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1.
J Anim Sci ; 98(1)2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31768533

RESUMO

Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.

2.
Appl Microbiol Biotechnol ; 104(4): 1809-1820, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31867694

RESUMO

Constructed wetlands (CWs) are effective ecological remediation technologies for various contaminated water bodies. Here, we queried for benzene-degrading microbes in a horizontal subsurface flow CW with reducing conditions in the pore water and fed with benzene-contaminated groundwater. For identification of relevant microbes, we employed in situ microcosms (BACTRAPs, which are made from granulated activated carbon) coupled with 13C-stable isotope probing and Illumina sequencing of 16S rRNA amplicons. A significant incorporation of 13C was detected in RNA isolated from BACTRAPs loaded with 13C-benzene and exposed in the CW for 28 days. A shorter incubation time did not result in detectable 13C incorporation. After 28 days, members from four genera, namely Dechloromonas, Hydrogenophaga, and Zoogloea from the Betaproteobacteria and Arcobacter from the Epsilonproteobacteria were significantly labeled with 13C and were abundant in the bacterial community on the BACTRAPs. Sequences affiliated to Geobacter were also numerous on the BACTRAPs but apparently those microbes did not metabolize benzene as no 13C label incorporation was detected. Instead, they may have metabolized plant-derived organic compounds while using the BACTRAPs as electron sink. In representative wetland samples, sequences affiliated with Dechloromonas, Zoogloea, and Hydrogenophaga were present at relative proportions of up to a few percent. Sequences affiliated with Arcobacter were present at < 0.01% in wetland samples. In conclusion, we identified microbes of likely significance for benzene degradation in a CW used for remediation of contaminated water.

3.
Nat Chem ; 12(2): 145-158, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31844194

RESUMO

New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effectively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, probably stem from the compound's polypharmacology.

4.
Front Immunol ; 10: 2552, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31772562

RESUMO

Staphylococcus aureus is one of the first and most prevalent pathogens cultured from the airways of cystic fibrosis (CF) patients, which can persist there for extended periods. Airway infections in CF patients are characterized by a strong inflammatory response of highly recruited neutrophils. One killing mechanism of neutrophils is the formation of neutrophil extracellular traps (NETs), which capture and eradicate bacteria by extracellular fibers of neutrophil chromatin decorated with antimicrobial granule proteins. S. aureus secretes nuclease, which can degrade NETs. We hypothesized, that S. aureus adapts to the airways of CF patients during persistent infection by escaping from NET-mediated killing via an increase of nuclease activity. Sputum samples of CF patients with chronic S. aureus infection were visualized by confocal microscopy after immuno-fluorescence staining for NET-specific markers, S. aureus bacteria and overall DNA structures. Nuclease activity was analyzed in sequential isogenic long persisting S. aureus isolates, as confirmed by whole genome sequencing, from an individual CF patient using a FRET-based nuclease activity assay. Additionally, some of these isolates were selected and analyzed by qRT-PCR to determine the expression of nuc1 and regulators of interest. NET-killing assays were performed with clinical S. aureus isolates to evaluate killing and bacterial survival depending on nuclease activity. To confirm the role of nuclease during NET-mediated killing, a clinical isolate with low nuclease activity was transformed with a nuclease expression vector (pCM28nuc). Furthermore, two sputa from an individual CF patient were subjected to RNA-sequence analysis to evaluate the activity of nuclease in vivo. In sputa, S. aureus was associated to extracellular DNA structures. Nuclease activity in clinical S. aureus isolates increased in a time-and phenotype-dependent manner. In the clinical isolates, the expression of nuc1 was inversely correlated to the activity of agr and was independent of saeS. NET-mediated killing was significantly higher in S. aureus isolates with low compared to isolates with high nuclease activity. Importantly, transformation of the clinical isolate with low nuclease activity with pCM28nuc conferred protection against NET-mediated killing confirming the beneficial role of nuclease for protection against NETs. Also, nuclease expression in in vivo sputa was high, which underlines the important role of nuclease within the highly inflamed CF airways. In conclusion, our data show that S. aureus adapts to the neutrophil-rich environment of CF airways with increasing nuclease expression most likely to avoid NET-killing during long-term persistence.

