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1.
J Med Microbiol ; 68(11): 1664-1670, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31553302

RESUMO

Purpose. To assess in vitro activities of nine antifungal agents (amphotericin B, fluconazole, voriconazole, itraconazole, posaconazole, caspofungin, micafungin, terbinafine and 5-flucytosine) against 93 strains of rare pathogenic fungi and the combined effects of drug combinations against several multidrug-resistant fungi.Methodology. The broth microdilution method M38-A3 and M27-A4 from the Clinical and Laboratory Standards Institute and the checkerboard method were performed in this study.Results. Low MICs for fluconazole were observed in moulds including Tritirachium oryzae, Exophiala attenuata and yeasts. MICs for amphotericin B>2 µg ml-1 were found among Aspergillus nidulans, Fusarium napiforme, Trichoderma longibrachiatum, Tritirachium oryzae, Cunninghamella bertholletiae, Cunninghamella phaeospora, Conidiobolus coronatus, Exophiala attenuata, Ochroconis mirabilis and Rhinocladiella basitona. Multidrug resistance was observed in Microascus spp., Lomentospora prolificans and Pythium insidiosum.Conclusion. Our study illustrated in vitro drug susceptibilities of some rare pathogenic fungi, which provide data to guide clinical treatment of fungal infections.


Assuntos
Antifúngicos/farmacologia , Fungos/efeitos dos fármacos , Micoses/microbiologia , Anfotericina B/farmacologia , Farmacorresistência Fúngica , Fluconazol/farmacologia , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Humanos , Itraconazol/farmacologia , Testes de Sensibilidade Microbiana , Triazóis/farmacologia , Voriconazol/farmacologia
2.
J Med Microbiol ; 68(10): 1544-1551, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31436523

RESUMO

Introduction. Breakthrough bloodstream infections (BSIs) are rare among non-neutropenic patients.Aim. Our goal was to determine the risk factors associated with development of breakthrough BSIs among critically ill non-neutropenic patients and its role in mortality.Methodology. During a 24-month period (August 2016 to July 2018), all BSIs among non-neutropenic patients hospitalized at the University General Hospital of Patras, Greece, were included. Antimicrobial resistance of isolates was interpreted according to EUCAST guidelines. BSIs were considered as breakthrough when blood cultures yielded a pathogen in a patient who, for at least the previous 72 h, had been receiving at least one antibiotic to which the isolated microorganism was susceptible.Results. Among 217 episodes of BSI, 118 (54.4 %) developed a breakthrough infection. Primary BSIs predominated (101; 46.5 %), followed by catheter-related BSIs (56; 25.8 %). Gram-negative bacteria represented the most common pathogens isolated (157; 72.4 %), followed by Gram-positive bacteria (36; 16.6 %) and fungi (36; 16.6 %). Factors independently associated with the development of breakthrough BSIs were immunosuppressive therapy, obesity (body mass index ≥30 kg m- 2), infection by Gram-positive bacteria, noradrenaline dose during 24 h from BSI onset, prior use of colistin and antifungal treatment. Overall 14-day mortality was 23.0 % (50 patients). Multivariate analysis revealed noradrenaline dose during 24 h from BSI onset as an independent predictor of mortality, while appropriate empiric antimicrobial treatment and breakthrough BSI were identified as predictors of good prognosis.Conclusion. Breakthrough BSIs were common among critically ill non-neutropenic patients and these patients were associated with better survival because they were de facto receiving appropriate antibiotics.


