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1.
BMC Ecol Evol ; 21(1): 53, 2021 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-33836663

RESUMO

BACKGROUND: Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. RESULTS: Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. CONCLUSIONS: Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.


Assuntos
Actinobacteria , Avidina , Actinobacteria/genética , Animais , Bacteroidetes/genética , Humanos , Proteobactérias/genética , Streptomyces
2.
Sci Total Environ ; 771: 144773, 2021 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-33548724

RESUMO

Surface water plays a significant role in world development by promoting economic growth and health benefits to humans and animals whose lives depend on good water quality in the ecosystem. Thus, this study investigated the differences in physical and chemical properties of surface water from two lakes (Lakes Jackson and Talquin) and a pond (Pedrick Pond). Also, the influence of environmental factors on the microbial communities that live within the water environment was examined. Genomic DNA was extracted from the water samples collected and 16S rRNA sequencing method was employed to characterize the microbial community compositions across the three locations. The results obtained suggest that the water sources met the recommended recreational water quality criteria standard for clean water. Overall, Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes were the main bacterial phyla present in the communities, while Archaea was mainly dominated by Euryachaeota. Pressure, conductivity, temperature, dissolved oxygen (DO), and pH accounted for 74.2% of the variation in the distribution of the microbial community in the three locations (P < 0.05), while 58.2% of the variation in the microbial community distribution was accounted for by pressure and conductivity. The high temperature observed in the Pedrick Pond correlated with the distribution of genera hgcl_clades and Legionella. While in Lake Talquin, water conductivity was significantly associated with the abundance of Cyanobium_PCC_6307, Sediminibacterium, and Conexibacter. The results from this study indicate that the microbial communities in the two lakes are different from the pond and all the environmental variables accounted for a significant portion of the total variation, but pressure, conductivity, and temperature are more important factors due to significant correlation with the distribution of the microbial communities.


Assuntos
Lagos , Metagenômica , Animais , Bacteroidetes/genética , Humanos , Proteobactérias/genética , RNA Ribossômico 16S/genética
3.
Carbohydr Polym ; 255: 117388, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33436217

RESUMO

Pectins are a part of daily diet as well as food additives that are indigestible polysaccharides by human enzymes, however, they can be easily degraded by gut bacteria with the production of short chain fatty acids (SCFAs). Knowledge of pectin gut homeostasis and further how pectin affect gut bacterial communities is insufficient and limited. This review focuses on providing the whole story of how pectin functions as prebiotics in the gut. Understanding the interplay between functional and immunological responses inside animal or human gut as influenced by pectin in diets is provided. The interaction between pectin and gut microbiota is presented from both sides, in terms of how pectin affects gut microbiome and or the fermentation products produced in response by gut bacteria. This knowledge can be used to define preferred dietary pectins, targeting beneficial bacteria, and favoring balanced microbiota communities in the gut to maximize pectins' health benefits.


Assuntos
Microbioma Gastrointestinal/imunologia , Homeostase/imunologia , Imunomodulação/fisiologia , Pectinas/farmacologia , Polissacarídeos/administração & dosagem , Prebióticos/administração & dosagem , Animais , Bacteroidetes/genética , Bacteroidetes/imunologia , Biotransformação , Ensaios Clínicos como Assunto , Dieta/métodos , Ácidos Graxos Voláteis/biossíntese , Fermentação , Firmicutes/genética , Firmicutes/imunologia , Humanos , Pectinas/imunologia , Pectinas/metabolismo , Polissacarídeos/análise , Prebióticos/análise
4.
Arch Microbiol ; 203(4): 1489-1497, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33398398

