Essential oils have great potential in the field of the food industry as they can effectively prevent the presence of several bacterial and fungal pathogens. Essential oils are complex volatile compounds, synthesized naturally in different plant parts during the process of the secondary metabolism. The main goal of this work is to perform a qualitative evaluation of the antibacterial properties of 24 chemotyped essential oils against the growth of Bacillus subtillis. These Gram-positive bacteria are responsible for “rope” disease in bread preservation processes. The study was carried out using the method of disk-diffusion in agar. Biological activity was observed in five essential oils: Cymbopogon martinii var. motia, Thymus vulgaris QT Linanol, Thymus satureioides, Mentha piperita and Eugenia caryophyllus. The first three have in common the presence of some mono terpenic derivatives—Geraniol, Linalool and Carvacrol, respectively—with strong antimicrobial effects. The Cymbopogon martinii essential oil is one of the botanicals with the highest geraniol content (up to 80.53%) and showed more activity antimicrobial than the others. A contributing role of this knowledge could be the design of Cymbopogon martinii essential oil formula, which can be used in bakery industry as a preservative, such as nano-encapsulation for bakery doughs, active packaging of baked products or surface disinfectants. Full article

The intensive development of agriculture leads to the depletion of land and a decrease in crop yields and in plant resistance to diseases. A large number of fertilizers and pesticides are currently used to solve these problems. Chemicals can enter the soil and penetrate into the groundwater and agricultural plants. Therefore, the primary task is to intensify agricultural production without causing additional damage to the environment. This problem can be partially solved using microorganisms with target properties. Microorganisms that combine several useful traits are especially valuable. The aim of this work was to search for new microbial strains that possess a complex, technologically significant potential, such as increasing the bioavailability of nutrients, phytostimulation, antifungal effect and degradation of pesticide residues and other xenobiotics. Few isolated Bacillus and Pseudomonas strains were characterized by high activity against fungal phytopathogens. One of the bacterial strains identified as Bacillus sp. on the basis of the 16S rRNA gene sequence was characterized by an unusual cellular morphology and development cycle, significantly different from all previously described bacteria of this genus. All isolated bacteria are capable of benzoate degradation, as a sign of the ability to degrade aromatic compounds. Isolated strains were shown to be perspective agents in biotechnologies. Full article

Sourdoughs represent an awesome example of ecosystem in which yeasts and lactic acid bacteria (LAB) interact with each other, defining the characteristics of the final product in terms of composition, texture, taste and flavor. Therefore, the identification of dominant yeasts and LAB involved in the fermentation process can lead to the selection of starters with suitable fermentation aptitude and capable of producing desired aromas and/or aromatic precursors. In this work, two sourdoughs samples (A and B) for Panettone production were collected from an artisan bakery. Yeasts and bacteria were isolated at different fermentation steps on selective agar media. A total of 120 isolates were obtained and firstly characterized by conventional microbiological methods. Afterward, genomic DNA was extracted from the cultures, and (GTG)5-PCR fingerprinting analysis was carried out to reduce the redundance among the isolates. Representative yeasts and LAB strains, having a unique profile, were identified by sequencing the D1/D2 domain of the 26S rRNA and the 16S rRNA genes, respectively. The results highlighted the occurrence of Kazachstania humilis and Fructilactobacillus sanfranciscensis in both sourdoughs. Among LAB, also some other strains belonging to Lactobacillus genus were found. Moreover, Saccharomyces cerevisiae and Staphylococcus spp. strains were detected in sample B. In this study, a pool of yeasts and LAB strains for producing starter cultures with specific technological traits for sourdoughs production was obtained. Full article

A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic. After long-term extensive cultivation at 15 °C, it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate, and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stain-positive. Optimum conditions for growth were 24–28 °C, pH 6.8–7.3, and 0.075–0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein-coding genes revealed 16S rRNA’s close relation to Methanosarcina mazei S-6^T (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M. mazei was 98.5%, which is higher than the values recommended for new species. Thus, strain JL01 (=VKM B-2370 = JCM 31898) represents the first M. mazei isolated from permanently subzero Arctic sediments. The long-term co-cultivation of JL01 with S. associata GLS2^T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2^T revealed putative genes involved in methanochondroitin catabolism. Full article