Assuntos
Bacteriemia/microbiologia , Bacteriemia/mortalidade , Bactérias/isolamento & purificação , Estado Terminal/epidemiologia , Fungemia/microbiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Antifúngicos/uso terapêutico , Bacteriemia/tratamento farmacológico , Bacteriemia/epidemiologia , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Estado Terminal/terapia , Feminino , Fungemia/epidemiologia , Fungemia/mortalidade , Fungos/classificação , Fungos/efeitos dos fármacos , Fungos/genética , Fungos/isolamento & purificação , Grécia/epidemiologia , Hospitais Universitários , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos
3.
J Med Microbiol ; 68(10): 1507-1516, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31460858

RESUMO

Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often are resistant to antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates are low, ca. 1-2 %, the overall increase in the sheer number of joint replacement surgeries results in an increase in patients at risk.Aims. This study investigates the consensus of microbial species comprising PJI ecology, which is currently lacking.Methodology. In this study, PJI populations from seven patients were analysed using combined culturing and whole-genome shotgun sequencing (WGSS) to establish population profiles and compare WGSS and culture methods for detection and identification of the PJI microbiome.Results. WGSS detected strains when culture did not, notably dormant, culture-resistant and rare microbes. The CosmosID algorithm was used to predict micro-organisms present in the PJI and discriminate contaminants. However, culturing indicated the presence of microbes falling below the WGSS algorithm threshold. In these instances, microbes cultured are believed to be minor species. The two strategies were combined to build a population profile.Conclusions. Variability between and among PJIs showed that most infections were distinct and unique. Comparative analysis of populations revealed PJIs to form clusters that were related to, but separate from, vaginal, skin and gut microbiomes. Fungi and protists were detected by WGSS, but the role of fungi is just beginning to be understood and for protists it is unknown. These micro-organisms and their novel and strain-specific microbial interactions remain to be determined in current clinical tests.


Assuntos
Bactérias/genética , Bactérias/isolamento & purificação , Fungos/isolamento & purificação , Artropatias/microbiologia , Microbiota , Infecções Relacionadas à Prótese/microbiologia , Bactérias/classificação , Feminino , Fungos/classificação , Fungos/genética , Humanos , Articulações/microbiologia , Articulações/cirurgia , Masculino , Próteses e Implantes/efeitos adversos , Próteses e Implantes/microbiologia , Infecções Relacionadas à Prótese/etiologia , Estudos Retrospectivos , Sequenciamento Completo do Genoma
4.
Microbiol Res ; 228: 126299, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31422231

RESUMO

Wastewaters from textile dyeing industries represent an ecological concern, notably due to the known toxicity of azo dyes to the local microbiome and human health. Although physicochemical approaches are the rule for the treatment of industrial effluents, biological strategies such as enzyme-mediated dye destaining is a promising alternative. Notwithstanding a broad range of microorganisms, including fungi, algae, yeast, and bacteria, display dye-destaining properties, most of the literature has focused in ligninolytic fungi, leaving other classes of organisms somehow ignored. In this study, six endophytic strains isolated from Maytenus ilicifolia were studied for their destaining activity. The phylogenetic and morphological analysis allowed the identification of strain LGMF1504 as Neopestalotiopsis sp. LGMF1504 that decolorized several commercial dyes as the result of a mycelium-associated laccase. The enzyme expression was modulated by carbon and nitrogen content in the culture medium, it was weakly affected by the presence of aromatic compounds and metal ions while some common laccase mediators improved the destaining activity onto dye substrates. The best culture condition observed for laccase activity was a basic culture medium containing 5 g L-1 starch and 15 g L-1 ammonium tartrate. The laccase activity showed low substrate specificity and almost unaltered performance in a wide range of pH values and NaCl concentrations, suggesting the potential of Neopestalotiopsis sp. LGMF1504 for biodegradation approaches.


Assuntos
Corantes/metabolismo , Endófitos/metabolismo , Lacase/metabolismo , Micélio/metabolismo , Compostos Azo/toxicidade , Biodegradação Ambiental , Carbono , Corantes/toxicidade , DNA Fúngico , Endófitos/classificação , Endófitos/isolamento & purificação , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Concentração de Íons de Hidrogênio , Metais , Tipagem de Sequências Multilocus , Nitrogênio , Filogenia , Cloreto de Sódio/análise , Indústria Têxtil , Águas Residuárias
5.
World J Microbiol Biotechnol ; 35(9): 139, 2019 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-31451943

