RESUMO
AIMS: The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho. METHODS AND RESULTS: Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated. CONCLUSIONS: The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a sauerkraut jar.
Assuntos
Fermentação , Alimentos Fermentados , Tecnologia de Alimentos/métodos , Microbiota , MusaceaeRESUMO
This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.
Assuntos
Ração Animal/microbiologia , Dípteros/microbiologia , Microbiota , Ração Animal/análise , Animais , Bélgica , Dípteros/crescimento & desenvolvimento , Larva/crescimento & desenvolvimento , Larva/microbiologia , Resíduos SólidosRESUMO
Gut microbial communities are critical for the health of many insect species. However, little is known about how gut microbial communities respond to anthropogenic changes and how such changes affect host-pathogen interactions. In this study, we used deep sequencing to investigate and compare the composition of gut microbial communities within the midgut and ileum (both bacteria and fungi) in Bombus terrestris queens collected from natural (forest) and urbanized habitats. Additionally, we investigated whether the variation in gut microbial communities under each habitat affected the prevalence of two important bumblebee pathogens that have recently been associated with Bombus declines (Crithidia bombi and Nosema bombi). Microbial community composition differed strongly among habitat types, both for fungi and bacteria. Fungi were almost exclusively associated with bumblebee queens from the forest habitats, and were not commonly detected in bumblebee queens from the urban sites. Further, gut bacterial communities of urban B. terrestris specimens were strongly dominated by bee-specific core bacteria like Snodgrassella (Betaproteobacteria) and Gilliamella (Gammaproteobacteria), whereas specimens from the forest sites contained a huge fraction of environmental bacteria. Pathogen infection was very low in urban populations and infection by Nosema was only observed in specimens collected from forest habitats. No significant relationship was found between pathogen prevalence and microbial gut diversity. However, there was a significant and negative relationship between prevalence of Nosema and relative abundance of the core resident Snodgrassella, supporting its role in pathogen defense. Overall, our results indicate that land-use change may lead to different microbial gut communities in bumblebees, which may have implications for bumblebee health, survival and overall fitness.
Assuntos
Abelhas/microbiologia , Ecossistema , Animais , Bactérias/isolamento & purificação , Bactérias/patogenicidade , Biodiversidade , Crithidia/isolamento & purificação , Crithidia/patogenicidade , Feminino , Fungos/isolamento & purificação , Microbioma Gastrointestinal , Nosema/isolamento & purificação , Nosema/patogenicidade , PrevalênciaRESUMO
Enset (Ensete ventricosum) provides staple food for 15 million people in Ethiopia after fermentation into kocho. The fermentation process has hardly been investigated and is prone to optimization. The aim of this study was to investigate the physicochemical and microbial dynamics of fermentation practices in the Gamo highlands. These practices show local variation, but two steps were omnipresent: scraping of the pseudostem and fermenting it in a pit or a bamboo basket. Enset plants were fragmented and fermented for two months in order to investigate the physicochemical (temperature, moisture content, pH and titratable acidity) and microbial dynamics (total viable aerobic counts, counts of Enterobacteriaceae, lactic acid bacteria, yeasts and moulds and Clostridium spores counts, and Illumina Miseq sequencing). Samples were taken on days 1, 7, 15, 17, 31 and 60. The pH decreased, whereas the titratable acidity increased during fermentation. Of all counts those of lactic acid bacteria and Clostridium spores increased during fermentation. Leuconostoc mesenteroides initiated the fermentation. Later on, Prevotella paludivivens, Lactobacillus sp. and Bifidobacterium minimum dominated. These three species are potential candidates for the development of a starter culture.
Assuntos
Lactobacillales/isolamento & purificação , Musaceae/microbiologia , Biodiversidade , Clostridium/classificação , Clostridium/genética , Clostridium/isolamento & purificação , Clostridium/metabolismo , Etiópia , Fermentação , Concentração de Íons de Hidrogênio , Lactobacillales/classificação , Lactobacillales/metabolismo , Musaceae/química , Musaceae/metabolismo , TemperaturaRESUMO
In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects.
Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Contaminação de Alimentos/análise , Tenebrio/microbiologia , Ração Animal/análise , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Inocuidade dos Alimentos , Humanos , Tenebrio/química , Tenebrio/metabolismoRESUMO
Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by (Para)bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas. In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies.
Assuntos
Bactérias/genética , Bactérias/isolamento & purificação , Gryllidae/microbiologia , Tenebrio/microbiologia , Animais , Bactérias/classificação , Contaminação de Alimentos/análise , Inocuidade dos Alimentos , Humanos , Larva/microbiologia , MetagenômicaRESUMO
OBJECTIVES: Rapid identification of Acinetobacter species is critical as members of the A. baumannii (Ab) group differ in antibiotic susceptibility and clinical outcomes. A. baumannii, A. pittii, and A. nosocomialis can be identified by MALDI-TOF/MS, while the novel species A. seifertii and A. dijkshoorniae cannot. Low identification rates for A. nosocomialis also have been reported. We evaluated the use of MALDI-TOF/MS to identify isolates of A. seifertii and A. dijkshoorniae and revisited the identification of A. nosocomialis to update the Bruker taxonomy database. METHODS: Species characterization was performed by rpoB-clustering and MLSA. MALDI-TOF/MS spectra were recovered from formic acid/acetonitrile bacterial extracts overlaid with α-cyano-4-hydroxy-cinnamic acid matrix on a MicroflexLT in linear positive mode and 2000-20 000 m/z range mass. Spectra were examined with the ClinProTools v2.2 software. Mean spectra (MSP) were created with the BioTyper software. RESULTS: Seventy-eight Acinetobacter isolates representative of the Ab group were used to calculate the average spectra/species and generate pattern recognition models. Species-specific peaks were identified for all species, and MSPs derived from three A. seifertii, two A. dijkshoorniae, and two A. nosocomialis strains were added to the Bruker taxonomy database, allowing successful identification of all isolates using spectra from either bacterial extracts or direct colonies, resulting in a positive predictive value (PPV) of 99.6% (777/780) and 96.8% (302/312), respectively. CONCLUSIONS: The use of post-processing data software identified statistically significant species-specific peaks to generate reference signatures for rapid accurate identification of species within the Ab group, providing relevant information for the clinical management of Acinetobacter infections.
Assuntos
Infecções por Acinetobacter/diagnóstico , Acinetobacter/classificação , Acinetobacter/isolamento & purificação , Técnicas Bacteriológicas/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Acinetobacter/química , Acinetobacter/genética , Análise por Conglomerados , RNA Polimerases Dirigidas por DNA/genética , Humanos , Tipagem de Sequências Multilocus , Valor Preditivo dos TestesRESUMO
The rising interest in insects for human consumption and the changing regulations in Europe require a profound insight into the food safety of insects reared and sold in Western society. The microbial quality of edible insects has only been studied occasionally. This study aimed at generating an overview of intrinsic parameters (pH, water activity and moisture content) and microbial quality of fresh mealworm larvae and crickets for several rearing companies and for several batches per rearer. In total, 21 batches obtained from 7 rearing companies were subjected to analysis of intrinsic parameters, a range of plate counts and presence-absence tests for Salmonella spp. and Listeria monocytogenes. The microbial counts of the fresh insects were generally high. Different rearing batches from a single rearing company showed differences in microbial counts which could not be explained by variations in intrinsic properties. The largest variations were found in numbers of bacterial endospores, psychrotrophs and fungi. Salmonella spp. and L. monocytogenes were not detected in any of the samples. Altogether, our study shows that large variations were found between batches from individual rearers. As a consequence, no overall differences between rearers could be observed.