Streptomyces spp. are known producers of therapeutically important secondary metabolites with diversity in structure and function. Optimization of different bioprocess parameters towards the improved productivity and activity profile is always considered to be of high significance. Peptone is an acclaimed source of nutrients that had been studied for its effect on the bioactivity of metabolites produced during media development. In the present communication, we report remarkable variation in the profile and anti-Candida activity of the metabolites produced by Streptomyces chrestomyceticus strain ADP4 in response to variation in the source of peptone. It was found that peptone procured from different manufactures (Himedia, CDH and Diffco) have shown noteworthy variation when used as a component of Sabouraud Dextrose Broth (SDB). The zone of inhibition, values of minimum inhibitory concentration (MIC₉₀) against C. krusei and the yield of metabolites varied significantly when the metabolites were produced in SDB medium using peptones from above mentioned sources. CDH-peptone was found to be the best for anti-Candida activity with highest zone of inhibition of 38 ± 2.0 mm and MIC₉₀ value of 2.877 ± 0.22 µg/mL against C. krusei ATCC 6258. Activity against C. albicans ATCC 10231, C. tropicalis ATCC 750, C. parapsilosis ATCC 90028 and C. auris CBS 12372 was also better as compared to the activities obtained using other peptones. The total yield of the metabolites was approximately twice in SDB with CDH-peptone as compared to those with peptone from HiMedia and Diffco. Analyses of the metabolites by using TLC and HPLC demonstrated a clear and significant difference in their profile. Since peptone is a major nitrogen source, it may be inferred that nitrogen source may play a critical role in regulation of biosynthetic gene clusters associated with synthesis of anti-Candida compounds by S. chrestomyceticus ADP4. Full article

Antimicrobial resistance is driving pharmaceutical companies to investigate different therapeutic approaches. One approach that has garnered growing consideration in drug development is the use of antimicrobial peptides (AMPs). Antibacterial peptides (ABPs), which occur naturally as part of the immune response, can serve as powerful, broad-spectrum antibiotics. However, conventional laboratory procedures for screening and discovering ABPs are expensive and time-consuming. Identification of ABPs can be significantly improved using computational methods. In this paper, we introduce a machine learning method for the fast and accurate prediction of ABPs. We gathered more than 6000 peptides from publicly available datasets and extracted 1209 features (peptide characteristics) from these sequences. We selected the set of optimal features by applying correlation-based and random forest feature selection techniques. Finally, we designed an ensemble gradient boosting model (GBM) to predict putative ABPs. We evaluated our model using receiver operating characteristic (ROC) curves, calculating the area under the curve (AUC) for several different models for comparison, including a recurrent neural network, a support vector machine, and iAMPpred. The AUC for the GBM was ~0.98, more than 3% better than any of the other models. Full article

Machine learning can be used as an alternative to similarity algorithms such as BLASTp when the latter fail to identify dissimilar antimicrobial-resistance genes (ARGs) in bacteria; however, determining the most informative characteristics, known as features, for antimicrobial resistance (AMR) is essential to obtain accurate predictions. In this paper, we introduce a feature selection algorithm called symmetrical uncertainty qualitative mutual information (SU-QMI), which selects features based on estimates of their relevance, redundancy, and interdependency. We use these together with graph theory to derive a feature selection method for identifying putative ARGs in Gram-negative bacteria. We extract physicochemical, evolutionary, and structural features from the protein sequences of five genera of Gram-negative bacteria—Acinetobacter, Klebsiella, Campylobacter, Salmonella, and Escherichia—which confer resistance to acetyltransferase (aac), β-lactamase (bla), and dihydrofolate reductase (dfr). Our SU-QMI algorithm is then used to find the best subset of features, and a support vector machine (SVM) model is trained for AMR prediction using this feature subset. We evaluate performance using an independent set of protein sequences from three Gram-negative bacterial genera—Pseudomonas, Vibrio, and Enterobacter—and achieve prediction accuracy ranging from 88 to 100%. Compared to the SU-QMI method, BLASTp requires similarity as low as 53% for comparable classification results. Our results indicate the effectiveness of the SU-QMI method for selecting the best protein features for AMR prediction in Gram-negative bacteria. Full article

Infectious diseases, such as lactococcosis caused by Lactococcus garvieae, are portrayed as critical limiting factors in aquaculture. The antimicrobial properties of lactic acid bacteria (LAB), mainly the production of organic acids and bacteriocins (e.g., the lanthionine containing nisins A and Z; NisA and NisZ, respectively), led to propose LAB as probiotics to be used as an alternative and/or complementary strategy to vaccination and chemotherapy in aquaculture. L. lactis RBT18, isolated from cultured rainbow trout (Oncorhynchus mykiss, Walbaum), exerts strong, direct, and extracellular antimicrobial activity against L. garvieae and other ichthyopathogens, with the latter being heat-resistant (100 °C, 10 min), and thus suggesting the involvement of a thermostable antimicrobial compound (i.e., bacteriocin). Cross-immunity tests using the agar well diffusion test (ADT) and PCR assays suggested that NisA/Z is the bacteriocin responsible for the extracellular antimicrobial activity exerted by L. lactis RBT18. To demonstrate this hypothesis, the bacteriocin was purified to homogeneity by two multi-chromatographic procedures. MALDI TOF-MS analyses of purified samples after the last reverse-phase chromatography step identified the presence of NisZ (3330 Da), and its oxidized form (3346 Da), derived from the oxidation of a lanthionine ring. The oxidized NisZ showed a diminished antimicrobial activity that would increase the chances of bacterial pathogens to evade its antimicrobial activity. Further experiments are necessary to assess the in vitro and in vivo safety and efficiency of L. lactis RBT18 as a probiotic in aquaculture, but also to optimize the environmental conditions to reduce bacteriocin oxidation and thus bacterial pathogen resistance. Full article