RESUMO

Exploitation of microbes, especially fungi, has the potential to help humankind meet the UN's sustainable development goals, help feed the worlds growing population and improve bioeconomies of poorer nations. The majority of the world's fungal genetic resources are held in collections in developed countries, primarily within the USA, Europe and Japan. Very little capacity exists in low to middle income countries, which are often rich in biodiversity but lack resources to be able to conserve and exploit their own microbial resources. In this paper we review the current challenges facing culture collections and the challenges of integrating new approaches, the worth of collaborative networks, and the importance of technology, taxonomy and data handling. We address the need to underpin research and development in developing countries through the need to build 'in country' infrastructure to address these challenges, whilst tackling the global challenges to meet the requirements of the research community through the impacts of legislation and the Nagoya protocol on access to biological resources.


Assuntos
Fungos , Desenvolvimento Sustentável/tendências , Biodiversidade , Bases de Dados Genéticas , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/fisiologia , Disseminação de Informação , Internacionalidade
6.
World J Microbiol Biotechnol ; 35(9): 131, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31432251

RESUMO

Cholesterol is a C27-sterol employed as starting material for the synthesis of valuable pharmaceutical steroids and precursors. The microbial transformations of cholesterol have been widely studied, since they are performed with high regio- and stereoselectivity and allow the production of steroidal compounds which are difficult to synthesize by classical chemical methods. In recent years, ongoing research is being conducted to discover novel biocatalysts and to develop biotechnological processes to improve existing biocatalysts and biotransformation reactions. The main objective of this review is to present the most remarkable advances in fungal and bacterial transformation of cholesterol, focusing on the different types of microbial reactions and biocatalysts, biotransformation products, and practical aspects related to sterol dispersion improvement, covering literature since 2000. It reviews the conversion of cholesterol by whole-cell biocatalysts and by purified enzymes that lead to various structural modifications, including side chain cleavage, hydroxylation, dehydrogenation/reduction, isomerization and esterification. Finally, approaches used to improve the poor solubility of cholesterol in aqueous media, such as the use of different sterol-solubilizing agents or two-phase conversion system, are also discussed.


Assuntos
Bactérias/metabolismo , Biotecnologia/métodos , Colesterol/metabolismo , Fungos/metabolismo , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Biotecnologia/tendências , Biotransformação , Enzimas/metabolismo , Fungos/genética , Fungos/crescimento & desenvolvimento
7.
J Microbiol ; 57(9): 717-724, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31452042

RESUMO

Salterns are hypersaline extreme environments with unique physicochemical properties such as a salinity gradient. Although the investigation of microbiota in salterns has focused on archaea and bacteria, diverse fungi also thrive in the brine and soil of salterns. Fungi isolated from salterns are represented by black yeasts (Hortaea werneckii, Phaeotheca triangularis, Aureobasidium pullulans, and Trimmatostroma salinum), Cladosporium, Aspergillus, and Penicillium species. Most studies on saltern-derived fungi gave attention to black yeasts and their physiological characteristics, including growth under various culture conditions. Since then, biochemical and molecular tools have been employed to explore adaptation of these fungi to salt stress. Genome databases of several fungi in salterns are now publicly available and being used to elucidate salt tolerance mechanisms and discover the target genes for agricultural and industrial applications. Notably, the number of enzymes and novel metabolites known to be produced by diverse saltern-derived fungi has increased significantly. Therefore, fungi in salterns are not only interesting and important subjects to study fungal biodiversity and adaptive mechanisms in extreme environments, but also valuable bioresources with potential for biotechnological applications.