5.
J Innate Immun ; : 1-13, 2019 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-31743913

RESUMO

A prominent feature of severe streptococcal infections is the profound inflammatory response that contributes to systemic toxicity. In sepsis the dysregulated host response involves both immunological and nonimmunological pathways. Here, we report a fatal case of an immunocompetent healthy female presenting with toxic shock and purpura fulminans caused by group B streptococcus (GBS; serotype III, CC19). The strain (LUMC16) was pigmented and hyperhemolytic. Stimulation of human primary cells with hyperhemolytic LUMC16 and STSS/NF-HH strains and pigment toxin resulted in a release of proinflammatory mediators, including tumor necrosis factor, interleukin (IL)-1ß, and IL-6. In addition, LUMC16 induced blood clotting and showed factor XII activity on its surface, which was linked to the presence of the pigment. The expression of pigment was not linked to a mutation within the CovR/S region. In conclusion, our study shows that the hemolytic lipid toxin contributes to the ability of GBS to cause systemic hyperinflammation and interferes with the coagulation system.

6.
Comput Struct Biotechnol J ; 17: 1016-1019, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31428294

RESUMO

The secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), formed by gut microbiota from primary bile acids via a multi-step 7α-dehydroxylation reaction, have wide-ranging effects on host metabolism and play an important role in health and disease. A few 7α-dehydroxylating strains have been isolated, where bile acid-inducible (bai) genes were organized in a gene cluster and encoded major enzymes involved. However, only little is known on diversity and abundance of intestinal bacteria catalysing DCA/LCA formation in the human gut in situ. In this study, we took the opportunity to screen metagenome-assembled genomes (MAGs) from sequence data of stool samples provided by two recent studies along with newly available gut-derived isolates for the presence of the bai gene cluster. We revealed in total 765 and 620 MAGs encoding the potential to form DCA/LCA that grouped into 21 and 26 metagenomic species, respectively. The majority of MAGs (92.4 and 90.3%) were associated with a Ruminococcaceae clade that still lacks an isolate, whereas less MAGs belonged to Lachnospiraceae along with eight new isolates (n total = 11) that contained the bai genes. Only a few MAGs were linked to Peptostreptococcaceae. Signatures for horizontal transfer of bai genes were observed. This study gives a comprehensive overview of the diversity of bai-exhibiting bacteria in the human gut highlighting the application of metagenomics to unravel potential functions hidden from current isolates. Eventually, isolates of the identified main MAG clade are required in order to prove their capability of 7α-dehydroxylating primary bile acids.

7.
Nat Commun ; 10(1): 3846, 2019 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-31451691

RESUMO

Necrotizing soft tissue infections (NSTIs) are devastating infections caused by either a single pathogen, predominantly Streptococcus pyogenes, or by multiple bacterial species. A better understanding of the pathogenic mechanisms underlying these different NSTI types could facilitate faster diagnostic and more effective therapeutic strategies. Here, we integrate microbial community profiling with host and pathogen(s) transcriptional analysis in patient biopsies to dissect the pathophysiology of streptococcal and polymicrobial NSTIs. We observe that the pathogenicity of polymicrobial communities is mediated by synergistic interactions between community members, fueling a cycle of bacterial colonization and inflammatory tissue destruction. In S. pyogenes NSTIs, expression of specialized virulence factors underlies infection pathophysiology. Furthermore, we identify a strong interferon-related response specific to S. pyogenes NSTIs that could be exploited as a potential diagnostic biomarker. Our study provides insights into the pathophysiology of mono- and polymicrobial NSTIs and highlights the potential of host-derived signatures for microbial diagnosis of NSTIs.