RESUMO

The composition of microorganisms in the gastrointestinal tract is closely related to the intestinal microenvironments and the exterior growth environments of host. In this study, 16S rDNA sequencing technology was adopted to investigate the influence of fermentation bed on the cecum microorganisms of ducks. Two feeding density treatment groups were set up, including group A (n = 4brids/m2) and group B (n = 6brids/m2). Samples were collected from the intermediate core fermentation layer (10-20 cm) of the fermented mattress materials and from the intestinal contents of ducks at 4, 6 and 8 weeks, respectively. Results showed that Bacteroidetes (20.12-27.17%) and Ruminococcaceae UCG-014 (2.97-10.1%) were the predominant microorganisms in duck cecum, while the Truepera (5.08-6.29%), Pricia (4.44-5.44%) and Luteimonas (3.62-4.99%) were the dominant microorganisms in fermentation mattress material. The cecum bacteria exhibited great difference among different growth periods of the ducks. Increasing the stocking density of ducks had a negative effect on the beneficial bacteria in the cecum. The microbial populations in fermentation mattress material were very different from that in the cecal. In summary, our findings can provide a scientific data for the rational use of fermentation bed feeding mode in poultry production.


Assuntos
Criação de Animais Domésticos , Ceco , Patos , Fermentação , Pisos e Cobertura de Pisos , Microbioma Gastrointestinal , Criação de Animais Domésticos/métodos , Animais , Bactérias/genética , Bactérias/metabolismo , Bacteroidetes/genética , Ceco/microbiologia , Patos/genética , Patos/microbiologia , Microbioma Gastrointestinal/fisiologia , Trato Gastrointestinal/microbiologia , RNA Ribossômico 16S/genética
5.
Chemosphere ; 263: 127959, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32814133

RESUMO

Di(2-ethylhexyl) phthalate (DEHP) is one of the most widespread environmental contaminants worldwide because of its massive production, extensive use in common products, and liability to leach from products. This study investigated the mechanisms of DEHP mediated alteration of lipid metabolism. Rats were treated with 0.5 mg kg-1 d-1 of DEHP for 23 weeks. Results showed that the treatment induced cholesterol imbalance. Further fecal transplantation experiments corroborated the involvement of gut microbiota in DEHP-induced cholesterol imbalance. In addition, 16S rRNA gene sequencing analysis of cecal contents showed that DEHP disrupted the gut microbiota diversity in rats and increased the ratio of Firmicutes to Bacteroidetes. Further cecal metabolomic analyses, bile salt hydrolase enzyme activity, and gene expression examination revealed that chronic DEHP exposure generated a bile acid profile in the gut that is a more potent activator of farnesoid X receptor (FXR). The activation of FXR in the gut induced the expression of fibroblast growth factor 15, which subsequently suppressed cytochrome P450 family 7 subfamily A member 1 in the liver and bile acid synthesis. These results suggest that DEHP might induce cholesterol imbalance by regulating bile acid metabolism via the remodeling of the gut microbiota.


Assuntos
Colesterol/metabolismo , Dietilexilftalato/toxicidade , Microbioma Gastrointestinal/efeitos dos fármacos , Animais , Bacteroidetes/genética , Ácidos e Sais Biliares/metabolismo , Ceco , Dietilexilftalato/metabolismo , Firmicutes/genética , Metabolismo dos Lipídeos/genética , Fígado/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , RNA Ribossômico 16S/metabolismo , Ratos
6.
Nucleic Acids Res ; 49(1): 547-567, 2021 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-33330920

RESUMO

Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein-bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.


Assuntos
Bacteroidetes/genética , Iniciação Traducional da Cadeia Peptídica , Sequências Reguladoras de Ácido Ribonucleico , Ribossomos/metabolismo , Sequência de Aminoácidos , Sequência de Bases , Códon de Iniciação , Microscopia Crioeletrônica , Cristalografia por Raios X , Escherichia coli/genética , Flavobacterium/genética , Regulação Bacteriana da Expressão Gênica , Modelos Moleculares , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica , Puromicina/farmacologia , RNA Bacteriano/genética , RNA Mensageiro/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , RNA Ribossômico 5S/genética , Ribossomos/ultraestrutura , Alinhamento de Sequência , Homologia de Sequência , Especificidade da Espécie
7.
Sci Rep ; 10(1): 22296, 2020 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-33339847

RESUMO

Although bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.