Assuntos
Fungos/fisiologia , Sais/química , Cloreto de Sódio/metabolismo , Solo/química , Adaptação Fisiológica , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Tolerância ao Sal
8.
J Sci Food Agric ; 99(14): 6522-6534, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31321764

RESUMO

BACKGROUND: Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study first investigated the metaproteome of bean sauce mash. This was followed by an analysis of its biological functions and its microbial community to reveal information about strains and about the expressed proteins to better understand the roles of the microbiota in bean sauce mash. RESULTS: The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of the Penicillium and Rhizopus genera and were classified into 100 cellular components, 238 biological processes, and 220 molecular function categories by gene ontology (GO) annotation. Enzymes associated with glycolysis metabolic pathways were also identified. These can provide the energy required for microbial fermentation. Illumina MiSeq sequencing technology results showed that the microorganism communities of bean sauce mash exhibited a high level of diversity. Microbiological analysis demonstrated that the Penicillium, Mucor, Fusarium, Aspergillus, and Rhizopus fungi, and Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium genera were predominant 22 samples. CONCLUSION: The profiles and insights in the current study are important for research on bean sauce mash and related products in terms of their food microbial ecology. The information obtained from this study will help the development of stable sufu starter cultures with unique sensory qualities. © 2019 Society of Chemical Industry.


Assuntos
Bactérias/enzimologia , Alimentos Fermentados/microbiologia , Fungos/enzimologia , Microbiota , Soja/microbiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , China , Fermentação , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Soja/metabolismo
9.
Sci Total Environ ; 690: 911-922, 2019 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-31302555

RESUMO

In the saline-affected ecosystem, fungi have huge potential to promote growth, induce disease resistance and enhance tolerance against salt-stress of host plants. Since areas of plowland are gradually decreasing, the reclamation of coastal saline lands could play a crucial role in maintaining agricultural productivity and crop security globally. Therefore, it is of great significance to explore the fungal diversity in the coastal saline ecosystem. Here, we collected saline soil samples from unflooded areas and tidal flat areas, the two typical distinct landforms in coastal saline ecosystems, and used ITS metabarcoding to depict the diversity of fungal communities. We found that fungal species evenness had a remarkably higher variation from the tidal flat compared to unflooded soil samples. Furthermore, we also confirmed that the fungal niches differentiation reports in the coastal saline ecosystem. Our ITS based DNA sequencing revealed that both unflooded and tidal flat soil were mainly composed of amplicon sequence variants (ASVs) belonging to Ascomycota (93.43% and 86.91% respectively). Based on our findings, understanding the associations and distinctions of fungal microbiome between unflooded soil and tidal flat could provide the basis for the development of reclamation in coastal saline lands.


Assuntos
Código de Barras de DNA Taxonômico , Ecossistema , Fungos/genética , Microbiologia do Solo , Agricultura , Ascomicetos , Biodiversidade , DNA Fúngico , Fungos/classificação , Micobioma , Nitrogênio , Plantas , Solo
10.
Nat Biotechnol ; 37(8): 869-876, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31285593

RESUMO

Engineering the synthesis of massive amounts of therapeutics, enzymes or commodity chemicals can select for subpopulations of nonproducer cells, owing to metabolic burden and product toxicity. Deep DNA sequencing can be used to detect undesirable genetic heterogeneity in producer populations and diagnose associated genetic error modes. Hotspots of genetic heterogeneity can pinpoint mechanisms that underlie load problems and product toxicity. Understanding genetic heterogeneity will inform metabolic engineering and synthetic biology strategies to minimize the emergence of nonproducer mutants in scaled-up fermentations and maximize product quality and yield.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Fungos/metabolismo , Heterogeneidade Genética , Sequenciamento de Nucleotídeos em Larga Escala , Engenharia Metabólica/métodos , Animais , Biotecnologia , Linhagem Celular , Indústria Farmacêutica , Fermentação , Fungos/genética , Humanos , Preparações Farmacêuticas , Biologia Sintética
11.
Plant Dis ; 103(10): 2634-2644, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31339440