Assuntos
Coinfecção/patologia , Infecções dos Tecidos Moles/patologia , Infecções Estreptocócicas/patologia , Fatores de Virulência/metabolismo , Adulto , Idoso , Técnicas de Tipagem Bacteriana , Bacteroides/genética , Bacteroides/isolamento & purificação , Bacteroides/metabolismo , Biópsia , Coinfecção/diagnóstico , Coinfecção/microbiologia , DNA Bacteriano/isolamento & purificação , Escherichia/genética , Escherichia/isolamento & purificação , Escherichia/metabolismo , Feminino , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , Necrose/diagnóstico , Necrose/microbiologia , Necrose/patologia , RNA Ribossômico 16S/genética , Infecções dos Tecidos Moles/diagnóstico , Infecções dos Tecidos Moles/microbiologia , Staphylococcus/genética , Staphylococcus/isolamento & purificação , Staphylococcus/metabolismo , Infecções Estreptocócicas/diagnóstico , Infecções Estreptocócicas/microbiologia , Streptococcus/genética , Streptococcus/isolamento & purificação , Streptococcus/metabolismo , Fatores de Virulência/genética
8.
Gastroenterology ; 157(4): 1081-1092.e3, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31175864

RESUMO

BACKGROUND & AIMS: The microbiome varies along the human gastrointestinal (GI) tract with exposure to luminal and mucosal factors. We analyzed active bacterial communities at 8 locations along the GI tract using high-throughput sequencing techniques. METHODS: We collected saliva, mucosal, and fecal samples from healthy adults (10 men and 11 women; mean age, 59 ± 12.3 years) who underwent upper and lower GI tract endoscopy in Germany from December 2015 through September 2016. Biopsies were taken from stomach, antrum, corpus, duodenum, terminal ileum, ascending colon, and descending colon. RNA was extracted from all samples and reverse transcribed into complementary DNA; V1-V2 regions of 16S ribosomal RNA genes were amplified and sequenced on an Illumina MiSeq platform. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices with the Bray-Curtis algorithm. Significant differences between a priori-defined groups were evaluated using analysis of similarity. RESULTS: After taxonomic annotation, 4045 phylotypes, belonging to 169 genera and 14 different phyla, were identified. Each subject had a different bacterial community. We identified distinct microbial consortia in saliva, upper GI tract, lower GI tract, and fecal samples. The predominant genera in the upper GI tract (Gemella, Veillonella, Neisseria, Fusobacterium, Streptococcus, Prevotella, Pseudomonas, and Actinomyces) were almost absent from the lower GI tract, where the microbial communities mainly comprised Faecalibacterium, Ruminococcus, and Bacteroides. The bacterial communities in the upper GI tract were characterized by greater richness and heterogeneity (measured by the Shannon index) than those in the lower GI tract. We detected Helicobacter pylori in only the upper GI tract. CONCLUSIONS: In an analysis of saliva, mucosal, and fecal samples from 21 healthy adults, we found each individual, and each GI region, to have a different bacterial community. The fecal microbiome is not representative of the mucosal microbiome. We propose a systematic method to analyze the bacterial communities of the GI tract.


Assuntos
Bactérias/genética , DNA Bacteriano/genética , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Regulação Bacteriana da Expressão Gênica , RNA Ribossômico 16S/genética , Ativação Transcricional , Idoso , Bactérias/classificação , Fezes/microbiologia , Feminino , Mucosa Gástrica/microbiologia , Alemanha , Voluntários Saudáveis , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mucosa Intestinal/microbiologia , Masculino , Pessoa de Meia-Idade , Filogenia , Ribotipagem , Saliva/microbiologia
9.
J Microbiol ; 57(7): 626-636, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31054134