Plants have been explored and used as sources for antimicrobial extract and compounds for many years, but galls—specialized structures forms on such by diversity of organisms—have been explored much less. Aphid galls host many insects in closed, humid and sugar rich environments for long periods. We have tested the antimicrobial properties of Slavum wertheimae aphid galls on Pistacia atlantica. Secondary metabolites were extracted from leaves and galls with organic solvents, and essential oils with Clevenger, and tested by disk diffusion assay and volatile effect on bacteria and fungi, respectively. The results demonstrated that gall extracts/essential oils had much stronger activity against the diversity of bacteria and fungi. The large diversity of galls suggest they could be explored as source for novel compounds. Full article

Polyphenol oxidases (PPOs) are a group of Cu-containing enzymes exhibiting two activities: catechol oxidase and tyrosinase. Their precise mechanism of action and the structural elements that determine the distinction between the two activities are yet to be fully understood. In nature, PPOs catalyze the oxidation of several phenols to o-quinones, considerably affecting the color and nutritional properties of numerous agricultural products. On the other hand, PPOs have been widely employed as biocatalysts in food, pharmaceutical, and cosmetic industries. TtPPO is a PPO from the thermophilic fungus Thermothelomyces thermophila (TtPPO), capable of degrading of chlorophenols (CPs), contagious by-products of various pesticides. The present work aims to clarify the structural determinants of TtPPO function, by performing protein-ligand docking experiments via YASARA software. The docking results are compared with biochemical data, and the role of specific amino acids in TtPPO function is investigated. The identification of the amino acids involved in binding of the different substrates to the active site of the enzyme would allow the structure-based design of a more efficient biocatalyst for wastewater treatment. Full article

The enterobacteria that produce β-lactamases are the main focus of infections in the healthcare environment. This is due to the difficulty they present in terms of treatment, their ease of transmission, and the impact they represent at the economic and personal level. The bacteria of greatest clinical relevance are those with resistance to third and fourth generation cephalosporins, extended spectrum β-lactamase and AmpC. Currently, carbapenemics are one of the few antimicrobials effective against multi-drug resistant organisms. However, the emergence of carbapenem-resistant enterobacteria has increased health concerns. These microorganisms include K. pneumoniae, a pan-resistant bacteria with high morbidity and mortality rates in public health facilities. In this work, we have carried out a review on the antimicrobial resistance genes found in its genome, as well as the resistance mechanisms involved. Finally, we will focus on the main outbreaks causing nosocomial infections during the last few years. Full article

: The present work was carried out on 133 halophilic strains isolated on MGM (Modified Growth Medium) medium with 12 and 23% (w/v) of salt. A screening of the extracellular proteolytic activities, carried out on the same medium supplemented with casein or gelatin at 1% (w/v), allowed us to select 24 bacterial and 21 archaeal strains presenting a precipitate around the colonies for casein and/or a translucent halo (after addition of Frazier’s reagent) for gelatin. The enzymatic test was performed on liquid medium in microculture in a 2 mL Eppendorf tube. The assay of the proteolytic activity, using Azocasein as substrate, followed two protocols—the first with PBS and the second with Tris HCl, with positive and negative controls—and demonstrated interesting results for 10 strains among the 45 tested including five bacteria and five archaea. These underwent morphological, physiological and molecular characterizations based on amplification and sequencing of the 16S ribosomal RNA gene. Full article

The human pathogen Mycobacterium tuberculosis (MTB) is indeed one of the renowned, important, longtime infectious diseases, tuberculosis (TB). Interestingly, MTB infection has become one of the world’s leading causes of human death. In trehalose synthase, the protein NCGM 946K2 146 found in MTB has an important role. For carbohydrate transport and metabolism, trehalose synthase is required. The protein is not clarified yet, though. In this research, an in silico approach was, therefore, formulated for functional and structural documentation of the uncharacterized protein NCGM946K2_146.Three distinct servers, including Modeller, Phyre2, and Swiss Model, were used to evaluate the predicted tertiary structure. The top materials are selected using structural evaluations conducted with the analysis of Ramachandran Plot, Swiss-Model Interactive Workplace, ProSA-web, Verify 3D, and Z scores. This analysis aimed to uncover the value of the NCGM946K2_146 protein of MTB. This research will, therefore, improve our pathogenesis awareness and give us a chance to target the protein compound. Full article