RESUMO

Greenhouse cultivation of ornamentals is subjected to a high incidence of soil-borne fungal pathogens. In Kalanchoe, these pathogens are responsible for root and stem rot, and for infection of the vascular tissue. Well-known soil-borne pathogens are believed to cause these diseases. Yet, a systematized survey of these pathogens is lacking for Kalanchoe produced commercially. Here, we studied the occurrence of soil-borne fungal pathogens associated with cultivation of Kalanchoe in Denmark and production of cuttings and stock plants in greenhouse facilities located in Turkey and Vietnam. Molecular identification of pathogens complemented mycological identification and pathogenicity testing of the soil-borne fungal pathogens. This study revealed that the fungi Corynespora cassiicola, Thielaviopsis basicola, Fusarium solani, and F. oxysporum are the most prevalent pathogens associated with root and stem rotting and wilt of Kalanchoe under the conditions studied. Furthermore, the study showed that some of the pathogens are part of an infection complex comprising both primary and opportunistic fungal species. The fact that some of the pathogens were present in some regions, while absent in others, suggests how they move between greenhouse facilities on infected plant material. This study generated important information about the soil-borne fungal complex affecting Kalanchoe, which is useful for a better understanding of the biology of the disease and for designing control strategies.


Assuntos
Kalanchoe , Microbiologia do Solo , Dinamarca , Fungos/classificação , Fungos/genética , Kalanchoe/microbiologia , Doenças das Plantas/microbiologia , Prevalência , Turquia , Vietnã
12.
Bioengineered ; 10(1): 316-334, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31347943

RESUMO

In the development of medicinally important Orchidaceae, the extent of fungal endophytes specificity is not presently very clear. Limited study has been available on natural products formed and its role on plant growth, defence mechanism by endophytes, and to characterize the chief treasure of bioactive molecules. Therefore, this review article presents an evaluation of the endophytes associated with Orchidaceae for physiology, metabolism, and genomics which have prominently contributed to the resurgence of novel metabolite research increasing our considerate of multifaceted mechanisms regulatory appearance of biosynthetic gene groups encoding diverse metabolites. Additionally, we presented the comprehensive recent development of bio-strategies for the cultivation of endophytes from Orchidaceae and integration of bioengineered 'Genomics with metabolism' approaches with emphases collective omics as powerful approach to discover novel metabolite compounds. The Orchidaceae-fungal endophytes' biodynamics for sustainable development of bioproducts and its applications are supported in large-scale biosynthesis of industrially and pharmaceutical important biomolecules.


Assuntos
Produtos Biológicos/química , Endófitos/metabolismo , Fungos/metabolismo , Orchidaceae/microbiologia , Simbiose/fisiologia , Produtos Biológicos/isolamento & purificação , Endófitos/classificação , Endófitos/genética , Fungos/classificação , Fungos/genética , Redes e Vias Metabólicas/fisiologia , Folhas de Planta/microbiologia , Raízes de Plantas/microbiologia , Caules de Planta/microbiologia , Metabolismo Secundário/fisiologia
13.
World J Microbiol Biotechnol ; 35(7): 107, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31267318

RESUMO

Marine microbial diversity offers enormous potential for discovery of compounds of crucial importance in healthcare, food security and bioindustry. However, access to it has been hampered by the difficulty of accessing and growing the organisms for study. The discovery and exploitation of marine bioproducts for research and commercial development requires state-of-the-art technologies and innovative approaches. Technologies and approaches are advancing rapidly and keeping pace is expensive and time consuming. There is a pressing need for clear guidance that will allow researchers to operate in a way that enables the optimal return on their efforts whilst being fully compliant with the current regulatory framework. One major initiative launched to achieve this, has been the advent of European Research Infrastructures. Research Infrastructures (RI) and associated centres of excellence currently build harmonized multidisciplinary workflows that support academic and private sector users. The European Marine Biological Research Infrastructure Cluster (EMBRIC) has brought together six such RIs in a European project to promote the blue bio-economy. The overarching objective is to develop coherent chains of high-quality services for access to biological, analytical and data resources providing improvements in the throughput and efficiency of workflows for discovery of novel marine products. In order to test the efficiency of this prototype pipeline for discovery, 248 rarely-grown organisms were isolated and analysed, some extracts demonstrated interesting biochemical properties and are currently undergoing further analysis. EMBRIC has established an overarching and operational structure to facilitate the integration of the multidisciplinary value chains of services to access such resources whilst enabling critical mass to focus on problem resolution.


