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1.
Chemosphere ; 238: 124629, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31524607

RESUMO

Despite wastewater treatment, sewage sludge is often contaminated with multiple pollutants. Their impact on the phylogenetic composition and diversity of prokaryotic communities in sludge samples remains largely unknown. In this study, we analyzed the phylogenetic structure of bacterial communities and diversity in sludge from six waste water treatment plants (WWTPs) and linked this information with the pollutants identified in these samples: eight potentially toxic metals (PTMs) and four groups of organic pollutants [polychlorinated biphenyls (PCBs), polyromantic hydrocarbons (PAHs), brominated flame retardants (BFRs) and organochlorine pesticides (OCPs)]. Alpha diversity measures and the distribution of dominant phyla varied among the samples, with the community from the thermophilic anaerobic digestion (TAD)-stabilized sample from Prague being the least rich and the least diverse and containing on average 36% of 16S rRNA gene sequence reads of the thermotolerant genus Coprothermobacter of the class Clostridia (phylum Firmicutes). Using weighted UniFrac distance-based redundancy analysis (dbRDA), we found that a collection of 5 PTMs: Cr, Cu, Ni, Pb, Zn, and a pair of BFRs: hexabromocyclododecane (HBCD) and tribromodiphenyl ethers (triBDEs) were significantly associated with the bacterial community structure in mesophilic anaerobic digestion (MAD)-stabilized samples, whereas PCBs were observed to be marginally significant. Altogether, 85% of the variance in bacterial community structure could be ascribed to these pollutants. The data presented here contribute to a greater understanding of the ecological effects of combined pollution on the composition and diversity of bacterial communities, hence have the potential to aid in predicting ecosystem functions and/or disruptions associated with pollution.


Assuntos
Bactérias/metabolismo , Retardadores de Chama/análise , Praguicidas/análise , Esgotos/química , Esgotos/microbiologia , Poluentes Químicos da Água/análise , Bactérias/classificação , Bactérias/genética , Ecossistema , Hidrocarbonetos Bromados/análise , Filogenia , Bifenil Polibromatos/análise , Bifenilos Policlorados/análise , RNA Ribossômico 16S/genética
2.
Food Chem ; 305: 125431, 2020 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-31610425

RESUMO

Recent European regulations require safety assessments of food enzymes (FE) before their commercialization. FE are mainly produced by micro-organisms, whose viable strains nor associated DNA can be present in the final products. Currently, no strategy targeting such impurities exists in enforcement laboratories. Therefore, a generic strategy of first line screening was developed to detect and identify, through PCR amplification and sequencing of the 16S-rRNA gene, the potential presence of FE producing bacteria in FE preparations. First, the specificity was verified using all microbial species reported to produce FE. Second, an in-house database, with 16S reference sequences from bacteria producing FE, was constructed for their fast identification through blast analysis. Third, the sensitivity was assessed on a spiked FE preparation. Finally, the applicability was verified using commercial FE preparations. Using straightforward PCR amplifications, Sanger sequencing and blast analysis, the proposed strategy was demonstrated to be convenient for implementation in enforcement laboratories.


Assuntos
Bactérias/isolamento & purificação , Código de Barras de DNA Taxonômico , RNA Ribossômico 16S/análise , Bactérias/genética , Bactérias/metabolismo , Manipulação de Alimentos , Reação em Cadeia da Polimerase
3.
Equine Vet J ; 52(1): 67-75, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31006119

