The use of fluorescein for labeling genomic probes in the checkerboard DNA-DNA hybridization method

Molecular methods that permit the simultaneous detection and quantification of a large number of microbial species are currently employed in the evaluation of complex ecosystems. The checkerboard DNA-DNA hybridization technique enables the simultaneous identification of distinct bacterial. species in a large number of dental samples. The original technique employed digoxigenin-labeled whole genomic DNA probes which were detected by chemiluminescence. In this study, we present an alternative protocol for labeling and detecting whole genomic DNA probes in the Checkerboard DNA-DNA hybridization method. Whole genomic DNA was extracted from five bacterial species and labeled with fluorescein. The fluorescein labeled whole genomic DNA probes were hybridized against whole genomic DNA or subgingival plaque samples in a checkerboard hybridization format, followed by chemiluminescent detection. Our results reveal that fluorescein is a viable and adequate alternative labeling reagent to be employed in the checkerboard DNA-DNA hybridization technique. (c) 2007 Elsevier GmbH. All rights reserved.

Microbial culture and checkerboard DNA-DNA hybridization assessment of bacteria in root canals of primary teeth pre- and post-endodontic therapy with a calcium hydroxide/chlorhexidine paste

Aim. To investigate the root canal microbiota of primary teeth with apical periodontitis and the in vivo antimicrobial effects of a calcium hydroxide/chlorhexidine paste used as root canal dressing. Design. Baseline samples were collected from 30 root canals of primary teeth with apical periodontitis. Then, the root canals were filled with a calcium hydroxide paste containing 1% chlorhexidine for 14 days and the second bacteriologic samples were taken prior to root canal filling. Samples were submitted to microbiologic culture procedure to detect root canal bacteria and processed for checkerboard DNA-DNA hybridization. Results. Baseline microbial culture revealed high prevalence and cfu number of anaerobic, black-pigmented bacteroides, Streptococcus, and aerobic microorganisms. Following root canal dressing, the overall number of cfu was dramatically diminished compared to initial contamination (P < 0.05), although prevalence did not change (P > 0.05). Of 35 probes used for checkerboard DNA-DNA hybridization, 31 (88.57%) were present at baseline, and following root canal dressing, the number of positive probes reduced to 13 (37.14%). Similarly, the number of bacterial cells diminished folowing application of calcium hydroxide/chlorhexidine root canal dressing (P = 0.006). Conclusion. Apical periodontitis is caused by a polymicrobial infection, and a calcium hydroxide/chlorhexidine paste is effective in reducing the number of bacteria inside root canals when applied as a root canal dressing.

Effects of dietary lipid composition bioavailability and inulin-type fructans on mineral in growing rats

Objective: This study reports the effects of feeding with a combination of inulin-type fructans (ITF) and fish oil (FO) on mineral absorption and bioavailability as part of a semipurified diet offered to rats. Methods: Male Wistar rats (n = 24) were fed a 15% lipid diet (soybean oil [SO] or a 1:0.3 fish:soybean oil mixture [FSO]) and diets containing the same sources of lipids supplemented with 10% ITF (Raftilose Synergy 1) ad libitum for 15 d. Feces and urine were collected for mineral analyses during the last 5 d of the test period. Fatty acid composition was determined in liver and cecal mucosa homogenates. Liver and bone mineral analyses were performed by atomic absorption spectrophotometry. Bone biomechanical analyses were evaluated by a 3-point bending test. Results: Compared with the controls, ITF-fed rats had enlarged ceca and a significant decrease in cecal content pH (P < 0.001). The apparent mineral absorption was improved in these rats, and this effect was enhanced by dietary combination with FO for all minerals except for magnesium. Addition of ITF to the diet resulted in higher bone mineral content (calcium and zinc) and bone strength, but increased bone mineral content was only statistically significant in FO-fed animals. A decrease in liver iron stores (P = 0.015) was observed in rats fed FO, considering that ITF consumption returned to levels comparable to the SO control group. Conclusion: These findings confirm the positive influence of ITF on mineral bioavailability, which was potentiated by addition of FO to the diet. (C) 2009 Published by Elsevier Inc.

