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  • Open access
  • 53 Reads
Decomposition of rice chaff using a cocultivation system of Thermobifida fusca and Ureibacillus thermosphaericus

Lignocellulosic biomass comprises cellulose, hemicellulose, and lignin and is a potential source of fuels and chemicals. Although this complex biomass is known to be a persistent compound, it can be cooperatively decomposed by a microbial consortium in nature. The cellulolytic and hemicellulolytic bacterium Thermobifida fusca and the lignolytic bacterium Ureibacillus thermosphaericus are moderately thermophilic and have similar optimal growth temperatures and pH values. In this study, the coculture of T. fusca and U. thermosphaericuswere used for the biodegradation of rice chaff at 50ºC.

The bacterial strains were incubated in the modified Brock’s basal salts medium (pH 8.0) supplemented with yeast extract (0.5%) and rice chaff (0.5%) at 50ºC 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 viable cells in each culture were counted as colony forming units.

The cell density of the coculture reached 4.6 × 108 CFU/mL on the second day and maintained a concentration of >3.3 × 107 CFU/mL throughout the study period. The concentrations of the reducing sugars in the cultures of T. fusca and U. thermosphaericus as well as in the mixed culture of the two strains after 7 days of incubation were 0.047 mg/mL, 0.040 mg/mL, 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 that cellulose and hemicellulose in the rice chaff were easily decomposed by the enzymes from T. fusca.

  • Open access
  • 239 Reads
Current promising antibiotics and future approaches in combating carbapenemase-producing Enterobacteriaceae

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, especiallyin 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 widevariety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemases 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 recently launched new 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 selectingfor 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.

  • Open access
  • 58 Reads
Individualized dietary supplements enriched with microbial propionic acid for athletes and elderly with benefits on gut microbiota

Personalised dietary supplements adapted to the individual needs of athletes and elderly enriched with microbial propionic acid are produced in form of a powder, ready to be mixed in drinks such as orang juices. Recent studies shown that fresh and pasteurized orange juices have a positive influence on gut microbiota, 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 have 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. On the other side, the short chain fatty acid propionic acid influences the gut-mediated immune regulation of people, and reduce lipogenesis and inhibit serum cholesterol synthesis.

  • Open access
  • 49 Reads
Future climate alters pathogens-microbiome co-occurrence networks in wheat straw residues during decomposition

The return of plant residues to the soil is used to promote soil carbon sequestration, improve soil structure, reduce evaporation, and help to fix carbon dioxide in the soil. Microbial communities colonize plant residues during decomposition is expected to be highly dynamic with diverse ecological functions. We aimed to characterize microbial communities colonizing wheat straw residues and their ecological functions during the early phase of decomposition. The experiment was conducted in 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 showed that future climate alters the dynamics of bacterial and fungal communities. We detected various microbial ecological functions within wheat straw residues such as plant growth promoting bacteria, N-fixing bacteria, saprotrophs and plant pathogens. 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 potential impacts of climate change on the interaction between pathogenic community and other bacterial and fungal microbiomes. The network of ambient climate consisted of 91 nodes and 129 correlations (edges). The highest number of connections was between the pathogen Mycosphaerella tassiana and Plectosphaerella oratosquillae with other microbes while the network of future climate consisted of 100 nodes and 170 correlations. The highest number of connections was between the pathogen Pseudopithomyces rosae and Gibellulopsis piscis with other microbes.

  • Open access
  • 64 Reads

Introduction: All the microorganisms inhabiting the particular human body regions or organs are collectively called a microbiome. The human body encompasses several various microbiomes that include specific populations of microorganisms. Gut microbial imbalance (dysbiosis) may lead to various diseases, including irritable bowel syndrome (IBS). While human microbiomes are abundant in non-breeding species, and traditional research methods based on classical microbiology have been proved to be ineffective, it is necessary to characterize in detail their composition to further evaluated function of particular microbiota. The knowledge about the microbial components of the intestinal ecosystem is still very limited, including Roseburia hominis.

Material and methods: The aim of the study was to identify Roseburia hominis in the faeces samples using PCR techniques. The study was conducted on samples obtained from patients with IBS (women, n=70, and men, n=50) and individuals without any intestinal symptoms (women, n=28, and men, n=23). After bacterial DNA extraction, qualitative identification of Roseburia hominis, based on the amplification of RHOM_14625 and RHOM_14635 gene fragments was performed. Then, a statistical analysis of the obtained data, using the Chi-square test was conducted.