(1) Background: Probiotics are a live microbial supplement that improve hosts’ health by maintaining intestinal microbiota. The evidence suggests that probiotics can be used as a therapeutic strategy to improve overall digestive health. Lactic acid bacteria strains have been extensively used as probiotics. (2) Method: To isolate lactic acid bacteria with probiotic potential from food samples. Probiotic properties such as tolerance to low pH, bile, sodium chloride, lysozyme, antibiotic susceptibility, cell surface hydrophobicity, and antimicrobial activity were determined. (3) Results: Ten different isolates were examined to study their probiotic potential. In this study, Lactobacillus brevis was isolated and showed most of the probiotic properties, such as10% sodium chloride tolerance, 1% bile tolerance, growth in pH 2, and antimicrobial activity against E. coli, S. aureus, K. pneumoniae, and P. aeruginosa. Formation of biofilm by Klebsiella pneumoniae and Pseudomonas aeruginosa was also inhibited by cell free extracts of L. brevis, which reveals its therapeutic relevance. In addition, it was found to be stable at low temperature (4°C). (4) Conclusion: The above-mentioned results of L. brevis suggest that it has promising potential to be considered “probiotic”. Further in vivo assessments could be carried out that would provide its dual role of prevention as well as use in therapy. Full article

Shiga toxin (Stx)-producing Escherichia coli strains are foodborne pathogens that can cause severe human diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Stxs are encoded by bacteriophages (Stx phages) which show remarkable variations in genome composition and harbour several genes of unknown function. Recently, a gene encoding a sialate O-acetylesterase (NanS-p) was identified in some relevant Stx2a phages and it was suggested that it could provide advantages for bacterial growth in the gut. The aim of this study was to analyse the presence and sequence of nanS-p genes in available Stx2a phage genomes. A total of 59 DNA sequences of Stx2a phages were extracted from the NCBI GenBank database with the BLAST program using the stx_2a sequence from phage 933W as a query sequence, either as complete phage genomes (45) or from bacterial genomes by subsequent analysis with the PHASTER web server (14). Comparative analysis revealed that nanS-p was located downstream of stx_2a in all genomes. Twenty different amino acid sequences of NanS-p were identified. Specifically, catalytic esterase domains showed only 11 possible sequences, with differences mainly observed in nine amino acid positions. Sequences corresponding to the N-terminal domain (DUF1737) showed three possible sequences, two of them closely related, while the C-terminal domain was highly variable, with four groups with structural differences. Since sialate O-acetylesterase activity has been determined from particular Stx2a phages, new studies are necessary to evaluate if the NanS-p subtypes identified in the present study also differ in their biological activity. Full article

Our aim was to evaluate the susceptibility of bacterial biofilm formation and the metabolic changes occurring in the bacterial cells by the action of ivy, strawberry tree, lavender, sulla and tree of heaven monofloral honeys. Listeria monocytogenes was the most sensitive bacteria with percentages of biofilm inhibition up to 72.20%. Pseudomonas aeruginosa was less sensitive, but tree of heaven and sulla honey caused an inhibition of biofilm up to 40.41% and 35.85%, respectively. The tree of heaven honey acted on the P. aeruginosa metabolism (75.24%). Staphylococcus aureus, majorly resistant to the biofilm-inhibitory action of the honey, was more sensitive at the metabolic level (61.63% inhibition in the presence of the tree of heaven honey). Full article

Urban soils are subject to significant anthropogenic impact, which affects the physicochemical composition of soils, as well as microbial natural diversity. Anthropogenic pollution of urban soils with lipids, in particular vegetable and mineral oils, can pose a certain danger to the biological balance in the soil ecosystem. For the quantitative determination of the number of heterotrophic microorganisms, MPA, a mineral medium with oil, was used for the isolation of lipolytic bacteria. In the first two weeks after the addition of lipids, a decrease was observed in relation to the control of the number of heterotrophic microorganisms in all variants of the experiment. The negative effect of lipid contamination on the native soil microbiota was short-lived, and by the fourth week of the experiment, a sharp increase in heterotrophic microorganisms was noted. Twenty six strains of bacteria were isolated from the mineral medium with oil. Nine strains were identified that predominated in their numbers over the rest of the bacteria in this environment. Six strains were identified as belonging to the order Enterobacterales, two strains belonged to the order Pseudomonadales, genus Pseudomonas, and one strain belonged to Rhizobium radiobacter. Full article