RESUMO

BACKGROUND: Although, peripheral caries (PC) affects almost half of UK horses, no comprehensive microbiological study has been performed on this disorder. As a high proportion of oral bacteria cannot be conventionally cultured, molecular microbiological techniques such as Next Generation Sequencing are required to examine the complex oral bacteria community. OBJECTIVES: To identify the microbiota involved in equine PC, including comparing microbiota at the more commonly and severely affected three caudal cheek teeth with the less commonly affected three rostral cheek teeth. STUDY DESIGN AND METHODS: Equine dental plaque samples were collected from the palatal aspects of cheek teeth of 63 horses. DNA was isolated and amplified using PCR, targeting the V4 region of the 16S rRNA gene and Next Generation Sequencing of these gene amplicons was performed. The acquired data were processed and analysed using Mothur and R. RESULTS: Streptococcus species was the genus most commonly associated with equine PC, whereas Gemella species was the genus most associated with the control group. In a further analysis where the rostral and caudal cheek teeth were compared with each other and with the control group. Veillonella species was the most commonly associated genus with PC of the rostral cheek teeth, Streptococcus species was the most associated genus with the caudal cheek teeth, and Corynebacterium with the control group. MAIN LIMITATIONS: Some bacteria can have multiple heterogeneous copies of the 16S rRNA gene, which can affect the estimation of their relative abundance. CONCLUSIONS: Similar to caries studies in other species, acidogenic and aciduric microorganisms including Streptococcus species were found to be associated with equine peripheral caries.


Assuntos
Bactérias/genética , Cárie Dentária/veterinária , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Doenças dos Cavalos/microbiologia , Animais , Bactérias/isolamento & purificação , Cárie Dentária/microbiologia , Placa Dentária/microbiologia , Placa Dentária/veterinária , Cavalos
4.
J Sci Food Agric ; 100(2): 705-713, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31599967

RESUMO

BACKGROUND: Despite the growing importance of probiotics apparent health benefits, an impediment to the use of new probiotic cultures is their safety. Hence there is a need to strictly examine the biosafety as well as health benefits of probiotics in in vivo model systems. RESULTS: In this study, two lactic acid bacterial (LAB) cultures Lactobacillus fermentum NCMR 2826 and FIX proven for their in vitro probiotic properties were investigated for their in vivo safety in Wistar rats. An acute toxicity study (14 days) with a high dose of biomass (1016 colony-forming units (CFU) mL-1 ) followed by a subchronic test for 13 weeks with oral feeding of the probiotic cultures in three different doses (107 , 108 and 1010 CFU mL-1 ) on a daily basis revealed the safety of the L. fermentum cultures. The probiotic feeding had no toxic effects on survival, body weight and food consumption with any of the dosages used throughout the treatment period. No statistically significant changes in relative organ weights and serum biochemical and hematological indices were found between the control and the probiotic fed animals. In addition to the safety attributes, the L. fermentum culture fed rats showed reduced serum cholesterol levels, macrovesicular steatosis and hepatocyte ballooning compared with control animals. Further, quantification of intestinal microbiota using real-time polymerase chain reaction (PCR) analysis from animal feces indicated a significant increase and stability of Lactobacillus and Bifidobacterium counts but a decrease of Escherichia coli numbers. CONCLUSION: This study of safety and beneficial features highlights the use of the two native L. fermentum isolates as potential probiotic food supplements. © 2019 Society of Chemical Industry.


Assuntos
Anticolesterolemiantes/administração & dosagem , Colesterol/metabolismo , Microbioma Gastrointestinal/efeitos dos fármacos , Lactobacillus fermentum/metabolismo , Probióticos/administração & dosagem , Animais , Anticolesterolemiantes/metabolismo , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/isolamento & purificação , Colesterol/sangue , Intestinos/efeitos dos fármacos , Intestinos/microbiologia , Lactobacillus fermentum/crescimento & desenvolvimento , Masculino , Probióticos/metabolismo , Ratos , Ratos Wistar
5.
Pol J Microbiol ; 68(3): 377-382, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31880883

