further validated by DNA-protein binding assays. The presence of the red cluster in Streptomyces sp. MBK6 provides a vivid example of horizontal gene transfer of an entire metabolic pathway followed by differential adaptation to a new environment through mutations in the receiver domain of the key regulatory protein MbkZ.

Environmental pH and gut transit rate are the key factors determining the dynamics of colonic microbiota. In this study, the effect of changing pH on the composition and metabolism of pooled faecal microbiota was elucidated at physiologically relevant dilution rates Dhigh = 0.2 and Dlow = 0.05 1/h. The results showed the best adaptability of Bacteroides ovatus within the pH range 6.0-8.0 at both dilution rates. The butyrate producing Faecalibacterium and Coprococcus comes were extremely sensitive to pH > 7.5, while the abundance of Akkermansia muciniphila increased significantly at pH >7 at Dhigh, causing a pH-dependant shift in the dynamics of mucin degrading species. Increased gas formation was observed at pH < 6.5. Substantially more CO2 was produced at Dlow than at Dhigh (18-29 vs 12-23 mmol per L medium, respectively). Methane was produced only at Dlow and pH > 7, consistent with the simultaneous increased abundance of Methanobrevibacter smithii. Our study confirmed the importance of pH in the development of faecal microbiota in pectin-supplemented medium. Fermentation of other dietary fibres can be studied using the same approach. The significance of pH should be more emphasized in gut research and diagnostics.

Cryptococcus neoformans is a leading cause of fungal meningitis in immunocompromized populations. Amphotericin B (AMB) and fluconazole (FLC) are common anticryptococcal agents. AMB treatment leads to severe side-effects. In contrast, FLC-based therapy is relatively safe, although C. neoformans often develops resistance to this drug. C. neoformans must adapt to the challenging environment of the human host. Environmental effects on potency of AMB and FLC and development of drug resistance remain poorly characterized. Here, the effects of nutrients, temperature and antioxidants on susceptibility of C. neoformans towards FLC and AMB were investigated. Limited nutrients led to a decrease and an increase of sensitivity towards FLC and AMB, respectively. Co-treatment with various antioxidants also demonstrated reciprocal effects on susceptibility towards FLC and AMB. In contrast, elevated temperature increased the efficacy of both drugs, although the effect on FLC was more drastic as compared to that of AMB. In addition, temperatures of 37°C and above prevented development of FLC resistance. Our study pointed to a critical role of the environment on susceptibility towards AMB and FLC and revealed reciprocal effects towards these antifungal drugs, reflecting contrasting modes of action of AMB and FLC.

The enzyme L-methionine-γ-lyase is commonly found in a wide range of bacteria and catalyzes the α-elimination and γ-elimination of L-methionine to produce methyl mercaptan, α-ketobutyrate and ammonia. Black cumin seed essential oil (BC oil) reportedly exhibits deodorizing activity against methyl mercaptan. Therefore, we hypothesized that BC oil may also suppress methyl mercaptan production. In this study, we aimed to evaluate the inhibitory effect of BC oil on L-methionine-γ-lyase activity in Fusobacterium nucleatum. Recombinant L-methionine-γ-lyase was incubated under appropriate conditions with BC oil and its constituent thymoquinone. To analyze L-methionine-γ-lyase activity, α-ketobutyric acid and ammonia concentrations were determined. The concentrations of α-ketobutyric acid and ammonia were significantly decreased by 10 µg mL-1 of BC oil (P < 0.01) and 16.4 µg/mL of thymoquinone (P < 0.05). An enzyme kinetic assay showed a mixed inhibition pattern between L-methionine-γ-lyase and thymoquinone. In conclusion, BC oil not only had a deodorizing effect against methyl mercaptan but also an inhibitory effect on methyl mercaptan production through the suppression of L-methionine-γ-lyase activity. Thymoquinone may be mainly responsible for these effects of BC oil. Thus, application of natural BC oil may be adapted not only for medical use but also in other areas of life.