Bacteria of the Rhizobium genus form a group of microorganisms existing in the environment in two forms: symbiotic, in the root nodules of Fabaceae sp. plants and free-living, and saprophytic in the soil environment. The subject of this study was genetic identification and characterization of metabolic activity of different strains from Rhizobium genus bacteria. The study was conducted on the 16 bacteria strains from the collection of the Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation in Puławy, Poland. Based on the sequencing of PCR products, we found that all strains belong to one species—Rhizobium leguminosarum. The study of metabolic activity was performed using the GEN III BIOLOG system method (Biolog Inc., Hayward, CA, USA). Metabolism analysis of all R. leguminosarum strains with the use of GEN III™ plates showed that carbohydrates (CH) were the most intensively utilised group of substrates. Between the Rhizobium leguminosarum strains, there are metabolic differences in terms of the studied features. Full article

The present work was aimed at investigating the effects of a four strains consortium—Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria—on crops of Allium cepa L. and its soil health. The bacterial consortium was inoculated on seeds of two different onion varieties; inoculated seeds and control ones (treated with autoclaved inoculum) were sown in open-field and followed until harvest. Plant growth development parameters, as well as soil physico-chemical and molecular profiles (DNA extraction and 16S community sequencing on the Mi-Seq Illumina platform), were investigated. The results showed a positive influence of bacterial application on plant growth, with increased plant height (+18%), total chlorophylls (+42%), crop yields (+13%), and bulbs dry matter (+3%) than the control. The differences between control and treated experimental conditions were also underlined in the bulb extracts in terms of total phenolic contents (+25%) and antioxidant activities (+20%). Soil fertility and microbial community structure and diversity were also positively affected by the bacterial inoculum. At harvest, the soil with the presence of the bacterial consortium showed an increase of total organic carbon, organic matter, and available P and higher concentrations of nutrients than control. The ecological indexes calculated on the molecular profiles showed that community diversity was positively affected by the bacterial treatment. The present work allowed to remark the effective use of plant growth-promoting bacteria as a valid fertilization strategy to improve yield in productive landscapes, whilst safeguarding soil biodiversity. Full article

Enteropathogenic Escherichia coli (EPEC) are important agents of acute diarrhea in children living in developing countries. A severe dysfunction of the intestinal epithelial barrier occurs during EPEC infection, leading to diarrhea and inflammation as consequences. EPEC main virulence factors include the adhesins intimin and bundle-forming pilus (BFP), as well as several effector proteins translocated to the enterocyte by the type-three secretion system. The initial interaction of EPEC with the host cell and the role of effector proteins in this process are well known. However, the role of the EPEC virulence factors in macrophage activation is not fully understood. Hence, we analyzed the ability of intimin and bundle-forming pilus (BfpA) to activate the innate response mediated by macrophages, where the production of the proinflammatory cytokines TNF-α, IL-1, IL-6 and IL-12, as well as the anti-inflammatory cytokine IL-10 and chemokine MCP-1, were evaluated. Our results showed that recombinant intimin and BfpA activate macrophages in a dose-dependent manner, and the stimulated cells produced TNF-α, IL-12, IL-6, IL-10 and MCP-1, but not IL-1β. No synergistic effect was observed in the production of pro-inflammatory cytokines by combining BfpA and intimin, although production of IL-10, an anti-inflammatory mediator, was potentiated at a higher dose. The effect observed was largely attributed to these proteins, as the treatment of proteins with polymyxin B did not alter the production of TNF-α. Thus, herein we showed that intimin and BfpA can activate the innate immune response, inducing the production of pro- and anti-inflammatory cytokines, as well as chemokines, playing additional role as inflammatory molecules in the early steps of EPEC infection. Full article

The return of plant residues to the ground is used to promote soil carbon sequestration, improve soil structure, reduce evaporation, and help to fix additional carbon dioxide in the soil. The microbial communities with diverse ecological functions that colonize plant residues during decomposition are expected to be highly dynamic. We aimed to characterize microbial communities colonizing wheat straw residues and their ecological functions during the early phase of straw decomposition. The experiment, run in Central Germany, was conducted in a conventional farming system under both ambient conditions and a future climate scenario expected in 50–70 years from now. We used MiSeq illumina sequencing and network analysis of bacterial 16S rRNA and fungal ITS genes. Our results show that future climate alters the dynamics of bacterial and fungal communities during decomposition. We detected various microbial ecological functions within wheat straw residues such as plant growth-promoting bacteria, N-fixing bacteria, saprotrophs, and plant pathogenic fungi. Interestingly, plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome under both ambient and future climate conditions. Therefore, we applied co-occurrence network analysis to predict the potential impacts of climate change on the interaction between pathogenic community and other bacterial and fungal microbiomes. The network under ambient climate consisted of 91 nodes and 129 correlations (edges). The highest numbers of connections were detected for the pathogens Mycosphaerella tassiana and Neosetophoma rosigena. The network under future climate consisted of 100 nodes and 170 correlations. The highest numbers of connections were detected for the pathogens Pseudopithomyces rosae and Gibellulopsis piscis. We conclude that the future climate significantly changes the interactions between plant pathogenic fungi and other microorganisms during the early phrase of decomposition. Full article