RESUMO

The aim of this study was to assess the periodontal status of cystic fibrosis (CF) adult patients and to evaluate whether there is a correlation between the bacterial population of the subgingival biofilm and the health status of the periodontal tissues in this group of adults. The study involved 22 cystic fibrosis adult patients. The periodontal condition was assessed using Plaque Index (PLI), Gingival Index (GI), and Probing Pocket Depth (PPD). The gingival sulcus samples were analyzed by the Real-Time PCR assay (RT-PCR). Majority of patients showed moderate or severe bacterial dental plaque accumulation, but none of them had clinical symptoms of periodontal diseases. RT-PCR showed the presence of periopathogens in 50% of patients. Red complex microorganisms were detected in 9.09%, orange complex in 27.27%, and green complex in 31.82% of the samples analyzed. In cystic fibrosis patients colonized by periopathogens, the periodontal markers were significantly higher in comparison to not colonized by periopathogens patients. Despite the widespread presence of bacterial dental deposits in the cystic fibrosis adult patients examined, none of them has clinical symptoms of periodontal disease; however, the presence of periodontal pathogens in subgingival biofilm may represent a possible risk factor of this disease in the future. An unsatisfactory level of oral hygiene in any patient with cystic fibrosis indicates a need to focus on standards of dental care for such patients.The aim of this study was to assess the periodontal status of cystic fibrosis (CF) adult patients and to evaluate whether there is a correlation between the bacterial population of the subgingival biofilm and the health status of the periodontal tissues in this group of adults. The study involved 22 cystic fibrosis adult patients. The periodontal condition was assessed using Plaque Index (PLI), Gingival Index (GI), and Probing Pocket Depth (PPD). The gingival sulcus samples were analyzed by the Real-Time PCR assay (RT-PCR). Majority of patients showed moderate or severe bacterial dental plaque accumulation, but none of them had clinical symptoms of periodontal diseases. RT-PCR showed the presence of periopathogens in 50% of patients. Red complex microorganisms were detected in 9.09%, orange complex in 27.27%, and green complex in 31.82% of the samples analyzed. In cystic fibrosis patients colonized by periopathogens, the periodontal markers were significantly higher in comparison to not colonized by periopathogens patients. Despite the widespread presence of bacterial dental deposits in the cystic fibrosis adult patients examined, none of them has clinical symptoms of periodontal disease; however, the presence of periodontal pathogens in subgingival biofilm may represent a possible risk factor of this disease in the future. An unsatisfactory level of oral hygiene in any patient with cystic fibrosis indicates a need to focus on standards of dental care for such patients.


Assuntos
Biofilmes , Fibrose Cística/microbiologia , Doenças Periodontais/microbiologia , Adulto , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Fenômenos Fisiológicos Bacterianos , Feminino , Gengiva/microbiologia , Humanos , Masculino , Pessoa de Meia-Idade , Índice Periodontal , Periodonto/microbiologia , Adulto Jovem
6.
Pol J Microbiol ; 68(4): 465-476, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31880891

RESUMO

The associated microbiota plays an essential role in the life process of jellyfish. The endobiotic bacterial communities from four common jellyfish Phyllorhiza punctata, Cyanea capillata, Chrysaora melanaster, and Aurelia coerulea were comparatively analyzed by 16S rDNA sequencing in this study. Several 1049 OTUs were harvested from a total of 130 183 reads. Tenericutes (68.4%) and Firmicutes (82.1%) are the most abundant phyla in P. punctata and C. melanaster, whereas C. capillata and A. coerulea share the same top phylum Proteobacteria (76.9% vs. 78.3%). The classified OTUs and bacterial abundance greatly decrease from the phylum to genus level. The top 20 matched genera only account for 9.03% of the total community in P. punctata, 48.9% in C. capillata, 83.05% in C. melanaster, and 58.1% in A. coerulea, respectively. The heatmap of the top 50 genera shows that the relative abundances in A. coerulea and C. capillata are far richer than that in P. punctata and C. melanaster. Moreover, a total of 41 predictive functional categories at KEGG level 2 were identified. Our study indicates the independent diversity of the bacterial communities in the four common Scyphomedusae, which might involve in the metabolism and environmental information processing of the hosts.The associated microbiota plays an essential role in the life process of jellyfish. The endobiotic bacterial communities from four common jellyfish Phyllorhiza punctata, Cyanea capillata, Chrysaora melanaster, and Aurelia coerulea were comparatively analyzed by 16S rDNA sequencing in this study. Several 1049 OTUs were harvested from a total of 130 183 reads. Tenericutes (68.4%) and Firmicutes (82.1%) are the most abundant phyla in P. punctata and C. melanaster, whereas C. capillata and A. coerulea share the same top phylum Proteobacteria (76.9% vs. 78.3%). The classified OTUs and bacterial abundance greatly decrease from the phylum to genus level. The top 20 matched genera only account for 9.03% of the total community in P. punctata, 48.9% in C. capillata, 83.05% in C. melanaster, and 58.1% in A. coerulea, respectively. The heatmap of the top 50 genera shows that the relative abundances in A. coerulea and C. capillata are far richer than that in P. punctata and C. melanaster. Moreover, a total of 41 predictive functional categories at KEGG level 2 were identified. Our study indicates the independent diversity of the bacterial communities in the four common Scyphomedusae, which might involve in the metabolism and environmental information processing of the hosts.


Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Cifozoários/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , Microbiota , Filogenia , RNA Ribossômico 16S/genética , Cifozoários/classificação
7.
Huan Jing Ke Xue ; 40(10): 4685-4690, 2019 Oct 08.
Artigo em Chinês | MEDLINE | ID: mdl-31854839

RESUMO

Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants. ARGs are frequently detected in municipal solid waste landfill and its leachate. In this study, high-throughput quantitative PCR techniques were used to investigate the dynamics of ARGs during the treatment process of landfill leachate. The results showed that ARGs in leachate were diverse and abundant, and leachate treatment could effectively reduce their abundance; the absolute abundance of ARGs was reduced to 9.2×1010 copies·L-1, which was five orders of magnitude less than the abundance of the influent. However, the range and abundance of antibiotic resistance genes in the leachate effluents were still high compared to the natural environment. Therefore, the secondary contamination of ARGs might be caused by leachate being directly discharged into municipal sewage system. In this regard, ecological and environmental risk is an inconvenient truth. Furthermore, strong correlations indicate that heavy metals and mobile genetic elements (MGEs) in landfill leachate might influence the transfer of ARGs.


Assuntos
Antibacterianos , Resistência Microbiana a Medicamentos , Resíduos Sólidos , Poluentes Químicos da Água , Bactérias/genética , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos , Instalações de Eliminação de Resíduos
8.
Adv Exp Med Biol ; 1168: 147-156, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31713170

RESUMO

The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.


Assuntos
Microbiota , Neoplasias , Bactérias/genética , Disbiose , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Metagenômica , Microbiota/genética , Microbiota/fisiologia , Neoplasias/microbiologia
9.
J Agric Food Chem ; 67(45): 12428-12440, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31668067

RESUMO

In the present study, the digestion and fermentation of blackberry polysaccharides (BBPs) with different molecular weights (Mw) were investigated. The results showed that the Mw decrease rates of BBP, BBP-8, BBP-16, and BBP-24 were 77.48, 69.61, 56.87, and 52.89%, respectively. The antioxidant and α-glucosidase inhibitory activities of BBPs were decreased under gastrointestinal condition, which might be due to the variation of Mw during digestion. The bile acid-binding ability of BBPs showed an Mw-dependent manner for higher Mw polysaccharides with higher viscosity. Through fermentation, the BBPs affected the ecosystem of the intestinal tract by promoting the production of short-chain fatty acids, lowering the pH of colon, and decreasing the ratio of Firmicutes to Bacteroidetes. All BBPs showed almost a similar modulation effect on the gut bacteria, but the lower Mw polysaccharide was more easily utilized by bacteria.