It takes guts for tolerance: The phenomenon of oral tolerance and the regulation of autoimmune response

The intestinal tract is a peculiar environment due to its constant contact with the microbiota agents, food antigens and other molecules. Such exposure requires the establishment of important regulatory mechanisms in order to avoid inflammatory response and self aggression. In this context, the GALT plays a very relevant role due to the presence of several different cellular populations which are the main players in this phenomenon. Moreover, it was described a while ago that the oral ingestion of a given molecule is able to induce systemic tolerance to the same molecule when it is used as an immunogen by parenteral route, known as oral tolerance. This observation led researches to use these mechanisms to induce tolerance against cognate antigens of different autoimmune diseases. In this context, in this review we focused on several tolerance inducing mechanisms which are relevant not only for the maintenance of intestinal tract but also for the suppression of T effector cells, such as Th1, Th2 and the newly described Th17 cells. To name a few, CD103(+) dendritic cells, Tr1 cells derived IL-10 secretion, Foxp3 conversion and CD4(+)LAP(+) regulatory cells induction are among the recently described features of the tolerogenic environment of the intestinal tract. (C) 2009 Elsevier B.V. All rights reserved.

Adherence and invasion of Bacteroidales isolated from the human intestinal tract

Members of the genera Bacteroides and Parabacteroides are important constituents of both human and animal intestinal microbiota, and are significant facultative pathogens. In this study, the ability of Bacteroides spp. and Parabacteroides distasonis isolated from both diarrhoeal and normal stools (n = 114) to adhere to and invade HEp-2 cells was evaluated. The presence of putative virulence factors such as capsule and fimbriae was also investigated. Adherence to HEp-2 cells was observed in 75.4% of the strains, which displayed non-localized clusters. Invasion was observed in 37.5% and 26% of the strains isolated from diarrhoeal and non-diarrhoeal stools, respectively. All strains displayed a capsule, whereas none of them showed fimbriae-like structures. This is the first report of the ability of Bacteroides spp. and P. distasonis to adhere to and invade cultured HEp-2 epithelial cells.

Vibrios dominate as culturable nitrogen-fixing bacteria of the Brazilian coral Mussismilia hispida

Taxonomic characterization was performed on the putative N-2-fixing microbiota associated with the coral species Mussismilia hispida, and with its sympatric species Palythoa caribaeorum, P. variabilis, and Zoanthus solanderi, off the coast of Sao Sebastiao (Sao Paulo State, Brazil). The 95 isolates belonged to the Gammaproteobacteria according to the 16S rDNA gene sequences. In order to identify the isolates unambiguously, pyrH gene sequencing was carried out. The majority of the isolates (n = 76) fell within the Vibrio core group, with the highest gene sequence similarity being towards Vibrio harveyi and Vibrio alginolyticus. Nineteen representative isolates belonging to V. harveyi (n = 7), V. alginolyticus (n = 8), V. campbellii (n = 3), and V parahaemolyticus (n = 1) were capable of growing six successive times in nitrogen-free medium and some of them showed strong nitrogenase activity by means of the acetylene reduction assay (ARA). It was concluded that nitrogen fixation is a common phenotypic trait among Vibrio species of the core group. The fact that different Vibrio species can fix N, might explain why they are so abundant in the mucus of different coral species. (C) 2008 Published by Elsevier GmbH.

Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis

Background/aim: The purpose of this study was to determine the bacterial diversity in the subgingival plaque of subjects with generalized aggressive periodontitis by using culture-independent molecular methods based on 16S ribosomal DNA cloning. Methods: Samples from 10 subjects with generalized aggressive periodontitis were selected. DNA was extracted and the 16S rRNA gene was amplified with the universal primer pairs 9F and 1525R. Amplified genes were cloned, sequenced, and identified by comparison with known 16S rRNA sequences. Results: One hundred and ten species were identified from 10 subjects and 1007 clones were sequenced. Of these, 70 species were most prevalent. Fifty-seven percent of the clone (40 taxa) sequences represented phylotypes for which no cultivated isolates have been reported. Several species of Selenomonas and Streptococcus were found at high prevalence and proportion in all subjects. Overall, 50% of the clone libraries were formed by these two genera. Selenomonas sputigena, the species most commonly detected, was found in nine of 10 subjects. Other species of Selenomonas were often present at high levels, including S. noxia, Selenomonas sp. EW084, Selenomonas sp. EW076, Selenomonas FT050, Selenomonas sp. P2PA_80, and Selenomonas sp. strain GAA14. The classical putative periodontal pathogens, such as, Aggregatibacter actinomycetemcomitans, was below the limit of detection and was not detected. Conclusion: These data suggest that other species, notably species of Selenomonas, may be associated with disease in generalized aggressive periodontitis subjects.

Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects

P>Aim To investigate the diversity, levels and proportions of Archaea in the subgingival biofilm of generalized aggressive periodontitis (GAgP; n=30) and periodontally healthy (PH; n=30) subjects. Materials and methods Diversity was determined by sequencing archaeal 16S rRNA gene libraries from 20 samples (10/group). The levels and proportions of Archaea were analysed by quantitative PCR (qPCR) in four and two samples/subject in GAgP and PH groups, respectively. Results Archaea were detected in 27/28 subjects and 68% of the sites of the GAgP group, and in 26/30 subjects and 58.3% sites of the PH group. Methanobrevibacter oralis was found in all 20 samples studied, Methanobacterium curvum/congolense in three GAgP and six PH samples, and Methanosarcina mazeii in four samples from each group. The levels and proportions of Archaea were higher in GAgP than in PH, whereas no differences were observed between the two probing depth category sites from the GAgP group. Conclusion Archaea were frequently found in subjects with periodontal health and GAgP, especially M. oralis. However, the higher levels and proportions (Archaea/total prokaryotes) of this domain observed in GAgP in comparison with PH subjects indicate a possible role of some of these microorganisms as an environmental modifier in GAgP.

Collagenase production and hemolytic activity related to 16S rRNA variability among Parvimonas micra oral isolates

Parvimonas micra are gram positive anaerobic cocci isolated from the oral cavity and frequently related to polymicrobial infections in humans. Despite reports about phenotypic differences, the genotypic variation of P. micra and its role in virulence are still not elucidated. The aim of this study was to determine the genotypic diversity of P. micra isolates obtained from the subgingival biofilm of subjects with different periodontal conditions and to correlate these findings with phenotypic traits. Three reference strains and 35 isolates of P. micro were genotyped by 16S rRNA PCR-RFLP and phenotypic traits such as collagenase production, elastolytic and hemolytic activities were evaluated. 16S rRNA PCR-RFLP showed that P. micra could be grouped into two main clusters: C1 and C2; cluster C1 harbored three genotypes (HG1259-like, HG1467-like and ICBM0583-like) while cluster C2 harbored two genotypes (ATC03270-like and ICBM036). A wide variability in collagenolytic activity intensities was observed among all isolates, while elastolytic activity was detected in only two isolates. There was an association between hemolytic activity in rabbit erythrocytes and cluster C2. There was an association between hemolytic activity in rabbit erythrocytes and cluster C1. Although these data suggest a possible association between P. micra genetic diversity and their pathogenic potential, further investigations are needed to confirm this hypothesis. (C) 2009 Elsevier Ltd. All rights reserved.

Microbiological profile of untreated subjects with localized aggressive periodontitis

Aim The microbial profile of localized aggressive periodontitis (LAgP) has not yet been determined. Therefore, the aim of this study was to evaluate the subgingival microbial composition of LAgP. Material and Methods One hundred and twenty subjects with LAgP (n=15), generalized aggressive periodontitis (GAgP, n=25), chronic periodontitis (ChP, n=30) or periodontal health (PH, n=50) underwent clinical and microbiological assessment. Nine subgingival plaque samples were collected from each subject and analysed for their content of 38 bacterial species using checkerboard DNA-DNA hybridization. Results Red complex and some orange complex species are the most numerous and prevalent periodontal pathogens in LAgP. The proportions of Aggregatibacter actinomycetemcomitans were elevated in shallow and intermediate pockets of LAgP subjects in comparison with those with GAgP or ChP, but not in deep sites. This species also showed a negative correlation with age and with the proportions of red complex pathogens. The host-compatible Actinomyces species were reduced in LAgP. Conclusion A. actinomycetemcomitans seems to be associated with the onset of LAgP, and Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Campylobacter gracilis, Eubacterium nodatum and Prevotella intermedia play an important role in disease progression. Successful treatment of LAgP would involve a reduction in these pathogens and an increase in the Actinomyces species.

Non-steroidal anti-inflammatory drugs may modulate the protease activity of Candida albicans