Assuntos
Contaminação de Alimentos/análise , Gryllidae/microbiologia , Larva/microbiologia , Tenebrio/microbiologia , Animais , Europa (Continente) , Inocuidade dos Alimentos , Fungos/crescimento & desenvolvimento , Fungos/isolamento & purificação , Humanos , Listeria monocytogenes/crescimento & desenvolvimento , Listeria monocytogenes/isolamento & purificação , Salmonella/crescimento & desenvolvimento , Salmonella/isolamento & purificaçãoRESUMO
Agar-based screening assays are the method of choice when evaluating antagonistic potential of bacterial biocontrol-candidates against pathogens. We showed that when using the same medium, but different agar compositions, the activity of a bacterial antagonist against Agrobacterium was strongly affected. Consequently, results from in vitro screenings should be interpreted cautiously.
Assuntos
Ágar/química , Antibiose , Técnicas Bacteriológicas/métodos , Doenças das Plantas/prevenção & controle , Doenças das Plantas/microbiologia , Raízes de Plantas/microbiologiaRESUMO
AIMS: Rhizogenic Agrobacterium strains are the causative agent of hairy root disease (HRD), an increasing problem in the hydroponic cultivation of tomato and cucumber in Europe. A previous study has demonstrated that different lineages of rhizogenic agrobacteria are able to form biofilms. Although hydrogen peroxide (H2 O2 ) is a frequently used biocide in hydroponic systems, until now its effectiveness to remove rhizogenic agrobacteria has not been unequivocally demonstrated. Therefore, the main objective of this study was to assess the efficacy of H2 O2 in controlling Agrobacterium-containing biofilms. METHODS AND RESULTS: Using lab-scale experiments, we found a huge variation between different rhizogenic Agrobacterium strains in EC50 values, ranging from 18·8 to 600 ppm H2 O2 , representing the lowest and highest concentration tested respectively. Using pilot-scale experiments in which different H2 O2 concentrations were tested, treatment with 25 ppm H2 O2 was found to be ineffective. In contrast, treatment with 50 ppm significantly affected a catalase-negative Agrobacterium population, while a catalase-positive population was only marginally affected. For the catalase-positive Agrobacterium population, a treatment of 100 ppm H2 O2 was required to be effective. Finally, H2 O2 treatment of HRD in two commercial greenhouses was monitored, and showed that the H2 O2 concentration decreased considerably towards the end of the irrigation circuits. Further, a clear correlation was found between the actual concentration of H2 O2 and the incidence of HRD. CONCLUSION: We showed that H2 O2 may be effective to reduce biofilm formation by rhizogenic bacteria. Nevertheless, it was clear from our results that the required H2 O2 concentration depends on the particular Agrobacterium strain(s) present in the greenhouse. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study that examined the effectiveness of H2 O2 to control HRD in hydroponic systems, and the effect of catalase activity on H2 O2 effectiveness. Our study has direct relevance for the highly intensive horticultural sector.
Assuntos
Agrobacterium/efeitos dos fármacos , Agrobacterium/fisiologia , Peróxido de Hidrogênio/farmacologia , Doenças das Plantas/microbiologia , Biofilmes/efeitos dos fármacos , Catalase/metabolismo , Europa (Continente) , Solanum lycopersicum/microbiologia , Doenças das Plantas/prevenção & controle , Raízes de Plantas/microbiologiaRESUMO
In Western countries, the popularity of edible insects as an alternative animal protein source is increasing. Nevertheless, there is a lack of profound insight into the microbial safety and shelf life of living insects sold for human consumption. The purpose of this study was to characterise the microflora of fresh edible mealworm larvae and grasshoppers in a quantitative and qualitative way. Therefore, culture-dependent analyses (the total viable aerobic count, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds, and bacterial endospores) and next-generation sequencing (454amplicon pyrosequencing) were performed. High microbial counts were obtained for both insect species. Different insect batches resulted in quite similar microbial numbers, except for bacterial endospores. However, the bacterial community composition differed between both insect species. The most abundant operational taxonomic unit in mealworm larvae was Propionibacterium. Also members of the genera Haemophilus, Staphylococcus and Clostridium were found. Grasshoppers were mainly dominated by Weissella, Lactococcus and Yersinia/Rahnella. Overall, a variety of potential spoilage bacteria and food pathogens were characterised. The results of this study suggest that a processing step with a microbiocidal effect is required to avoid or minimize risks involved with the consumption of edible insects.