Assuntos
Extratos Vegetais/química , Extratos Vegetais/metabolismo , Polissacarídeos/química , Polissacarídeos/metabolismo , Rubus/metabolismo , Adulto , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Digestão , Ácidos Graxos Voláteis/metabolismo , Feminino , Microbioma Gastrointestinal , Humanos , Masculino , Peso Molecular , Rubus/química , Estômago/microbiologia , Adulto Jovem
10.
J Agric Food Chem ; 67(45): 12441-12451, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31674783

RESUMO

Sesamin, a lignan from sesame seed, has been reported to attenuate chronic mild stress-induced depressive-like behaviors. Gut microbiota play pivotal roles in mediating psychological behaviors by regulating gut barrier integrity and systemic inflammatory responses. Here, we found that oral sesamin administration (50 mg/kg·bodyweight/day) significantly attenuated depressive, aversive, repetitive, and anxiety-like behaviors in a long-term multiple nonsocial stress-treated mice model. Sesamin inhibited stress-induced gut barrier integrity damage, reduced circulating lipopolysaccharide (LPS) levels, and suppressed neuroinflammatory responses. Moreover, sesamin treatment also restructured the gut microbiome by enhancing the relative abundances of Bacteroidales and S24-7. The correlation analysis indicated that the microbiota composition changes were strongly correlated with behavioral disorders, serotonin, norepinephrine, and LPS levels. In conclusion, sesamin has preventive effects on stress-induced behavioral and psychological disorders, which might be highly related to the reshaped microbiota composition. This study provides a clue for understanding the systemic mechanism of anti-depression effects of sesamin.


Assuntos
Depressão/tratamento farmacológico , Suplementos Nutricionais/análise , Dioxóis/administração & dosagem , Microbioma Gastrointestinal/efeitos dos fármacos , Lignanas/administração & dosagem , Extratos Vegetais/administração & dosagem , Sesamum/química , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Comportamento/efeitos dos fármacos , Depressão/microbiologia , Depressão/psicologia , Humanos , Masculino , Camundongos , Estresse Oxidativo/efeitos dos fármacos , Sementes/química , Estresse Psicológico
11.
Int Heart J ; 60(5): 1176-1183, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31564708

RESUMO

Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.


Assuntos
Bactérias/classificação , Microbioma Gastrointestinal/efeitos dos fármacos , Insuficiência Cardíaca/microbiologia , Isoproterenol/efeitos adversos , Metagenômica/métodos , Animais , Bactérias/genética , Modelos Animais de Doenças , Ecocardiografia , Insuficiência Cardíaca/induzido quimicamente , Insuficiência Cardíaca/diagnóstico por imagem , Sequenciamento de Nucleotídeos em Larga Escala , Injeções Intraperitoneais , Isoproterenol/farmacologia , Masculino , Filogenia , Ratos , Análise de Sequência de DNA
12.
J Agric Food Chem ; 67(42): 11584-11590, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31566380

RESUMO

Ureolytic microbes play a pivotal role in the maintenance of soil fertility. Soil aggregates are supposed to provide heterogeneous habitats for microorganisms, which may result in distinct metabolic functions. However, limited information is available regarding the distribution patterns, driving factors, and activity of ureolytic microbiota at the aggregate scale. In this study, we characterized the ureolytic microbiota and urease activity of three soil aggregate fractions from an Inceptisol subjected to 5 years of different fertilization regimes. Correlations between soil chemical characteristics and ureolytic microbial communities were analyzed. The results showed that the total abundance as well as the relative abundance of copiotrophic ureolytic microbes generally increased with the increasing soil aggregate size. This trend was in line with the nutrient distribution patterns, including labile carbon, NH4+, total carbon, nitrogen, and phosphorus. Soil urease activity also increased significantly with the increasing soil aggregate size and was positively correlated with copiotrophic ureolyric microbes, such as Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Thus, we speculated that larger size soil aggregates with greater availability of labile carbon support more copiotrophic ureolyric microbes with a high growth rate, leading to a high density of total ureolytic microbes and higher urease activity. Smaller aggregates with less available carbon were associated with more oligotrophs, higher abundances of total ureolytic microbes, and higher urease activity. Our results suggest that larger soil aggregates and associated ureolyric microbes play a more important role in nutrient cycling for crop growth in this Inceptisol ecosystem.