The establishment of a sustainable circular bioeconomy requires the effective material recycling from biomass and biowaste beyond composting/fertilizer or anaerobic digestion/bioenergy. Recently, volatile fatty acids attracted much attention due to their potential application as carbon source for the microbial production of high added-value products. Their low-cost production from different types of wastes through dark fermentation is a key aspect, which will potentially lead to the sustainable production of fuels, materials or chemicals, while diminishing the waste volume. This article reviews the utilization of a volatile fatty acid platform for the microbial production of polyhydroxyalkanoates, single cell oil and omega-3 fatty acids, giving emphasis on the fermentation challenges for the efficient implementation of the bioprocess and how they were addressed. These challenges were addressed through a research project funded by the European Commission under the Horizon 2020 programme entitled 'VOLATILE-Biowaste derived volatile fatty acid platform for biopolymers, bioactive compounds and chemical building blocks'.

Foodborne, disease-causing microorganisms are increasingly resistant to commercial antibiotics. Thus, there is a need for the development of new agents capable of acting efficiently in the control of these pathogens. Terpenoids and phenylpropanoids stand out for having high biological activity and a broad spectrum of action. The objectives of this study were to evaluate the antibacterial potential of limonene, β-citronellol, carvone, carvacrol, eugenol and trans-cinnamaldehyde and to investigate the mechanism of activity of these compounds against the bacteria Escherichia coli and Staphylococcus aureus. The terpene and phenylpropanoid compoundswere purchased and their antibacterial potential was assessed by macrodilution. The mechanism of action was verified by tests of potassium ion efflux, salt tolerance, extravasation of cellular contents, absorption of crystal violet and morphological changes analyzed by electron microscopy. Bacteriostatic and bactericidal effects caused by the compounds carvone, carvacrol, eugenol and transcinemaldehyde were observed in both species; antibacterial activity against only S. aureus was observed for β-citronelol and limonene. Reduced salt tolerance was found for strains of E. coli treated with carvacrol and S. aureus treated with β-citronelol. There was extravasation of cellular materials induced by treatments with carvone, carvacrol, eugenol and trans-cinnamaldehyde in both microorganisms. The absorption of crystal violet increased for E. coli after incubation with each treatment. Deleterious effects and morphological changes were observed. Therefore, the monoterpenes and phenylpropanoids under study are potentially applicable for antimicrobial use against E. coli and S. aureus, and the mechanism of action involves changes in membrane permeability without cell lysis.

Annually, the EU produces more than 100 million tonnes of urban biowaste, which is largely under-valorized and in some cases even still landfilled without any energy or material recovery. If Europe wants to be ready for the future, it will need to make better use of this large biomass potential within a circular economy approach. The research project funded by the European Commission under the Horizon 2020 programme entitled 'VOLATILE-Biowaste derived volatile fatty acid platform for biopolymers, bioactive compounds and chemical building blocks' aimed to produce volatile fatty acids (VFAs) from biowaste for reprocessing into products, materials or substances to close the material loop. During the project, the partners were able to obtain average volatile fatty acid yields of 627 g COD/kg organic matter (OM) for food waste, 448 g COD/kg OM for separately collected vegetable, garden and fruit waste (VGF) and 384 g COD/kg OM for the organic fraction of municipal solid waste (OF-MSW) at concentrations ranging from 12 to 48 g/L, 6 to 40 g/L and 13 to 26 g/L, respectively. A membrane filtration cascade consisting of micro-, ultra- and nano-filtration followed by reverse osmosis was identified as a feasible way to purify and concentrate the VFA effluent, making them a suitable carbon source for further fermentation processes. Besides technical optimization, socio-economic and legal aspects associated with this platform technology were also studied and show that although this technology is still in development, it is providing an answer to changing societal and market expectations both regarding organic waste treatment and bio-based production strategies. Based on the current technological, economic and market evolutions, it is expected that the VFAP will play an important role in organic waste treatment in the coming years.