Assuntos
Bacteroidetes/genética , Ecossistema , Filogenia , Plâncton/genética , Organismos Aquáticos/genética , China , Cianobactérias/genética , Cianobactérias/metabolismo , Cadeia Alimentar , Plâncton/metabolismo , RNA Ribossômico 16S/genética
8.
PLoS One ; 15(10): e0239987, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33031424

RESUMO

The microbial communities colonize the mucosal immune inductive sites could be captured by hosts, which could initiate the mucosal immune responses. The aggregated lymphoid nodule area (ALNA) and the ileal Payer's patches (PPs) in Bactrian camels are both the mucosal immune inductive sites of the gastrointestinal tract. Here, the bacteria community associated with the ALNA and ileal PPs were analyzed using of 16S rDNA-Illumina Miseq sequencing. The mutual dominant bacterial phyla at the two sites were the Bacteroidetes, Firmicutes, Verrucomicrobia and Proteobacteria, and the mutual dominant genus in both sits was Prevotella. The abundances of the Fibrobacter, Campylobacter and RFP12 were all higher in ALNA than in ileal PPs. While, the abundances of the 5-7N15, Clostridium, and Escherichia were all higher in ileal PPs than in ALNA. The results suggested that the host's intestinal microenvironment is selective for the symbiotic bacteria colonizing the corresponding sites, on the contrary, the symbiotic bacteria could impact on the physiological functions of this local site. In ALNA and ileal PPs of Bactrian camel, the bacteria which colonized different immune inductive sites have the potential to stimulate different immune responses, which is the result of the mutual selection and adaptation between microbial communities and their host.


Assuntos
Trato Gastrointestinal/microbiologia , Imunidade nas Mucosas , Tecido Linfoide/microbiologia , Microbiota , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Biodiversidade , Camelus , Fibrobacter/genética , Fibrobacter/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Tecido Linfoide/imunologia , Análise de Componente Principal , RNA Ribossômico 16S/química , RNA Ribossômico 16S/metabolismo , Simbiose
9.
Med Oral Patol Oral Cir Bucal ; 25(5): e668-e674, 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32851984

RESUMO

BACKGROUND: The objective of this study was to describe the bacterial communities associated with pediatric patients with endodontic infections of temporal teeth by targeting the 16S rRNA gene using pyrosequencing. MATERIAL AND METHODS: Microbiological samples were obtained from the lower primary molars of thirteen 13 pediatric patients with dental infections. An aspiration method for microbiological sampling was used. The identification of microbiota employing the pyrosequencing method by targeting the 16S gene was performed. RESULTS: Ribosomal 16S RNA gene sequences were amplified, obtaining a total of 16,182 sequences from 13 primary infected molars (13 different individuals) by pyrosequencing. Bacteroidetes phyla (35.15%) were the most abundant followed by Firmicutes (33.3%) and Fusobacteria (10.05%); the presence of specific pathogenic bacteria was determined as well. CONCLUSIONS: The infected root canal of primary teeth contains a high diversity of anaerobic bacteria, and Bacteroidetes, Firmicutes, and Fusobacteria phyla were the most abundant; Prevotella and Streptococcus genera were the most prevalent.


Assuntos
Bactérias , Bacteroidetes/genética , Criança , Humanos , RNA Ribossômico 16S , Análise de Sequência de DNA , Dente Decíduo
10.
Aquat Toxicol ; 227: 105591, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32853898

RESUMO

The effects of allelopathy and the potential harm of several isolated allelochemicals have been studied in detail. Microorganisms in the phycosphere play an important role in algal growth, decay and nutrient cycling. However, it is unknown and often neglected whether allelochemicals affect the phycosphere. The present study selected a phenolic acid protocatechuic acid (PA) - previously shown to be an allelochemical. We studied PA at a half maximal effective concentration of 0.20 mM (30 mg L-1) against Scrippsiella trochoidea to assess the effect of PA on its phycosphere in an acute time period (48 h). The results showed that: 1) OTUs (operational taxonomic units) in the treatment groups (31.4 ± 0.55) exceeded those of the control groups (28.2 ± 1.30) and the Shannon and Simpson indices were lower than the control groups (3.31 ± 0.08 and 0.84 ± 0.02, 3.45 ± 0.09 and 0.88 ± 0.01); 2) Gammaproteobacteria predominated in the treatment groups (44.71 ± 2.13 %) while Alphaproteobacteria dominated in the controls (67.17 ± 3.87 %); 3) Gammaproteobacteria and Alphaproteobacteria were important biomarkers in the treatment and control groups respectively (LDA > 4.0). PA improved the relative abundance of Alteromonas significantly and decreased the one of Rhodobacteraceae. PICRUSt analysis showed that the decrease of Rhodobacterceae was closely related with the decline of most functional genes in metabolism such as amino acid, carbohydrate, xenobiotics, cofactors and vitamins metabolism after PA-treated.