Assuntos
Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Microbiologia do Solo , Solo/química , Ureia/metabolismo , Urease/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Microbiota , Nitrogênio/metabolismo , Tamanho da Partícula , Fósforo/metabolismo
13.
J Microbiol ; 57(10): 865-873, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31571125

RESUMO

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil's metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.


Assuntos
Bactérias/enzimologia , Bactérias/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Lignina/metabolismo , Metagenoma , Microbiologia do Solo , Regiões Antárticas , Bactérias/classificação , Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Biocombustíveis/análise , Temperatura Baixa , Filogenia , Solo/química , Tundra
14.
World J Microbiol Biotechnol ; 35(10): 155, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31576428

RESUMO

Biosurfactants are amphiphilic molecules produced by a variety of microorganisms, including bacteria, yeast and filamentous fungi. Unlike chemically synthesized surfactants, biosurfactants present advantages, such as biodegradability, low toxicity, high selectivity and activity under extreme temperature, pH and salinity conditions, as well as a low critical micelle concentration. Moreover, they can be produced from agro-industrial waste and renewable sources. Their structural diversity and functional properties mean that they have potential applications in various industrial processes as wetting agents, dispersants, emulsifiers, foaming agents, food additives and detergents, as well as in the field of environmental biotechnology. However, opportunities for their commercialization have been limited due to the low yields obtained in the fermentation processes involved in their production as well as the use of refined raw materials, which means higher cost in production. In an attempt to solve these limitations on the commercialization of biosurfactants, various research groups have focused on testing the use of inexpensive alternative sources, such as agro-industrial waste, as substrates for the production of different biosurfactants. In addition to enabling the economical production of biosurfactants, the use of such waste aims to reduce the accumulation of compounds that cause environmental damage. This review shows advances in biosurfactant production carried out using different waste materials or by-products from agro-industrial activities.


Assuntos
Bactérias/metabolismo , Resíduos Industriais/análise , Tensoativos/metabolismo , Leveduras/metabolismo , Bactérias/genética , Biodegradação Ambiental , Biotecnologia , Fermentação , Leveduras/genética
15.
J Agric Food Chem ; 67(45): 12335-12340, 2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31617360

RESUMO

The Human Microbiome Project has prompted unprecedented advancement in microbiome science. Personalized microbiome modulation with precision (PMMP) is one of the emerging yet challenging fields in microbiome research. Carbohydrate-based prebiotics (CBPs) have been shown to modulate the gut microbiome to various extents according to different structural characteristics, such as degree of polymerization, branching, glycosidic linkage, monosaccharide profile, and chemical modification. Subsequently, a targeted modulation of the microbiome might be achieved by using CBPs with a specific structure. A multidimensional database can be established based on the structure-microbiome and structure-microbial-marker relationships. Such relationships could facilitate the development of synbiotics and PMMP.


Assuntos
Carboidratos/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Prebióticos/análise , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Carboidratos/química , Humanos , Intestinos/microbiologia
16.
J Agric Food Chem ; 67(46): 12796-12805, 2019 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-31659898

RESUMO

Whole-grain dietary fiber is rich in bound-form phenolics, and the biological activity of this special structural feature has attracted increasing attention. In this study, rice bran dietary fiber (RBDF) was subjected to in vitro gastrointestinal digestion and colonic fermentation to investigate the liberation of bound phenolics and their potential activities. Bound phenolics were released at a higher ratio during colonic fermentation (27.57%) than gastrointestinal digestion (2.68%). Nine phenolic compounds were detected from the fermentation supernatants. The released phenolics showed radical scavenging activity (DPPH and ABTS assays) and α-glucosidase inhibitory activity (IC50 = 19.11 µg GAE/mL). Compared with phenolics-removed RBDF (PR-RBDF), RBDF had a significantly stronger prebiotic effect on the microbes associated with diabetes (Lactobacillus spp., Akkermansia muciniphila, and Faecalibacterium prausnitzii). These findings indicate that bound phenolics may act as important functional components that could contribute to the health benefits of whole-grain dietary fiber.