Kocuria isolates collected from the sake brewing process have inhabited the Narimasa Sake Brewery in Toyama, Japan. To investigate the effect of these actinobacterial isolates on the growth and metabolism of sake yeast, co-cultivation of sake yeast and Kocuria isolates was performed in a medium containing tryptone, glucose and yeast extract (TGY), and a solution containing koji (steamed rice covered with Aspergillus oryzae) and glucose. In the TGY medium, the ethanol concentration and the number of living cells of each microorganism were measured. In the koji solution, the concentrations of ethanol and organic acids (citric acid, lactic acid and succinic acid) were measured. The results showed that in TGY media, the growth of each Kocuria isolate in the co-culture of the two Kocuria isolates was similar to that in each monoculture. However, the growth of both Kocuria isolates was inhibited in the co-cultures of sake yeast and Kocuria isolates. On the other hand, the growth and ethanol productivity of sake yeast did not differ between its monoculture and co-cultures with Kocuria isolates. In the koji solution, Kocuria isolates TGY1120_3 and TGY1127_2 affected the concentrations of ethanol and lactic acid, respectively. Thus, Kocuria isolates affected the microbial metabolism, but the effects were not identical between the two isolates. This strongly suggests that bacteria inhabiting a sake brewery may influence the flavor and taste of sake products of the brewery.

Stachys pilifera Benth is an endemic species of Stachys family found in Iran with a wide application as an herbal tea. The objective of this research was to evaluate the antimicrobial, antioxidant and cytotoxic activity of the essential oil from the aerial parts of S. pilifera. Essential oil (EO) composition analysis showed that cis-Chrysanthenyl acetate (24.9%), viridiflorol (18.3%), trans-Caryophyllene (9.8%), caryophyllene oxide (4.6%), α-terpineol (3.3%) and linalool (3.1%) were the most abundant components. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the EO showed a higher antimicrobial activity against Gram-positive bacteria (Bacillus cereus and Staphylococcus aureus) than Gram-negative organisms (Escherichia coli, Shigella sonnei, Pseudomonas aeruginosa and Salmonella enterica subsp. Enterica). The antioxidant activity of EO was studied using DPPH, FRAP and β-carotene/linoleic acid assays. IC50 for the DPPH, FRAP and β-carotene/linoleic acid tests were 23.2, 28.7 and 16.1 µg/mL, respectively, that it was higher than the results for BHT (P ≤ 0.05). The cytotoxic activity of the EO was evaluated using HT29 and HUVEC cells and it was observed that by increasing in EO concentration from 0.026 to 19.4 ug/mL, the viability of the cells for HT29 and HUVEC reduced to 6.8 and 7.1%, respectively. The results from this study suggest the possibility to use the essential oils from S. pilifera Benth as a natural preservative in processed or packaged food due to its high antibacterial, antioxidant and cytotoxic activities.

Rhodococcus spp. have broad potential applications related to the degradation of organic contaminants and the transformation or synthesis of useful compounds. However, some Gram-positive bacteria are difficult to manipulate genetically due to low transformation efficiency. In this study, we investigated the effects of chemicals including glycine, isonicotinic acid hydrazide (INH), Tween 80 and penicillin G, as well as cell growth status, competent cell concentration, electroporation field strength, electroporation time and heat shock time, on the electrotransformation efficiency of the tetrahydrofuran-degrading bacterium Rhodococcus ruber YYL with low transformation efficiency. The highest electrotransformation efficiency was 1.60 × 106 CFU/µg DNA after parameter optimization. GmhD (D-glycero-D-manno-heptose 1-phosphate guanosyltransferase) gene, which is important in the biosynthesis of lipopolysaccharide, was deleted via the optimized electrotransformation method. Compared with wild-type strain, YYL ΔgmhD showed extremely high electrotransformation efficiency because the surface of it had no mushroom-like extracellular polymeric substances (EPS). In addition, the results showed that cell wall-weakening reagents might cause some translucent substances like EPS, to detach from the cells, increasing the electrotransformation efficiency of strain YYL. We propose that these results could provide a new strategy for unique bacteria that are rich in EPS, for which genetic manipulation systems are difficult to establish.