Assuntos
Produtos Biológicos , Biotecnologia , Oceanos e Mares , Água do Mar/microbiologia , Organismos Aquáticos/genética , Organismos Aquáticos/metabolismo , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Descoberta de Drogas , Fungos/genética , Fungos/metabolismo , Metabolômica
14.
World J Microbiol Biotechnol ; 35(7): 113, 2019 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-31289918

RESUMO

Camellia taliensis (W. W. Smith) Melchior is a wild tea plant endemic from the west and southwest of Yunnan province of China to the north of Myanmar and is used commonly to produce tea by the local people of its growing areas. Its chemical constituents are closely related to those of C. sinensis var. assamica, a widely cultivated tea plant. In this study, the α diversity and phylogeny of endophytic fungi in the branches of C. taliensis were explored for the first time. A total of 160 fungal strains were obtained and grouped into 42 species from 29 genera, which were identified based on rDNA internal transcribed spacer sequence analysis. Diversity analysis showed that the endophytic fungal community of the branches of C. taliensis had high species richness S (42), Margalef index D' (8.0785), Shannon-Wiener index H' (2.8494), Simpson diversity index DS (0.8891), PIE index (0.8947) and evenness Pielou index J (0.7623) but a low dominant index λ (0.1109). By contrast, that in the branches of C. taliensis had abundant species and high species evenness. Diaporthe tectonigena, Acrocalymma sp. and Colletotrichum magnisporum were the dominant endophytic fungi. The phylogenetic tree was established by maximum parsimony analysis, and the 11 orders observed for endophytic fungi belonging to Ascomycota and Basidiomycota were grouped into 4 classes.


Assuntos
Camellia/microbiologia , Endófitos/classificação , Endófitos/isolamento & purificação , Fungos/classificação , Fungos/isolamento & purificação , Filogenia , Chá , Ascomicetos/classificação , Ascomicetos/genética , Ascomicetos/isolamento & purificação , Basidiomycota/classificação , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Biodiversidade , China , Análise por Conglomerados , DNA Ribossômico/genética , Endófitos/genética , Fungos/genética , Mianmar , Análise de Sequência
15.
Microbiol Res ; 226: 1-9, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284938

RESUMO

Citrus crops have great economic importance worldwide. However, citrus production faces many diseases caused by different pathogens, such as bacteria, oomycetes, fungi and viruses. To overcome important plant diseases in general, new technologies have been developed and applied to crop protection, including RNA interference (RNAi) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) systems. RNAi has been demonstrated to be a powerful tool for application in plant defence mechanisms against different pathogens as well as their respective vectors, and CRISPR/Cas system has become widely used in gene editing or reprogramming or knocking out any chosen DNA/RNA sequence. In this article, we provide an overview of the use of RNAi and CRISPR/Cas technologies in management strategies to control several plants diseases, and we discuss how these strategies can be potentially used against citrus pathogens.


Assuntos
Citrus/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Doenças das Plantas/genética , Doenças das Plantas/prevenção & controle , Interferência de RNA , Bactérias/genética , Bactérias/patogenicidade , Sistemas CRISPR-Cas , Citrus/microbiologia , Produtos Agrícolas , Fungos/genética , Fungos/patogenicidade , Edição de Genes/métodos , Engenharia Genética , Vírus/genética , Vírus/patogenicidade
16.
J Sci Food Agric ; 99(13): 5687-5695, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31150112