Assuntos
Colo/metabolismo , Fibras na Dieta/análise , Trato Gastrointestinal/metabolismo , Oryza/metabolismo , Fenóis/química , Compostos Fitoquímicos/química , Prebióticos/análise , Adulto , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Colo/microbiologia , Fibras na Dieta/metabolismo , Feminino , Fermentação , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Humanos , Masculino , Oryza/química , Fenóis/metabolismo , Compostos Fitoquímicos/metabolismo , Adulto Jovem
17.
J Agric Food Chem ; 67(42): 11665-11674, 2019 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-31588753

RESUMO

A long-term high-fat diet (HFD) can cause a range of health problems. Gut microbiota plays a decisive role in the development of HFD-associated inflammation, involved in function of T cells. This study was designed to probe the regulative effects of dietary stachyose, a functional oligosaccharide, on HFD-induced weight gain, inflammation, gut microbiota dysbiosis, and T cell abnormality in C57Bl/6 mice. Mice were divided into three groups which received normal chow, HFD and HFD plus stachyose (400 mg/kg), respectively. Results showed that administration of stachyose diminished the HFD-induced upregulation of serum TNF-α level and elevation of peripheral blood leukocyte populations to alleviate the HFD-caused colonic and hepatic inflammation in mice. Analysis of gut microbiota revealed that stachyose improved the intestinal homeostasis of HFD-fed mice by improving the bacterial diversity with the increases in the relative abundances of the Prevotellaceae_NK3B31_group, Parasutterella, Christensenellaceae_R-7_group, and Anaerovorax, as well as the fecal level of butanoic acid, while decreasing the ratio of Firmicutes-to-Bacteroidetes and the abundances of the Lachnospiraceae_NK4A136_group, Desulfovibrio, Anaerotruncus, Mucispirillum, Roseburia, and Odoribacter. Flow cytometric analysis showed that stachyose antagonized the HFD-induced decrease of peripheral CD4+ T cell population in mice. Conclusively, these findings suggest that long-term consumption of stachyose can ameliorate the HFD-associated colonic and hepatic inflammation and its complications by modulating gut microbiota.


Assuntos
Linfócitos T CD4-Positivos/imunologia , Colo/imunologia , Disbiose/dietoterapia , Microbioma Gastrointestinal , Fígado/imunologia , Oligossacarídeos/metabolismo , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Colo/microbiologia , Dieta Hiperlipídica/efeitos adversos , Disbiose/imunologia , Disbiose/microbiologia , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL
18.
BMC Bioinformatics ; 20(1): 517, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31651233

RESUMO

BACKGROUND: One of the main challenges for the CRISPR-Cas9 system is selecting optimal single-guide RNAs (sgRNAs). Recently, deep learning has enhanced sgRNA prediction in eukaryotes. However, the prokaryotic chromatin structure is different from eukaryotes, so models trained on eukaryotes may not apply to prokaryotes. RESULTS: We designed and implemented a convolutional neural network to predict sgRNA activity in Escherichia coli. The network was trained and tested on the recently-released sgRNA activity dataset. Our convolutional neural network achieved excellent performance, yielding average Spearman correlation coefficients of 0.5817, 0.7105, and 0.3602, respectively for Cas9, eSpCas9 and Cas9 with a recA coding region deletion. We confirmed that the sgRNA prediction models trained on prokaryotes do not apply to eukaryotes and vice versa. We adopted perturbation-based approaches to analyze distinct biological patterns between prokaryotic and eukaryotic editing. Then, we improved the predictive performance of the prokaryotic Cas9 system by transfer learning. Finally, we determined that potential off-target scores accumulated on a genome-wide scale affect on-target activity, which could slightly improve on-target predictive performance. CONCLUSIONS: We developed convolutional neural networks to predict sgRNA activity for wild type and mutant Cas9 in prokaryotes. Our results show that the prediction accuracy of our method is improved over state-of-the-art models.