Assuntos
Alelopatia/efeitos dos fármacos , Dinoflagelados/efeitos dos fármacos , Proliferação Nociva de Algas/efeitos dos fármacos , Hidroxibenzoatos/farmacologia , Microbiota/efeitos dos fármacos , Feromônios/farmacologia , Alelopatia/genética , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Dinoflagelados/genética , Dinoflagelados/crescimento & desenvolvimento , Microbiota/genética , Proteobactérias/efeitos dos fármacos , Proteobactérias/genética , Proteobactérias/isolamento & purificação
11.
Arch Microbiol ; 202(10): 2663-2669, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32719948

RESUMO

A Gram-stain-negative, non-motile and yellow-colored bacterium, designated 17J68-12T, was isolated from soil in Jeju Island, Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 17J68-12T formed a distinct lineage within the family Chitinophagaceae and was mostly related to members of Flaviaesturariibacter luteus (97.5%), Flaviaesturariibacter amylovorans (96.8%) and Flaviaesturariibacter terrae (96.8%). Growth was observed at 18-42 °C (optimum 30 °C) in R2A broth at pH 7.0. The major cellular fatty acids of the strain 17J68-12 T were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), summed feature 1 (C15:1 iso-H and/or C13:0 3-OH), and iso-C15:0. The predominant respiratory quinones are MK-7 and MK-6. The major polar lipid was identified as phosphatidylethanolamine. Based on biochemical, chemotaxonomic and phylogenetic characteristics, the strain 17J68-12T represents a novel bacterial species within the family Chitinophagaceae, for which the name Flaviaesturariibacter flavus sp. nov. is proposed. The type strain of Flaviaesturariibacter flavus is 17J68-12T (= KCTC 62219T = JCM 33179T).


Assuntos
Bacteroidetes/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , RNA Ribossômico 16S/genética , República da Coreia , Especificidade da Espécie
12.
PLoS One ; 15(7): e0218636, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32639969

RESUMO

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.


Assuntos
Osso e Ossos/microbiologia , Microbiota , Antropologia , Ascomicetos/genética , Ascomicetos/isolamento & purificação , Autopsia , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , DNA/química , DNA/metabolismo , Humanos , Masculino , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Dente/microbiologia
13.
Sci Rep ; 10(1): 7809, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32385374

RESUMO

Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements. Our objective was to characterize gut microbes in wild mammals and relate those findings to host body-size scaling. Two large (Petaurista philippensis grandis and P. alborufus lena), one medium (Trogopterus xanthipes) and one small (Pteromys volans orii) species of flying squirrels (FS) were studied. Using 16S rRNA genes, 1,104 OTUs were detected from four FS, with 1.99% of OTUs shared among all FS. Although all FS gut microbiota were dominated by Firmicutes, they were constituted by different bacterial families. Moreover, Bacteroidetes accounted for up to 19% of gut microbiota in small FS, but was absent in large FS. Finally, based on metagenome predictions, carbohydrate and amino acid metabolism genes were enriched in small body-size FS. In conclusion, gut microbiota compositions and predictive metabolic functions were characteristic of body-size in FS, consistent with their adaptations to folivorous dietary niches.


Assuntos
Microbioma Gastrointestinal/genética , Variação Genética , Metagenoma/genética , Sciuridae/microbiologia , Animais , Bacteroidetes/genética , Tamanho Corporal , Dieta , Fezes/microbiologia , Firmicutes/genética , Filogenia , RNA Ribossômico 16S/genética , Sciuridae/genética , Sciuridae/metabolismo
14.
PLoS One ; 15(5): e0232699, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32374760

RESUMO

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95-105 versus 36-44). In these treatments the share of subdominant Actinobacteria (0.4-0.8%), Firmicutes (0.5-0.9%) and Bacteroidetes (0.2-0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.