Assuntos
Bactérias/isolamento & purificação , Fungos/isolamento & purificação , Larva/microbiologia , Locusta migratoria/microbiologia , Tenebrio/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Biodiversidade , Qualidade de Produtos para o Consumidor , Inocuidade dos Alimentos , Fungos/classificação , Fungos/genética , Fungos/crescimento & desenvolvimento , HumanosRESUMO
Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and ß-glycosides as well as α- and ß-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and ß-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a ß-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.
Assuntos
Brettanomyces/genética , Brettanomyces/fisiologia , Carbono/metabolismo , Variação Genética , Redes e Vias Metabólicas/genética , Nitrogênio/metabolismo , Cerveja/microbiologia , Brettanomyces/classificação , Brettanomyces/isolamento & purificação , Bebidas Gaseificadas/microbiologia , DNA Fúngico/genética , Genômica , Genótipo , Fenótipo , Reação em Cadeia da Polimerase , Deleção de Sequência , Vinho/microbiologia , alfa-Glucosidases/genética , alfa-Glucosidases/metabolismo , beta-Glucosidase/genética , beta-Glucosidase/metabolismoRESUMO
Since minced meat is very susceptible for microbial growth, characterisation of the bacterial community dynamics during storage is important to optimise preservation strategies. The purpose of this study was to investigate the effect of different production batches and the use of different preservatives on the composition of the bacterial community in minced meat during 9 days of cold storage under modified atmosphere (66% O2, 25% CO2 and 9% N2). To this end, both culture-dependent (viable aerobic and anaerobic counts) and culture-independent (454 pyrosequencing) analyses were performed. Initially, microbial counts of fresh minced meat showed microbial loads between 3.5 and 5.0 log cfu/g. The observed microbial diversity was relatively high, and the most abundant bacteria differed among the samples. During storage an increase of microbial counts coincided with a dramatic decrease in bacterial diversity. At the end of the storage period, most samples showed microbial counts above the spoilage level of 7 log cfu/g. A relatively similar bacterial community was obtained regardless of the manufacturing batch and the preservative used, with Lactobacillus algidus and Leuconostoc sp. as the most dominant microorganisms. This suggests that both bacteria played an important role in the spoilage of minced meat packaged under modified atmosphere.
Assuntos
Bactérias/crescimento & desenvolvimento , Biodiversidade , Conservantes de Alimentos/farmacologia , Produtos da Carne/microbiologia , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/isolamento & purificação , Embalagem de Alimentos , Conservação de Alimentos , Armazenamento de AlimentosRESUMO
AIMS: To screen and identify biosurfactant-producing Pseudomonas strains isolated from floral nectar; to characterize the produced biosurfactants; and to investigate the effect of different carbon sources on biosurfactant production. METHODS AND RESULTS: Four of eight nectar Pseudomonas isolates were found to produce biosurfactants. Phylogenetic analysis based on three housekeeping genes (16S rRNA gene, rpoB and gyrB) classified the isolates into two groups, including one group closely related to Pseudomonas fluorescens and another group closely related to Pseudomonas fragi and Pseudomonas jessenii. Although our nectar pseudomonads were able to grow on a variety of water-soluble and water-immiscible carbon sources, surface active agents were only produced when using vegetable oil as sole carbon source, including olive oil, sunflower oil or waste frying sunflower oil. Structural characterization based on thin layer chromatography (TLC) and ultra high performance liquid chromatography-accurate mass mass spectrometry (UHPLC-amMS) revealed that biosurfactant activity was most probably due to the production of fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof. CONCLUSIONS: Four biosurfactant-producing nectar pseudomonads were identified. The active compounds were identified as fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof, produced by hydrolysis of triglycerides of the feedstock. SIGNIFICANCE AND IMPACT OF THE STUDY: Studies on biosurfactant-producing micro-organisms have mainly focused on microbes isolated from soils and aquatic environments. Here, for the first time, nectar environments were screened as a novel source for biosurfactant producers. As nectars represent harsh environments with high osmotic pressure and varying pH levels, further screening of nectar habitats for biosurfactant-producing microbes may lead to the discovery of novel biosurfactants with broad tolerance towards different environmental conditions.