RESUMO

Beta haemolytic Group A streptococcus (GAS) or Streptococcus pyogenes are strict human pathogens responsible for mild to severe fatal invasive infections. Even with enormous number of reports exploring the role of S. pyogenes exotoxins in its pathogenesis, inadequate knowledge on the biofilm process and the potential role of exotoxins in bacterial dissemination from matured biofilms has been a hindrance in development of effective and targeted treatments. Therefore, the present study was aimed in investigating the uncharted role of these exotoxins in biofilm process. Through our study the putative role of ciaRH in the SpeA dependent ablation of biofilm formation could be speculated and thus helping in bacterial dissemination. The seed-dispersal effect of SpeA was time and concentration dependent and seen to be consistent within various streptococcal species. Transcriptome analysis of SpeA treated S. pyogenes biofilms revealed the involvement of many transcriptional regulators (ciaRH) and response genes (luxS, shr, shp, SPy_0572), hinting towards specific mechanisms underlying the dispersal effect by SpeA. This finding opens up a discussion towards understanding a new mechanism involved in the pathogenesis of Streptococcus pyogenes and might help in understanding the bacterial infections in a better way.


Assuntos
Proteínas de Bactérias , Biofilmes/efeitos dos fármacos , Exotoxinas , Proteínas de Membrana , Infecções Estreptocócicas/microbiologia , Streptococcus pyogenes , Proteínas de Bactérias/farmacologia , Proteínas de Bactérias/fisiologia , Exotoxinas/farmacologia , Exotoxinas/fisiologia , Perfilação da Expressão Gênica/métodos , Humanos , Proteínas de Membrana/farmacologia , Proteínas de Membrana/fisiologia , Streptococcus pyogenes/efeitos dos fármacos , Streptococcus pyogenes/genética , Streptococcus pyogenes/patogenicidade , Superantígenos/fisiologia
13.
J Nutr ; 149(3): 451-462, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30715385

RESUMO

BACKGROUND: Excess dietary fat and sugar are linked to obesity and metabolic syndrome. Polyamines such as spermidine are implicated in fat accumulation and may support activity-induced weight loss. OBJECTIVE: This study tested interventional spermidine supplementation and voluntary activity against fat- and sucrose-induced systemic and gut microbiota changes. METHODS: A 3-factorial study design (3 × 2 × 2) was used to test the factors diet, activity, and spermidine. Male 6-wk-old C57BL/6N mice were fed a control diet (CD; carbohydrate:protein:fat, 70%:20%:10% of energy; 7% sucrose), a high-fat diet (HFD; carbohydrate:protein:fat, 20%:20%:60% of energy; 7% sucrose), or a high-sucrose diet (HSD; carbohydrate:protein:fat, 70%:20%:10% of energy; 35% sucrose). Diet groups were left untreated (+0) or had unlimited access to running wheels (+A) or were supplemented with 3 mM spermidine via drinking water (+S) or a combination of both (+A+S) for 30 wk (n = 7-10). RESULTS: In comparison to the CD, the HFD enhanced body weights (by 36%, P < 0.001), plasma lipids (cholesterol by 24%, P < 0.001; triglycerides by 27%, P = 0.004), and glucose concentrations (by 18%, P < 0.001), whereas the HSD increased weight by 13% (P < 0.001) and fasting glucose by 17% (P < 0.001) but did not increase plasma lipids. Microbiota taxonomic composition changed upon the HFD and HSD (both P < 0.001); however, only the HSD increased microbial diversity (P < 0.001) compared with the CD. Activity influenced microbiota composition (P < 0.01) and reduced glucose concentrations in HSD-fed (P = 0.021) and HFD-fed (P < 0.001) mice compared with nonactive mice. The combination of activity and spermidine affected energy intake (P-interaction = 0.037) and reduced body weights of HSD+A+S mice compared with HSD+0 mice (P = 0.024). CONCLUSIONS: In male C57BL/6N mice, dietary sucrose and fat caused diverse metabolic and microbiota changes that were differentially susceptible to physical exercise. Spermidine has the potential to augment activity-induced beneficial effects, particularly for sucrose-induced obesity.