Results: Assessed RHOM_14625 gene fragments were recognized in samples derived from 9 female and 21 male IBS patients, and in 15 and 7 female and male control individuals, respectively. The presence of the RHOM_14635 gene fragment was detected in 35 and 33 samples obtained from female and male patients, respectively, and in 18 and 7 samples from female and male control individuals. Differences in the analyzed genes distribution were statistically significant (p-value = 0.0001, and p-value = 0.02, respectively).

Conclusion: Further molecular studies are necessary to evaluate the role of Roseburia hominis in the intestinal microbiome in IBS patients.

Funding: Grant Preludium - NCN 2016/21/N/NZ5/01423 (principal: Paulina Pecyna).

  • Open access
  • 56 Reads
Catabolism of branched chain and aromatic amino transferases, route to fusel alcohols and acetates by the Ceratocystidaceae.

Fungi in the family Ceratocystidaceae produce fusel alcohols and acetates that have fruity and floral odours. Since fusel alcohols are produced in fungi from amino acids via the Ehrlich pathway in a three-step catabolic process, we identified and characterized the genes encoding enzymes involved in catalysing the first and second steps in this pathway. We identified three putative branched-chain amino transferases, three putative aromatic amino transferases and a putative pyruvate decarboxylase in each of the Bretziella, Berkeleyomyces, Ceratocystis, Davidsoniella, Endoconidiophora, Huntiella and Thielaviopsis genomes. Using gas chromatography coupled to mass spectrometry (GC-MS), also revealed that all the strains included in this study produced high levels of isoamyl acetate. In contrast, only some members of Bretziella, Berkeleyomyces, Ceratocystis and Huntiella produced isobutyl acetate, while only the Berkeleyomyces, Ceratocystis and Huntiella strains produced 2-phenylethyl acetate in low quantities. Either by accepting the branched-chain amino acid substrates (valine and leucine) or accepting the aromatic amino acid substrate (phenylalanine). Fusel alcohols and acetates produced by fungi in the Ceratocystidaceae can therefore be used as additives of food products, perfumes and soaps. In addition, identified fusel alcohols can potentially be utilized as biofuels or biodiesels, bringing solutions to the problems associated with limited fossil resources and climate change.

  • Open access
  • 86 Reads
The Vaginal and Fecal Microbiota associated to cervical cancer development in a mice model.

Introduction. Cervical cancer is an important health issue worldwide. Many factors are related to this condition as persistent human papillomavirus infection, the use of hormonal contraceptives, pH changes, and bacterial vaginosis. The association between the microbiota and cervical cancer is an interesting issue; given that environmental and hormonal factors changing the vaginal microbiota may contribute to cancer. Methods Using High-throughput DNA sequencing of V3-16S rDNA libraries, we determined the bacterial diversity in cervicovaginal lavages and fecal samples at different stages of cervical cancer development in the K14HPV16E7 mice model under +/- 17β-estradiol (E2) stimulus and compared it with an isogenic control (FVB). Results. We found that continuous E2 administration during 6 months in the model with type 16 E7 expression causing the development of cancer, is associated with significant changes in the microbiota diversity in the cervicovaginal lavages. Similar results were not observed in the model when no E2 was administered neither in the FVB mice. Comparable changes in the microbiota diversity of fecal samples were not observed. Conclusions. The persistent expression of E7 oncogene or the 17β-estradiol for longer periods of time, cause changes in the vaginal microbiota diversity and the cervical epithelium not necessarily leading to cervical cancer; however, the combined action of both, causes cervical carcinoma and defined changes in the abundance of bacterial taxa in the cervicovaginal lavages, suggesting a specific organ effect of E7 expression associated to E2 on the vaginal microbiota. Acknowledgments. Work supported by Cinvestav and CONACyT 163235 INFR-2011-01, FONSEC SS/IMSS/ISSSTE-CONACYT-233361, and CONACyT 0201904 grants.