Assuntos
Flores/microbiologia , Néctar de Plantas/química , Pseudomonas/metabolismo , Tensoativos/metabolismo , DNA Bacteriano/genética , Flores/química , Dados de Sequência Molecular , Filogenia , Pseudomonas/classificação , Pseudomonas/genética , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Tensoativos/químicaRESUMO
Vibrio anguillarum is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. However, the diversity and virulence mechanisms of this pathogen are still insufficiently known. In this study, we aimed to increase our understanding of V. anguillarum diversity and virulence through comparative genome analysis of 15 V. anguillarum strains, obtained from different hosts or non-host niches and geographical regions, among which 10 and 5 strains were found to be virulent and avirulent, respectively, against sea bass larvae. First, the 15 draft genomes were annotated and screened for putative virulence factors, including genes encoding iron uptake systems, transport systems and non-ribosomal peptide synthetases. Second, comparative genome analysis was performed, focusing on single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). Five V. anguillarum strains showed a remarkably high nucleotide identity. However, these strains comprise both virulent and avirulent strains towards sea bass larvae, suggesting that differences in virulence may be caused by subtle nucleotide variations. Clearly, the draft genome sequence of these 15 strains represents a starting point for further genetic research of this economically important fish pathogen.
Assuntos
Variação Genética , Genoma Bacteriano/genética , Vibrio/genética , Vibrio/patogenicidade , Animais , Bass/microbiologia , Deleção de Genes , Mutagênese Insercional , Polimorfismo de Nucleotídeo Único , Virulência/genéticaRESUMO
Characterization of the microflora during malting is an essential step towards process management and optimization. Up till now, however, microbial characterization in the malting process has mostly been done using culture-dependent methods, probably leading to biased estimates of microbial diversity. The aim of this study was to characterize the bacterial communities using two culture-independent methods, including Terminal Restriction Fragment Length Polymorphism (T-RFLP) and 454 pyrosequencing, targeting the 16S rRNA gene. Studied samples originated from two harvest years and two malting houses malting the same batch of barley. Besides targeting the entire bacterial community (T-RFLP), emphasis was put on lactic acid bacteria (LAB) (T-RFLP and 454 pyrosequencing). The overall bacterial community richness was limited, but the community structure changed during the process. Zooming in on the LAB community using 454 pyrosequencing revealed a total of 47 species-level operational taxonomic units (OTUs). LAB diversity appeared relatively limited since 88% of the sequences were covered by the same five OTUs (representing members of Weissella, Lactobacillus and Leuconostoc) present in all samples investigated. Fluctuations in the relative abundances of the dominant LAB were observed with the process conditions. In addition, both the year of harvest and malting house influenced the LAB community structure.