Assuntos
Carboidratos da Dieta/efeitos adversos , Gorduras na Dieta/efeitos adversos , Espermidina/farmacologia , Sacarose/efeitos adversos , Ração Animal , Animais , Glicemia , Dieta , Ingestão de Energia , Microbioma Gastrointestinal , Glucose/metabolismo , Homeostase , Lipídeos/sangue , Masculino , Camundongos , Atividade Motora
14.
Mucosal Immunol ; 12(3): 691-702, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30659231

RESUMO

Disease activity in Interleukin-10-deficient (Il10-/-) mice, a model for IBD, depends on genetic background and microbiome composition. B6.129P2/JZtm-Il10tm1Cgn (B6-Il10-/-) mice are partially resistant to colitis, whereas mice carrying the Cdcs1C3Bir haplotype on chromosome 3, B6.Cg-Il10tm1CgnMMU3(D3Mit11-D3Mit348)/JZtm (BC-R3-Il10-/-), are susceptible. This study was performed to clarify Cdcs1 and candidate gene effects on the colitogenic potential of hematopoietic cells using bone marrow (BM) and T-cell transfer models. Acute and chronic graft versus host reaction was excluded by high-density genotyping, in vitro and in vivo approaches. BM-chimeras were created with animals housed in two barriers (I and II) with distinct microbiota composition as identified by sequencing. BM-chimeras of all groups developed comparable moderate-to-severe colitis in Barrier I, however, in Barrier II only recipients of BC-R3-Il10-/- BM. Subsequent adoptive T cell transfers pointed to a new subcongenic interval within Cdcs1 affecting their colitogenic potential. Transfers excluded Larp7 and Alpk1 but highlighted Ifi44 as potential candidate genes. In this model-system, colitis development after cell transfer heavily depends on microbiome, though Cdcs1 acts mainly independently in hematopoietic cells. A new subcongenic interval, provisionally named Cdcs1.4, modifies colitogenic T cell function. Within this locus, Ifi44 represents an important candidate gene for colitis expression.


Assuntos
Colite/imunologia , Doenças Inflamatórias Intestinais/imunologia , Microbiota/imunologia , Linfócitos T/imunologia , Transferência Adotiva , Animais , Transplante de Medula Óssea , Células Cultivadas , Colite/genética , Modelos Animais de Doenças , Hematopoese , Humanos , Interleucina-10/genética , Camundongos , Camundongos Knockout , Mutação/genética
15.
BMC Microbiol ; 19(1): 1, 2019 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-30616583

RESUMO

BACKGROUND: Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants' nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers. RESULTS: For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection. CONCLUSIONS: Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.


Assuntos
Biodiversidade , Microbiota , Cavidade Nasal/microbiologia , Infecções por Picornaviridae/microbiologia , Pré-Escolar , Feminino , Variação Genética , Humanos , Lactente , Masculino , RNA Ribossômico 16S/genética , Fatores de Tempo
16.
Extremophiles ; 23(2): 177-187, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30600357

RESUMO

Here we report the chemical and microbial characterization of the surface water of a CO2-rich hydrothermal vent known in Costa Rica as Borbollones, located at Tenorio Volcano National Park. The Borbollones showed a temperature surrounding 60 °C, a pH of 2.4 and the gas released has a composition of ~ 97% CO2, ~ 0.07% H2S, ~ 2.3% N2 and ~ 0.12% CH4. Other chemical species such as sulfate and iron were found at high levels with respect to typical fresh water bodies. Analysis by 16S rRNA gene metabarcoding revealed that in Borbollones predominates an archaeon from the order Thermoplasmatales and one bacterium from the genus Sulfurimonas. Other sulfur- (genera Thiomonas, Acidithiobacillus, Sulfuriferula, and Sulfuricurvum) and iron-oxidizing bacteria (genera Sideroxydans, Gallionella, and Ferrovum) were identified. Our results show that CO2-influenced surface water of Borbollones contains microorganisms that are usually found in acid rock drainage environments or sulfur-rich hydrothermal vents. To our knowledge, this is the first microbiological characterization of a CO2-dominated hydrothermal spring from Central America and expands our understanding of those extreme ecosystems.