Personalized dietary supplements adapted to the individual needs of athletes and the elderly enriched with microbial propionic acid were produced in form of a powder, ready to be mixed in drinks such as orange juices. Studies have shown that fresh and pasteurized orange juices have a positive influence on gut microbiota, and exhibit selective prebiotic activity, particularly in terms of gut microbiota, by increasing Lactobacillus spp., Enterococcus spp., Bifidobacterium spp., and Clostridium spp., and reducing Enterobacteria. Besides, studies been reported the effect of the combined use of probiotics and organic salts, such as propionic acid salts, on the in vitro inhibition of microorganisms. Additionally, the short chain fatty acid propionic acid influences the gut-mediated immune regulation of people, reduces lipogenesis, and inhibits serum cholesterol synthesis. Full article

Staphylococcus aureus is a Gram-positive opportunistic pathogen that imposes a heavy burden on society. What sets this pathogen apart is the sheer spectrum of infections it can cause, which range from benign skin and soft tissue infections to lethal endocarditis and bacteraemia. The ability of S. aureus to cause this gamut of infections is conferred by its arsenal of virulence factors that are under the control of the Accessory Gene Regulator (Agr) system. However, a large proportion of clinical isolates have inactivating mutations in this important regulatory system. We previously showed that, contrary to the common dogma, not all these mutations are evolutionary ‘dead-ends’ and a fraction are phase variants which can revert to an Agr active state. Here we report that some Agr deficient isolates can revert a haemolytic phenotype without repairing their Agr system. We collected a series of 30 Agr negative primary patient samples in order to assess the significance of our previous findings on the existence of Agr phase variants. We used primary samples to avoid strains that had undergone multiple clonal expansions before being tested for reversibility. We assessed Agr reversibility by serially passaging strains and screening for phenotypic reversion of haemolysis. We show that two strains reverted haemolysis and one reverted alpha haemolysin activity without any genetic changes in agr (and hla for the alpha revertant). These results add further complexity to the phenomenon of Agr shutdown observed in the clinical setting and corroborate recent findings of compensatory mutations arising in Agr deficient clinical strains. Full article

Carbapenem-resistant (CR) Gram-negative bacilli, including Enterobacteriaceae and the non-fermenters, represent the most notorious pathogens due to the high incidence of morbidity and mortality, especially in immunocompromised patients in intensive care units. Carbapenem resistance is mainly associated with the production of carbapenemases, which are β-lactamases belonging to different Ambler classes (A, B, D) that can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, hydrolyzing a wide variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are both clinical, posing significant challenges in the treatment of healthcare-associated infections by compromising the activity of the last-resort antibiotics, and epidemiological, due to their dissemination across almost all geographic regions. An important advancement is a handful of newly launched antibiotics targeting some of the current most problematic Gram-negative pathogens, namely carbapenem-resistant Enterobacteriaceae (CRE). The most appropriate antimicrobial therapy to treat CRE infections is still controversial. Combination therapy is preferred over monotherapy due to its broad-spectrum coverage, synergic activity, and low probability of selecting resistance. In this mini-review, current and future promising antibiotics that are currently under investigation for winning the war against the emerging CRE are discussed. Full article

Cholera outbreaks are prevalent in countries with a low Human Development Index (HDI) where people have limited access to safe drinking water, sanitation and hygiene (WASH). Intriguingly, the state of Kerala which records the highest HDI in India is endemic to cholera. We discuss the epidemiology of a cholera outbreak reported among migrant workers of Kerala in 2017. Virulence genes of Vibrio cholerae, toxR and ctxA, were detected in the river and ground water samples collected from the outbreaks sites which indicates need of enhanced awareness on WASH practices among migrant workers. The pathogenic Vibrio cholerae isolated from four patients in two districts had a similar DNA band pattern when analysed using repetitive extragenic palindromic-PCR (BOX), which indicates their single clonal origin. The four isolates were serotyped as O1 Ogawa. These isolates were resistant to multiple antibiotics including the carbapenem like imipenem. Nevertheless, isolates of these pathogenic bacteria were susceptible to tetracycline, identical to clinical isolates of Vibrio cholera reported earlier from this region. The current study highlights the importance of generating awareness on WASH protocols among migrant workers to prevent the outbreaks and considers community-based data as socioeconomic variable to predict the incidence of cholera. Full article