Assuntos
Cádmio/farmacologia , Cromo/farmacologia , Gleiquênias/microbiologia , Chumbo/farmacologia , Microbiota/efeitos dos fármacos , Microbiota/genética , Poluentes do Solo/farmacologia , Actinobacteria/efeitos dos fármacos , Actinobacteria/genética , Actinobacteria/metabolismo , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/metabolismo , Biodegradação Ambiental , Cádmio/metabolismo , Cromo/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Firmicutes/efeitos dos fármacos , Firmicutes/genética , Firmicutes/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Chumbo/metabolismo , RNA Ribossômico 16S/genética , Microbiologia do Solo
15.
Chemosphere ; 253: 126584, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32278186

RESUMO

Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.


Assuntos
Monitoramento Ambiental , Microbiota , Mineração , Rios/microbiologia , Poluentes Químicos da Água/análise , Bactérias/genética , Bacteroidetes/genética , Compostos Férricos/análise , Sedimentos Geológicos/química , RNA Ribossômico 16S/genética , Rios/química , Esgotos/análise , Tsunamis
16.
PLoS One ; 15(4): e0231237, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32267892

RESUMO

Consumption of either monosodium glutamate (MSG) or high-fat and high-fructose (HFF) diets changes the gut microbiome and hence contributes to development of several diseases. In this study, with an emphasis on kidney injury, hamsters were divided into 4 groups as follows: (1) hamsters fed with standard diet (control); (2) hamsters fed with standard diet and MSG in drinking water (MSG); (3) hamsters fed with high-fat and high-fructose diets (HFF), and (4) animals fed MSG+HFF. After 8 months, the animals were used for the study. Despite showing normal kidney function, hamsters fed with MSG+HFF exhibited signs of kidney damage as demonstrated by the highest expression levels of high-mobility group box-1 and kidney injury molecule-1 in kidney tissues, while slight changes of histopathological features in H&E-stained sections and normal levels of creatinine were observed, indicating possible early stages of kidney injury. Sequencing of the microbial 16S rRNA gene revealed that animals fed with the MSG+HFF diet had a higher ratio of gut Firmicutes/Bacteroidetes along with marked changes in abundance and diversity of gut microbiome compared to hamsters fed with MSG or HFF alone. In addition, 1H Nuclear magnetic resonance spectroscopy showed an elevation of urine p-cresol sulfate levels in the MSG+HFF group. These results indicate that consumption of both MSG and HFF increases the risk of kidney injury, induces gut dysbiosis and an increase in the amount of p-cresol sulfate in hamsters.


Assuntos
Dieta da Carga de Carboidratos/efeitos adversos , Dieta Hiperlipídica/efeitos adversos , Disbiose/etiologia , Frutose/administração & dosagem , Microbioma Gastrointestinal/efeitos dos fármacos , Insuficiência Renal/etiologia , Glutamato de Sódio/farmacologia , Animais , Bacteroidetes/genética , Cresóis/urina , Cricetinae , Firmicutes/genética , Proteína HMGB1/metabolismo , Receptor Celular 1 do Vírus da Hepatite A/metabolismo , Rim/efeitos dos fármacos , Rim/metabolismo , Masculino , Mesocricetus , RNA Ribossômico 16S , Insuficiência Renal/urina , Ésteres do Ácido Sulfúrico/urina
17.
Sci Rep ; 10(1): 3895, 2020 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-32127609