RESUMO

BACKGROUND: The quality of soy sauce is strongly affected by microorganisms and raw materials (defatted soybean or whole soybean). The present study investigated the effect of two types of fortified pattern, including inoculation with starters (Tetragenococcus halophilus combined with Zygosaccharomyces rouxii and Candida versatilis), and adding culture medium (saccharified rice flour solution), on the metabolite profiles and microbial community of soy sauce produced from defatted soybean (DP) and whole soybean (HD). Relationships between microbes and volatiles, and their interactions, were shown. RESULTS: The dominant metabolites differed in the soy sauce samples except for isoflavones. Alcohols and phenols were higher in DP moromi. Two classes of dominant esters, long-chain fatty acid esters (LFAE) and unsaturated-short-chain fatty acid esters (USFAE), were higher in HD moromi than DP. Weissella, Leuconostoc, and Aspergillus were the dominant microbes. Leuconostoc, and Aspergillus increased, and Weissella decreased in moromi inoculated with starters compared with a control. Similar changes to Leuconostoc were observed in moromi added culture medium. CONCLUSIONS: The microbes were responsible for the formation of volatiles. The intergeneric interactions with microbes were affected by fortified pattern. The effect of starters or culture medium on microbial community and metabolites of soy sauce depended on the raw material. © 2019 Society of Chemical Industry.


Assuntos
Bactérias/isolamento & purificação , Fungos/isolamento & purificação , Microbiota , Alimentos de Soja/microbiologia , Soja/microbiologia , Álcoois/análise , Álcoois/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Candida/metabolismo , Enterococcaceae/metabolismo , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Fermentação , Fungos/classificação , Fungos/genética , Fungos/metabolismo , Fenóis/análise , Fenóis/metabolismo , Alimentos de Soja/análise , Soja/metabolismo , Zygosaccharomyces/metabolismo
17.
BMC Genomics ; 20(Suppl 5): 423, 2019 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-31167634

RESUMO

BACKGROUND: High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes. RESULTS: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project. CONCLUSIONS: MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .


Assuntos
Biologia Computacional/métodos , Fungos/genética , Marcadores Genéticos , Metagenômica/métodos , Microbiota , Análise de Sequência de DNA/métodos , Vírus/genética , Algoritmos , Fungos/classificação , Genoma Fúngico , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Vírus/classificação
18.
Ecotoxicol Environ Saf ; 181: 395-403, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31212188

RESUMO

The aims of this work was to investigate, in soil microcosms, the effects on soil microbial community structure and function of increasing concentrations of 4-Nonylphenol (NP). The lasts is a product of degradation of NPEOs (Nonylphenol polyethoxylates) with a known toxic and estrogenic capacity able to disrupt animal's hormonal systems. The effect of increasing concentrations of NP (0, 10, 30, 90, and 270 mg NP kg-1 of dry soil) in soil microcosms in three sampling dates (28, 56, and 112 days) over soil microbial activity and function were assessed. Soil microbial activity was estimated by microbial ATP content, and both bacterial and fungal communities composition were estimated using the terminal restriction fragment length polymorphism technique (T-RFLP). Abundance of ammonia-oxidizing bacteria (AOB) was estimated by qPCR of gene encoding for the bacterial ammonia-monoxygenase (amoA). Changes in biologically mediated soil properties were also assessed, namely water-soluble NH+4, NO-2 and NO-3 content, the two last allowing the assessment of mineralization rates. NP-spiking had some unexpected impacts on microbial community structure and functions, since (i) impacted both bacterial and fungal communities structure at the highest NP concentration tested, bacterial communities were resistant to lower concentrations, while fungal communities were increasingly impacted until the end of the incubation at day 112; (ii) no community structure resilience was observed in bacteria at the highest NP concentration nor for fungi at any concentration; (iii) microbial activity decreased with NP after 28 and 56 d, but increased in the last sampling at the highest concentrations tests, coupled to an enrichment in AOB taxa after 56 and 112 days, that at least partly explain also explain the observed speed up of nitrification rates.


Assuntos
Estrogênios não Esteroides/toxicidade , Microbiota/efeitos dos fármacos , Nitrogênio , Fenóis/toxicidade , Microbiologia do Solo , Poluentes do Solo/toxicidade , Amônia/análise , Amônia/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Fungos/genética , Fungos/isolamento & purificação , Minerais , Nitratos/análise , Nitrificação , Nitritos/análise , Solo/química
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