Rhizobacteria play an important role in maintaining soil balance. Among these bacteria, there are those taht have shown their ability to promote the growth of plants, known as Plant Growth Promoting Rhizobacteria (PGPR). In our work, we are interested in characterizing 110 bacterial strains isolated in the field in the region of Ben Badis (Constantine Algeria) from 5 varieties of faba bean. Phenotypic and biochemical characterization showed that most of the isolates are cream-colored, slightly raised, flat and opaque, Gram−, catalase+ and oxidase−, and Bacillus form. PCA analysis allowed us to select 40 isolates with a high degree of variability to continue our work. The results obtained have directed us towards different taxonomic groups (rhizobium, Pseudomonas, Bacillus etc.). The evaluation of the PGPR potential of bacteria (phytostimulation, biofertilization and biocontrol), showed that 100% of bacteria are able to produce auxin at different concentrations, with the highest concentration (177.77 µg/mL) for the isolate 6, and that more than 50% of isolates are capable of producing nitrogen, ammonia and phytate mineralization. These PGPR traits have a direct effect on plant growth of five varieties of the faba bean and can be used to select the best performing bacteria for inoculation tests. Full article

Various products coded by genes recognized in microbiota are involved in many biochemical pathways in thehuman body. Bacteria composition in the gastrointestinal tract may be an important aspect of selected diseases’ pathogenesis, including irritable bowel syndrome (IBS). Traditional research methods based on classical microbiology, using selective media for bacterial growth, have proven to be ineffective. The use of genetic methods allows the identification of unidentified microbiota, including anaerobes. Roseburia hominis is a flagellated gut anaerobic commensal bacterium, producing short-fatty acids. The knowledge about the microbial components of the intestinal ecosystem is still very limited, including Roseburia hominis. This study aimed to identify Roseburia hominis in the faeces samples obtained from IBS patients and healthy individuals, using PCR techniques. The differences between studied groups were observed, and it was concluded that R. hominis may play a role in IBS etiology. Full article

Prickly pear [Opuntia ficus-indica (L.) Mill.] is a succulent plant that is globally diffused. The oil obtained from its seeds has antimicrobial and antioxidant properties. We evaluated the antibiofilm of the oil and its capacity to block the metabolic changes taking place in the microbial cells included in the biofilm. The oil was capable to inhibit at 38.75% the biofilm of Escherichia coli, Pseudomonas aeruginosa, and Pectobacterium carotovorum (38.75%, 71.84%, and 63.06% inhibition, respectively). The metabolic activity of the microbial cells within the biofilm was also strongly inhibited. The action of the prickly pear seeds oil was effective also in blocking at 64.97% the metabolism of Listeria monocytogenes cells. Full article

An approach of new and sustainable uses for by-products generated in the wine production industry, one of the agro-food sectors of importance, has been studied. Wine lees, a sediment obtained in different processes of decantation of wine, have been used to produce biomass of microalgae enriched in carotenoids as high added value biomolecules. Experiments to incorporate chemical components of wine lees into microalgae biomass to understand the effect of these residues on the growth and biosynthesis of carotenoids into commercial microalgae Chlorella sorokiniana have been done. Algal culture system has been optimized and preparation of culture media have been obtained by extracting in water the soluble nutrients contained in the lees at different concentrations between 5% and 50% w/v. Optimal growth was obtained using extraction of wine residues at 5% and 10% w/v. At 10% oxidative stress, measured as carotenoids production (specially lutein) and antioxidant activity (DPPH method), was more intense than the obtained using residues at 5%. Our results show that growth in culture media prepared with wine lees extracts stimulated the antioxidant activity and the production of carotenoids in C. sorokiniana cells. Preliminary information, not only to produce sustainable growth media for biomass of microalgae enriched in high value molecules, but also to reuse nutrients contained in wine industry by-products what is of particular interest in the context of a circular economy is provided. Full article

Lignocellulosic biomass comprises cellulose, hemicellulose, and lignin and is a potential source of fuels and chemicals. Although this complex biomass is persistent, it can be cooperatively decomposed by a microbial consortium in nature. In this study, a coculture of the moderately thermophilic bacteria Thermobifida fusca and Ureibacillus thermosphaericus was used for biodegradation of rice chaff. The bacterial strains were incubated in modified Brock’s basal salt medium (pH 8.0) supplemented with yeast extract and rice chaff at 50 °C for 7 days. The concentration of reducing sugars and the enzymatic activities of laccase, lignin peroxidase, cellulase, and xylanase in the supernatant of the culture medium were measured every day. The concentrations of reducing sugars in solo cultures of T. fusca and U. thermosphaericus and a mixed culture of the two strains after 7 days of incubation were 0.047, 0.040, and 0.195 mg/mL, respectively, indicating that the decomposition of rice chaff was enhanced in the coculture. Based on the results, it is thought that the lignin surrounding the cellulose was decomposed by laccase and lignin peroxidase secreted from U. thermosphaericus, resulting in cellulose and hemicellulose in the rice chaff being easily decomposed by enzymes from T. fusca. Full article