The phenotypic pressure exerted by non-steroidal anti-inflammatory drugs (NSAIDs) on autochthonous and pathogenic microbiota remains sparsely known. In this study, we investigated if some NSAIDs increment or diminish the secretion of aspartyl-proteases (Sap) by Candida albicans grown under different phenotypes and oxygen availability using a set of SAP knock-out mutants and other set for genes (EFG1 and CPH1) that codify transcription factors involved in filamentation and protease secretion. Preconditioned cells were grown under planktonic and biofilm phenotypes, in normoxia and anoxia, in the presence of plasma concentrations of acetylsalicylic acid, diclofenac, indomethacin, nimesulide, piroxicam, ibuprofen, and acetaminophen. For diclofenac, indomethacin, nimesulide, and piroxicam the secretion rates of Sap by SAP1-6, EFG1. and CPH1 mutants were similar or, even, inferior to parental wildtype strain. This suggests that neither Sap 1-6 isoenzymes nor Efg1/Cph1 pathways may be entirely responsible for protease release when exposed to these NSAIDs. Ibuprofen and acetaminophen enhanced Sap secretion rates in three environmental conditions (normoxic biofilm, normoxic planktonic and anoxic planktonic). In other hand, aspirin seems to reduce the Sap-related pathogenic behavior of candidal biofilms. Modulation of Sap activity may occur according to candidal phenotypic state, oxygen availability, and type of NSAID to which the cells are exposed. (C) 2010 Elsevier Ltd. All rights reserved.

Estudo da bile por drenagem nasobilar na coledocolitiase apos esfincterotomia endoscopica : descricao de tecnica e analise bacteriologica

Esse trabalho teve como objetivo principal salientar o potencial da drenagem nasobiliar (DNB) como uma forma não cirúrgica de acesso à bile, utilizando como modelo uma téc- nica de DNB no estudo bacteriológico da bile em pesquisa. Para tal, foram estudados 17 pacientes portadores de coledo- colitíase submetidos eletivamente à colangiopancreatografia endoscópica retrógrada na Unidade de Endoscopia do Hospital de Clínicas de Porto Alegre. Foram realizadas DNB por até três dias com coletas seriadas de bile no momento do exame e a cada 24 horas, visando analisar os germes mais prevalentes e o perfil evolutivo da microbiota bacteriana. Correlacionou- se infecção biliar(IB), definida como 105 unidades formadoras de colônias (UFC)/ml de bile, com dados clínico-laboratori- ais obtidos dos prontuários (idade, sexo, presença ou não de febre, icterícia, leucocitose, elevação de fosfatase alca- lina, divertículos justapapilares, uso de antibióticos e co- lecistectomia prévia). A única intercorrência foi desconfor- to na retrofaringe em 28% dos casos. Foram tomadas medidas preventivas visando reduzir a contaminação do sistema. As enterobacteriácias (Klebsiella e E. coli) foram os germes mais encontrados. Ocorreu crescimento bacteriano em 71% dos casos na primeira coleta, embora 30% tivessem IB. Houve al- teração da microbiota biliar em 58% dos casos da primeira para a segunda coleta e em 81% dos casos desta para a terceira. Enquanto IB foi identificada em 30% dos casos na primeira coleta, esta atingiu 50% na segunda, 90% na terceira e 100% na última coleta, embora todos os pacientes tivessem evoluído satisfatóriamente. O perfil bacteriano qualitativo também se alterou, havendo predominância de Klebsiella e E. coli na primeira coleta, acréscimo de Streptococcus faecalis na segunda e apenas Pseudomonas na última. A associação entre IB e os dados clínico-laboratoriais não foi estatisticamente significativa. Concluiu-se que as enterobacteriácias Gram - foram os germes mais prevalentes nos pacientes com coledocolitíase, sendo que o perfil bacteriológico foi significativamente alterado com a DNB, embora sem implicação no quadro clínico. Além disto, não houve associação entre os dados clínico-laboratoriais estudados e a presença de IB.

Simulação da codisposição de resíduos de Manzate 800 com resíduos sólidos urbanos durante a fase metanogênica

Para tentar elucidar os efeitos da codisposição de embalagens de agrotóxico no âmbito de um aterro sanitário, foram monitoradas oito células de aterro, em tamanho reduzido. O resíduo sólido urbano utilizado nas oito células foi proveniente do município de Porto Alegre, tendo sido caracterizado antes da montagem do experimento. Os reatores foram submetidos a regas semanais por água, simulando uma situação média de chuva para a região. Acompanhou-se a degradação do RSU através de análises do percolado até a fase de fermentação metanogênica. A partir do 250o dia, passou-se a introduzir diferentes doses do agrotóxico Manzateâ 800, sendo três diferentes concentrações em duplicata e dois brancos. O acompanhamento estendeu-se então até os 460 dias. Os resultados de análises do percolado das oito células não apresentaram diferenças estatísticas significativas entre si, antes e depois da aplicação do agrotóxico. Também não foram constatadas mudanças no comportamento da degradação anaeróbia do resíduo ao longo do tempo. As análises de metais realizadas no material sólido coletado ao final do experimento mostraram uma maior concentração de manganês e zinco, metais constituintes do agrotóxico utilizado, nas amostras provenientes dos reatores que receberam cargas do mesmo. Adicionalmente ao experimento, testou-se a influência do Manzateâ 800 em percolado proveniente de célula de aterro sanitário de escala real, também de caráter experimental, contendo apenas RSU. Os testes foram feitos em bateladas, com quatro concentrações diferentes do agrotóxico e um branco e compararam-se as concentrações de DBO5. Os valores obtidos apresentaram diferenças estatísticas significativas, sendo maiores as concentrações de DBO5 das amostras com maior concentração de Manzateâ 800. Tais resultados evidenciam a degradação do agrotóxico pelos microrganismos presentes no percolado.