  • Open access
  • 66 Reads
Production of biocatalysts and bioactive compounds from Greek basidiomycete wild strains grown in different induction media

White-rot basidiomycetes are the only microorganisms with the ability to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for degrading cellulose/hemicellulose and lignin, while they are also capable of oxidizing a wide range of aromatic or toxic compounds. In addition, they produce secondary metabolites with applications in the cosmetics industry. In the present work, three wild strains of Basidiomycete fungi (Pleurotus citrinopileatus, Abortiporus biennis and Ganoderma lucidum) from Greek habitats were grown in different media (agroindustrial residues, such as olive oil mill wastewater, and corn cob). The cultures were examined in regard to the production of biotechnologically relevant enzymes and bioactive compounds. All strains were found to be preferential lignin degraders, similarly to most white-rot fungi. Bioinformatic analyses were performed on the proteome of the strains P. citrinopileatus and A. biennis, focusing on CAZymes with biotechnological relevance, and the results were compared with the enzyme activities in the culture supernatants. In terms of secondary metabolism, compounds production and bioactivity of the extracts have been evaluated in relation to the different types of culture media. Principal components analysis (PCA) and volcano plots were generated based on ultra-high-performance liquid chromatography - high resolution mass spectrometry (UHPLC-HRMS) data to reveal significant variations in bioactive compounds amongst the extracellular fluids and fungal biomasses of cultures. Overall, all three Basidiomycete strains were shown to be potent producers of secondary metabolites, but also of oxidative enzymes of special interest for biomass conversion applications.

  • Open access
  • 72 Reads
Variation of the human milk bacterial diversity during the time of the day.

Introduction. In previous studies, it has been observed that the concentration of some components of breast milk such as proteins, carbohydrates, lipids among others vary throughout the day. In the same way, it has been observed that bacteria diversity undergoes changes at the same time interval. In human milk there are also beneficial bacteria from the mother that are transferred to the newborn by breastfeeding, being the main source of colonizing bacteria of the newborn's gastrointestinal tract. Many of these bacterial communities display oscillations throughout the day, contributing to homeostasis and play an important role in various physiological processes. It is reported that the healthy human microbiome is regulated by the circadian cycle, where fluctuations in abundance of the bacterial community occur, in addition to a relationship in feeding times and sleep cycles of the mother. The aim of this work was to identify possible fluctuations and variations in bacterial diversity and composition on human milk throughout the day. Methods Human milk samples were collected during 5 consecutive days from Monday to Friday at three different times, approximately every 8 hours: Morning (7:00 am), Afternoon (3:00 pm), and night (10:00 pm). Samples were manually collected in aseptic conditions and immediately freeze at -20° C. Bacterial DNA was extracted using the Favorgen stool kit. The diversity was characterized by high-throughput DNA sequencing of V3-16S rDNA libraries. The sequencing data were analyzed using the QIIME pipeline and taxonomy was assigned by comparison of the sequences against the Greengenes reference database. Alpha diversity was determined using Phyloseq and ggplot2 packages in the R environment (v3.4.4). For beta diversity, the dissimilarity was estimated using unweighted Bray Curtis analysis. The linear discriminant analysis effect size program (LEfSe v1.0) was used to detect significant differences in the relative abundances of bacterial taxa. Results. The human milk microbiota shows changes in the bacterial composition between morning and night; also, we observed significant changes in the Shannon diversity index between both groups. On the other hand, no differences were observed in the bacterial composition or alfa diversity in the afternoon samples compared with the morning and night samples. For beta diversity analysis, no clustering was observed among all the samples. As previously has been reported, Lactobacillus was found more enriched in the night milk of samples with statistical significance; same was observed for environmental proteobacteria and actinobacteria. The family Micrococcaceae was detected as more abundant in samples collected in the morning. Conclusions. As for other human milk components, the human milk microbiota seems to be affected by the daytime changes. The results presented in this work suggest that the milk microbiota exhibits diurnal fluctuation resulting in a time-of-day specific taxonomic arrangement. Acknowledgments. Work supported by Cinvestav and CONACyT 163235 INFR-2011-01 grant; and CONACYT doctorate scholarship 777953 (KCC), 291236 (FHQ), and master’s degree scholarship 997494 (NGZT).

  • Open access
  • 42 Reads
Virulence Reversion in Staphylococcus aureus

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 as 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.