Ready-to-eat food microbiota are the microorganisms present in the dishes that are currently consumed during meals. These microorganisms include those that may have a health benefit, are potentially pathogenic or have not yet been given a function. Foods suitable for consumption are not free of microorganisms; however, within the food industry only yeasts have been given a beneficial function, while other microorganisms such as filamentous fungi and bacteria have been studied for their negative effects on food. We determined the bacterial diversity in samples of highly demanded, freshly prepared, unspoiled ready-to-eat dishes by high-throughput DNA sequencing of 16S rDNA libraries. We found a great bacterial diversity, whereby the most abundant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, TM7 and Thermi, among others. These phyla included bacteria with remarkable abundances in some dishes. The alfa diversity analyses showed that the main dishes had the largest diversity. The beta-diversity analyses clustered the bacterial communities of soups, side plates, desserts, and beverages, and some main dishes. Based on our results we conclude that unspoiled ready-to-eat Mexican dishes contain a rich bacterial diversity, which may contribute to the organoleptic properties of the dishes without representing a sanitary risk for the consumers. Full article

Many bacterial communities display oscillations throughout the day; it has been shown that in humans, the healthy gut microbiome also shows fluctuations in the abundance of bacterial community, related with feeding times and sleep cycles. Likewise, in human milk there are beneficial bacteria that undergo changes in the same time interval and are transferred to the newborn by breastfeeding, colonizing the gastrointestinal tract. The aim of this work was to identify changes in the bacterial diversity of human milk throughout the day. Human milk samples were collected from a single donor three times during the day (morning, afternoon, night) for 5 consecutive days, and bacterial DNA was extracted. Bacterial diversity was characterized by high-throughput DNA sequencing of 16S rDNA libraries, and taxonomy was assigned by comparison of sequences against a database. Finally, the significant differences in relative abundance and alpha and beta diversity were determined. The analysis of human milk displayed changes in the bacterial diversity during the day, with significant changes in the Shannon diversity index. Our data show that human milk seems to be affected by the daytime change, and these changes could influence the infant gut microbiota. Full article

Though therapeutic compounds can be extracted directly from medicinal plant tissues; it is now known that many phytotherapeutic compounds are actually produced by associated microorganisms or due to their interaction with the plant. Bouvardia ternifolia is a medicinal plant that can be considered a potential source of therapeutic compounds, such as the antitumoral molecule bouvardin. We characterized the endophytic, endophytic+epiphyte and soil bacterial microbiota in the flower, leaves, stems and roots in specimens of this plant through 16S rDNA sequencing. We found that Proteobacteria followed by Actinobacteria were the most abundant bacteria phyla in this plant. On the other hand, the most representative genera living endophytically were Propionibacterium, Paraccocus, Lactobacillus, Kaistobacter, Methylobacterium and Erwinia. This study provides evidence of the composition and diversity of the bacterial communities present in soil and tissues of B. ternifolia which can be considered for subsequent analysis and understanding of the therapeutic compounds that give this species its medicinal properties. Full article

Patterns of trees’ endogenous rhythmic growth (ERG) and paralleled C allocation shift between root and shoot systems have been studied, but there is still a need to understand their impact in shaping soil microbiomes. Moreover, the impact of plants on soil microbial communities can be modulated or overweighed by time-induced plant and/or seasonal changes. Thus, we intended to analyze the structure of soil microbiomes as response to simultaneous alternated host tree root and shoot flushes and time-induced changes within one vegetation period at two sites in Central Germany. In this study, we utilized oak phytometers (Quercus robur L., clone DF159) as host trees, and made use of their ERG, whereby consecutive root and shoot flushes make a complete growth cycle. We studied two complete growth cycles during the same vegetation period, performed a non-destructive soil sampling and applied high-throughput amplicon sequencing of the bacterial 16S gene and the fungal ITS2 region. As C allocation shifts between the tree root and shoot, released root exudates and consequently the nutrient availability alternate for soil microorganisms. We therefore anticipated different microbial communities in the host tree root zone along the growth cycles until autumnal leaf senescence. In our results, the bacterial community exhibited a directional change over time along the vegetation period. In contrast, the fungal community appeared sample specific. Our findings enlarge the current understanding of the temporal microbial assembly in the host tree root zone. Full article