Swainsonine, an indolizidine alkaloid, is a promising anti-tumorigenic compound. Biological production of swainsonine was prospective, but the low swainsonine yield of wild type Alternaria oxytropis limited its production on a large scale. In present work, a stable A. oxytropis mutant UO1 with swanisonine yield of 14.84% higher than the wild-type strain was successfully obtained after heavy-ion irradiation. The A. oxytropis mutant UO1 and original wild-type strain were futher evaluated for SW concentrations under different factors. Results showed that the optimum culture temperature was 25°C. The optimum initial medium pH was 6.5 and the optimum inoculum size was 2 mL per 200 mL. Addition of the biosynthetic precursor L-pipecolic acids and L-lysine appropriately could increase the SW synthesis. These findings provided a theoretical basis and scientific data for the industrial production of swainsonine.

Equol, which produced from daidzein (one of the principal isoflavones), is recognized to be the most resultful in stimulating an estrogenic and antioxidant response. The daidzein transformation was studied during fermentation of five growth media inoculated with feces from a healthy human, and a daidzein conversion strain was isolated. To enrich the bacterial population involved in daidzein metabolism in a complex mixture, fecal samples were treated with antibiotics. The improved propidium monoazide combined with the quantitative polymerase chain reaction (PMAxx-qPCR) assay showed that the ampicillin treatment of samples did result in a reduction of the total visible bacteria counts by 52.2% compared to the treatment without antibiotics. On this basis, the newly isolated rod-shaped, Gram-positive anaerobic bacterium, named strain Y11 (MN560033), was able to metabolize daidzein to equol under anaerobic conditions, with a conversion ratio (equol ratio: the amount of equol produced/amount of supplemented daizein) of 0.56 over 120 h. The 16S rRNA partial sequence of the strain Y11 exhibited 99.8% identity to that of Slackia equolifaciens strain DZE (NR116295). This study will provide new insights into the biotransformation of equol from daidzein by intestinal microbiota from the strain-level and explore the possibility of probiotic interventions.

Mycetoma is a chronic human infectious disease that produces severe deformation frequently in the lower extremities. Etiological agents include fungi (eumycetoma) and bacteria (actinomycetoma) that produce similar clinical and microscopic changes. The clinical appearance includes swelling, abscesses, ulcers, scars and sinuses that drain purulent material with microbe microcolonies. The pathogenesis of actinomycetoma has been studied mainly in rodents. Using this approach, it was found that Nocardia brasiliensis produces proteases that may play a role in tissue damage, as well as immunosuppressive molecules, such as brasilicardin A. Nitric oxide (NO) is a molecule with biological activities depending on its local concentration. Its effect on killing intracellular bacteria such as Mycobacterium tuberculosis has been known for decades. NO plays an important role in innate and adaptive immunity. It can promote or suppress some biological activities despite its short half-ife. NO is produced by three different nitric oxide synthases (NOS). We used the genetic blockade of eNOS in C57BL/6 mice to demonstrate the role of NO in actinomycetoma development. Inflammation and actinomycetoma were prevented in genetically modified mice infected with N. brasiliensis. T cell proliferation was increased in these rodents, and antibody production, IL-6 and IL-10 expression were similar and TNF-α was lower.

The CoMiniGut in vitro model mimicking the small intestine of piglets was used to evaluate four probiotic strains for their potential as a preventive measure against development of diarrhea in weaned pigs. In the in vitro system, piglet digesta was inoculated with pathogenic enterotoxigenic Escherichia coli F4 (ETEC F4), and the short-chain fatty acid profile and the gut microbiota composition were assessed. A total of four probiotic strains were evaluated: Enterococcus faecium (CHCC 10669), Lactobacillus rhamnosus (CHCC 11994), Bifidobacterium breve (CHCC 15268) and Faecalibacterium prausnitzii (CHCC 28556). The significant differences observed in metabolite concetration and bacterial enumeration were attributed to variation in inoculating material or pathogen challenge rather than probiotic treatment. Probiotic administration influenced the microbiota composition to a small extend. Learnings from the present study indicate that the experimental setup, including incubation time and choice of inoculating material, should be chosen with care.