Assuntos
Bactérias/genética , Aprendizado Profundo , Edição de Genes , RNA Guia/genética , Sistemas CRISPR-Cas , Deleção de Sequência
19.
Postepy Biochem ; 65(3): 202-211, 2019 10 01.
Artigo em Polonês | MEDLINE | ID: mdl-31643167

RESUMO

Advances in high resolution microscopy techniques and development of high throughput DNA analyses allow to reconsider the views concerning bacterial chromosome (nucleoid). Recent reports show that nucleoid exhibits a hierarchical organization, similarly to the eukaryotic chromatin. However, bacterial chromosome undergoes constant modifications and topological rearrangements due to the ongoing DNA replication, transcription and translation processes. Organization of dynamic and highly compacted nucleoid structure depends on physical factors acting on chromosome molecule inside small cell compartment, and is a consequence of action of many different DNA-binding proteins. The main goal of this review is to present the recent reports on bacterial chromatin structure and to elucidate the physical and molecular factors influencing its intracellular organization.


Assuntos
Bactérias/genética , Cromatina/metabolismo , Cromossomos Bacterianos/metabolismo , DNA Bacteriano/metabolismo , Proteínas de Bactérias/metabolismo , Cromatina/química , Cromatina/genética , Cromossomos Bacterianos/química , Cromossomos Bacterianos/genética , Replicação do DNA , DNA Bacteriano/química , DNA Bacteriano/genética , Proteínas de Ligação a DNA/metabolismo
20.
J Med Microbiol ; 68(11): 1585-1590, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31647400

RESUMO

Purpose. Acute bacterial meningitis continues to be a potentially life threatening condition. Hospital-acquired meningitis is rapidly increasing and adding an immense burden to the health system due to the emergence of multidrug resistance isolates. The purpose of this study is to find the antibiotic susceptibility pattern of the bacteria detected from hospital- and community-acquired meningitis.Methodology. A total of 400 Cerebrospinal fluid (CSF) samples from the suspected meningitis cases were collected and processed for cell count, biochemical examination, Gram staining, latex agglutination and culture. Bacteria grown on blood, chocolate and Mac-conkey agar were identified by matrix-assisted laser desorption/ionization-time of flight. Antibiotic susceptibility tests were performed as per Clinical and Laboratory Standard Institute guidelines.Results. Of the isolates, most prevalent Gram negative organisms in hospital-acquired bacterial meningitis were Escherichia coli 13 (27.08 %), Acinetobacter baumannii 12 (25 %), Klebsiella pneumoniae 5 (10.42 %), Pseudomonas aeruginosa 4 (8.33 %) and Gram positive organisms were Staphylococcus aureus 4 (8.33 %), Enterococcus faecium 3 (6.25 %) and CONS 2 (4.16 %). Streptococcus pneumoniae 3 (6.25 %) was the predominant organism in community-acquired bacterial meningitis. All the Gram negative isolates were multidrug resistance. Only colistin and imipenem were effective antibiotics against them. Likewise Gram positive organisms were susceptible to most of the antibiotics tested. However, E. faecium was only susceptible to Vanco+Teicoplanin.Conclusion. In hospital-acquired bacterial meningitis, multidrug resistance Gram negative bacteria are a huge challenge for the treatment of patients. Hence, antimicrobial stewardship should be followed to counteract with the emerging multidrug resistance isolates.


Assuntos
Bactérias/efeitos dos fármacos , Infecção Hospitalar/microbiologia , Farmacorresistência Bacteriana Múltipla , Meningites Bacterianas/microbiologia , Antibacterianos/farmacologia , Gestão de Antimicrobianos , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Colistina/farmacologia , Humanos , Imipenem/farmacologia , Índia , Testes de Sensibilidade Microbiana , Centros de Atenção Terciária/estatística & dados numéricos , Vancomicina/farmacologia
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