RESUMO

Ursodeoxycholic acid (UDCA) treatment can reduce itch and lower endogenous serum bile acids in intrahepatic cholestasis of pregnancy (ICP). We sought to determine how it could influence the gut environment in ICP to alter enterohepatic signalling. The gut microbiota and bile acid content were determined in faeces from 35 pregnant women (14 with uncomplicated pregnancies and 21 with ICP, 17 receiving UDCA). Faecal bile salt hydrolase activity was measured using a precipitation assay. Serum fibroblast growth factor 19 (FGF19) and 7α-hydroxy-4-cholesten-3-one (C4) concentrations were measured following a standardised diet for 21 hours. Women with a high ratio of Bacteroidetes to Firmicutes were more likely to be treated with UDCA (Fisher's exact test p = 0.0178) than those with a lower ratio. Bile salt hydrolase activity was reduced in women with low Bacteroidetes:Firmicutes. Women taking UDCA had higher faecal lithocholic acid (p < 0.0001), with more unconjugated bile acids than women with untreated ICP or uncomplicated pregnancy. UDCA-treatment increased serum FGF19, and reduced C4 (reflecting lower bile acid synthesis). During ICP, UDCA treatment can be associated with enrichment of the gut microbiota with Bacteroidetes. These demonstrate high bile salt hydrolase activity, which deconjugates bile acids enabling secondary modification to FXR agonists, enhancing enterohepatic feedback via FGF19.


Assuntos
Amidoidrolases/genética , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Colestase Intra-Hepática/microbiologia , Regulação Bacteriana da Expressão Gênica , Intestinos/microbiologia , Complicações na Gravidez/microbiologia , Ácido Ursodesoxicólico/farmacologia , Animais , Estudos de Casos e Controles , Feminino , Microbioma Gastrointestinal/efeitos dos fármacos , Humanos , Camundongos , Gravidez
18.
PLoS One ; 15(3): e0230071, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32210450

RESUMO

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.


Assuntos
Bacteroidetes/classificação , Biodiversidade , Cianobactérias/classificação , Água Doce/microbiologia , Sedimentos Geológicos/microbiologia , Microbiota , Proteobactérias/classificação , Bacteroidetes/genética , Bacteroidetes/crescimento & desenvolvimento , Cianobactérias/genética , Cianobactérias/crescimento & desenvolvimento , Sedimentos Geológicos/análise , Sequenciamento de Nucleotídeos em Larga Escala , México , Nutrientes , Filogenia , Proteobactérias/genética , Proteobactérias/crescimento & desenvolvimento , RNA Ribossômico 16S/genética
19.
BMC Res Notes ; 13(1): 94, 2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32093782

RESUMO

OBJECTIVES: The silkworm Bombyx mori (B. mori) is an important domesticated lepidopteran model for basic and applied research. They produce silk fibres that have great economic value. The gut microbiome plays an important role in the growth of organisms. Spermidine (Spd) is shown to be important for the growth of all living cells. The effect of spermidine feeding on the gut microbiome of 5th instar B. mori larvae was checked. The B. mori gut samples from control and spermidine fed larvae were subjected to next-generation sequencing analysis to unravel changes in the bacterial community upon spermidine supplementation. DATA DESCRIPTION: The changes in gut bacteriota after spermidine feeding is not studied before. B. mori larvae were divided into two groups of 50 worms each and were fed with normal mulberry leaves and mulberry leaves fortified with 50 µM spermidine. The gut tissues were isolated aseptically and total genomic DNA was extracted, 16S rRNA region amplified and sequenced using Illumina platform. The spermidine fed gut samples were shown to have abundance and diversity of the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria.


Assuntos
Bactérias/genética , Bombyx/microbiologia , Microbioma Gastrointestinal/efeitos dos fármacos , Preparações de Plantas/farmacologia , RNA Ribossômico 16S/genética , Espermidina/farmacologia , Actinobacteria/classificação , Actinobacteria/genética , Animais , Bactérias/classificação , Bacteroidetes/classificação , Bacteroidetes/genética , DNA Bacteriano/análise , DNA Bacteriano/genética , Firmicutes/classificação , Firmicutes/genética , Microbioma Gastrointestinal/genética , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Larva/microbiologia , Morus/química , Folhas de Planta/química , Proteobactérias/classificação , Proteobactérias/genética
20.
Syst Appl Microbiol ; 43(2): 126065, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32057584

RESUMO

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.


Assuntos
Adaptação Fisiológica/genética , Bacteroidetes/genética , Evolução Molecular , Genoma Bacteriano/genética , Proteínas de Bactérias/genética , Sistemas de Secreção Bacterianos/genética , Bacteroidetes/classificação , Bacteroidetes/fisiologia , Transporte de Elétrons/genética , Locomoção/genética , Filogenia
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