Assuntos
Bactérias/isolamento & purificação , Fontes Termais/microbiologia , Microbiota , Enxofre/metabolismo , Thermoplasmales/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Thermoplasmales/classificação , Thermoplasmales/genética , Termotolerância
17.
Microb Ecol ; 78(1): 243-256, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30413836

RESUMO

Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.


Assuntos
Bactérias/isolamento & purificação , Microbiota , Água do Mar/química , Xestospongia/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Fenômenos Fisiológicos Bacterianos , Biodiversidade , Região do Caribe , Recifes de Corais , Panamá , Filogenia , Estações do Ano , Água do Mar/microbiologia , Simbiose , Xestospongia/fisiologia
18.
Extremophiles ; 23(1): 35-48, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30284641

RESUMO

Genotypic and morphological diversity of cyanobacteria in the Rupite hot spring (Bulgaria) was investigated by means of optical microscopy, cultivation, single-cell PCR, and 16S rRNA gene amplicon sequencing. Altogether, 34 sites were investigated along the 71-39 °C temperature gradient. Analysis of samples from eight representative sites shown that Illumina, optical microscopy, and Roche 454 identified 72, 45 and 19% respective occurrences of all cumulatively present taxa. Optical microscopy failed to detect species of minor occurrence; whereas, amplicon sequencing technologies suffered from failed primer annealing and the presence of species with extensive extracellular polysaccharides production. Amplicon sequencing of the 16S rRNA gene V5-V6 region performed by Illumina identified the cyanobacteria most reliably to the generic level. Nevertheless, only the combined use of optical microscopy, cultivation and sequencing methods allowed for reliable estimate of the cyanobacterial diversity. Here, we show that Rupite hot-spring system hosts one of the richest cyanobacterial flora reported from a single site above 50 °C. Chlorogloeopsis sp. was the most abundant at the highest temperature (68 °C), followed by Leptolyngbya boryana, Thermoleptolyngbya albertanoae, Synechococcus bigranulatus, Oculatella sp., and Desertifilum sp. thriving above 60 °C, while Leptolyngbya geysericola, Geitlerinema splendidum, and Cyanobacterium aponinum were found above 50 °C.


Assuntos
Cianobactérias/genética , Fontes Termais/microbiologia , Microbiota , Cianobactérias/classificação , Cianobactérias/citologia , Cianobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
19.
Proc Natl Acad Sci U S A ; 115(42): 10702-10707, 2018 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-30275328

RESUMO

Cyanobacteria are ecologically versatile microorganisms inhabiting most environments, ranging from marine systems to arid deserts. Although they possess several pathways for light-independent energy generation, until now their ecological range appeared to be restricted to environments with at least occasional exposure to sunlight. Here we present molecular, microscopic, and metagenomic evidence that cyanobacteria predominate in deep subsurface rock samples from the Iberian Pyrite Belt Mars analog (southwestern Spain). Metagenomics showed the potential for a hydrogen-based lithoautotrophic cyanobacterial metabolism. Collectively, our results suggest that they may play an important role as primary producers within the deep-Earth biosphere. Our description of this previously unknown ecological niche for cyanobacteria paves the way for models on their origin and evolution, as well as on their potential presence in current or primitive biospheres in other planetary bodies, and on the extant, primitive, and putative extraterrestrial biospheres.


Assuntos
Cianobactérias/crescimento & desenvolvimento , Ecossistema , Sedimentos Geológicos/análise , Metagenômica , Microscopia de Fluorescência , Análise Serial de Proteínas , Evolução Biológica , Cianobactérias/genética , Cianobactérias/metabolismo
20.
BMC Microbiol ; 18(1): 108, 2018 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-30189831

RESUMO

BACKGROUND: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems. RESULTS: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols. CONCLUSIONS: LCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems.


Assuntos
Delftia/metabolismo , Fenóis/química , Fenóis/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Delftia/classificação , Delftia/genética , Delftia/isolamento & purificação , Isomerismo , Oxigenases de Função Mista/genética , Oxigenases de Função Mista/metabolismo , Filogenia , Microbiologia do Solo , Áreas Alagadas
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