Assuntos
Biodiversidade , Hordeum/microbiologia , Lactobacillaceae/isolamento & purificação , Manipulação de Alimentos , Hordeum/química , Ácido Láctico/metabolismo , Lactobacillaceae/classificação , Lactobacillaceae/genética , Dados de Sequência Molecular , Filogenia , Polimorfismo de Fragmento de RestriçãoRESUMO
Most bacteria recovered so far from sugar thick juice during storage represent strains of the species Tetragenococcus halophilus. Recently, several Gram-positive, non-motile, non-spore-forming cocci with other physiological and genetic traits were isolated from sugar thick juice samples from different origins. In this study, representative isolates were investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%. The level of DNA-DNA relatedness between isolate T1(T), representing the newly found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic features demonstrated that the isolates represent a novel species, for which the name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from high-salt and high-sugar environments showed clear differences in several physiological and genetic characteristics like RAPD fingerprints and 16S rRNA gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness between osmophilic and halophilic T. halophilus isolates, demonstrating that the different strains belong to the same species. Based on the phenotypic and genotypic differences observed, as well as the different origins of the strains and the industrial relevance of thick juice degradation, two subspecies of T. halophilus are described in this manuscript: T. halophilus subsp. halophilus subsp. nov. for the strains isolated from salt media and T. halophilus subsp. flandriensis subsp. nov. for the strains isolated from sugar-rich environments, which were first isolated in Flanders, Belgium. The type strains for the subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T) =DSM 23766(T)), respectively.
Assuntos
Enterococcaceae/classificação , Enterococcaceae/isolamento & purificação , Microbiologia de Alimentos , Técnicas de Tipagem Bacteriana , Composição de Bases , Bélgica , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Enterococcaceae/genética , Enterococcaceae/fisiologia , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
PCR-based DNA array technology is one of the most suitable techniques to detect and identify multiple pathogens in a single assay. Out of the different array platforms that currently exist, membrane-based DNA macroarrays are the most convenient for plant disease diagnosis because of low costs, great sensitivity, and modest equipment requirements. Here we describe a protocol for routine detection of plant pathogens using DNA macroarrays, i.e., from sampling to analysis of hybridization results. Diagnosis can be completed within 36 h after sample collection.
Assuntos
Fungos/genética , Fungos/isolamento & purificação , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Doenças das Plantas/microbiologia , Plantas/microbiologia , Microbiologia do Solo , DNA Fúngico/genética , DNA Fúngico/isolamento & purificação , Medições Luminescentes , Hibridização de Ácido Nucleico/métodos , Reação em Cadeia da Polimerase/métodosRESUMO
Fish diseases can be caused by a variety of diverse organisms, including bacteria, fungi, viruses and protozoa, and pose a universal threat to the ornamental fish industry and aquaculture. The lack of rapid, accurate and reliable means by which fish pathogens can be detected and identified has been one of the main limitations in fish pathogen diagnosis and fish disease management and has consequently stimulated the search for alternative diagnostic techniques. Here, we describe a method based on multiplex and broad-range PCR amplification combined with DNA array hybridization for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV-1, CyHV-2 and CyHV-3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were targeted. For bacterial identification, the ribosomal RNA gene was used. The developed methodology permitted 100% specificity for the identification of the target species. Detection sensitivity was equivalent to 10 viral genomes or less than a picogram of bacterial DNA. The utility and power of the array for sensitive pathogen detection and identification in complex samples such as infected tissue is demonstrated in this study.
Assuntos
Infecções Bacterianas/veterinária , Doenças dos Peixes/diagnóstico , Pesqueiros/métodos , Infecções por Flavobacteriaceae/veterinária , Infecções por Herpesviridae/veterinária , Reação em Cadeia da Polimerase Multiplex/veterinária , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Animais , Infecções Bacterianas/diagnóstico , Carpas , DNA Helicases/genética , DNA Polimerase Dirigida por DNA/genética , Infecções por Flavobacteriaceae/diagnóstico , Flavobacterium/genética , Herpesviridae/genética , Infecções por Herpesviridae/diagnóstico , RNA Ribossômico 16S/genética , Reprodutibilidade dos Testes , Sensibilidade e EspecificidadeRESUMO
Vibrio anguillarum, also known as Listonella anguillarum, is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. In both aquaculture and larviculture, this disease is responsible for severe economic losses worldwide. Because of its high morbidity and mortality rates, substantial research has been carried out to elucidate the virulence mechanisms of this pathogen and to develop rapid detection techniques and effective disease-prevention strategies. This review summarizes the current state of knowledge pertaining to V. anguillarum, focusing on pathogenesis, known virulence factors, diagnosis, prevention and treatment.