Dessorção do herbicida atrazina e atividade microbiana em duas classes de solos do Estado do Rio Grande do Sul

A atrazina (ATZ) foi utilizada em experimentos de laboratório para estudos de mineralização e dessorção em amostras de Argissolo Vermelho (PV) e Vertissolo Ebânico (VE), sob campo nativo, com o intuito de identificar os atributos do solo que afetam estes processos. A influência da umidade do solo sobre a atividade microbiana foi avaliada variando-se os teores de umidade em 20, 40, 65 e 85% da capacidade de água disponível do solo (CAD) e aplicando-se 1,5 kg de princípio ativo ha-1 (menor dose recomendada (DR)). Para a avaliação do efeito das doses do herbicida ATZ sobre a atividade microbiana e sobre a taxa de degradação do herbicida foram feitas aplicações de 1x, 2x, 4x, 7x e 10x a DR. Na avaliação do efeito da matéria orgânica sobre a atividade microbiana e sobre a taxa de degradação da ATZ foi feita a aplicação de 10x a DR. Num estudo adicional foram testados quatro métodos de desinfestação de solos (fumigação, tindalização, autoclavagem e irradiação em forno de microondas). A determinação da ATZ na solução foi feita por cromatografia gasosa em extratos de metanol. A atividade microbiana foi monitorada pela evolução de CO2 e a microbiota foi avaliada pela contagem de unidades formadoras de colônias Os resultados indicam que a população microbiana apresenta maior atividade entre 65 e 85% de umidade da CAD e que o aumento das doses de aplicação da ATZ não provoca alterações relevantes na atividade microbiana. Aproximadamente 70% do herbicida aplicado fica sorvido ao solo, independentemente de dose de ATZ aplicada e da classe de solo estudada (PV e VE). As taxas de degradação da ATZ lábil foram baixas e dependentes de doses e tipos de solos, sendo maiores em doses mais elevadas e em solos com maior teor de C. Dentre os métodos de desinfestação, a irradiação em forno de microondas foi o mais adequado, uma vez que apresentou um comportamento similar à testemunha quanto à sorção do herbicida e foi eficiente na redução da população microbiana do solo.

Comparação de diferentes etapas de enriquecimento seletivo no isolamento de Salmonella sp. a partir de fezes de suínos de terminação

A detecção de Salmonella sp. é fundamental nos programas de controle de salmonelose. Métodos de detecção mais eficientes permitem uma melhor determinação do nível de infecção dos rebanhos, um melhor entendimento da epidemiologia da infecção por Salmonella sp. e o desenvolvimento de programas de controle do patógeno, que visem a segurança biológica do alimento. Nos métodos convencionais, o enriquecimento seletivo é uma etapa crítica, pois inibe a microbiota competitiva e permite a multiplicação de Salmonella sp. Vários caldos de enriquecimento seletivo têm sido comparados quanto à eficiência na recuperação de Salmonella sp. a partir de alimentos, contudo existem poucos estudos relativos a fezes de suínos. O objetivo deste trabalho foi comparar caldos de enriquecimento seletivo para o isolamento de Salmonella sp. a partir de fezes de suínos. Numa primeira fase, amostras de fezes foram contaminadas artificialmente e os caldos Rappaport-Vassiliadis incubado a 42°C (RV), Tetrationato Müller-Kauffmann a 37°C (TMK37) e 42°C (TMK42), e Selenito Cistina (SC) a 37°C foram testados, em associação com meios sólidos seletivos: Rambach (RA), Xilose Lisina Tergitol 4 (XLT4), e Verde Brilhante Vermelho de Fenol Lactose Sacarose (VB). Na segunda fase os caldos RV, TMK37 e TMK42, semeados nos meios XLT4 e VB, foram testados com amostras naturalmente contaminadas. Na primeira fase o RV, TMK42 e TMK37 foram mais eficientes que o SC. No isolamento de Salmonella sp. em amostras naturalmente contaminadas os caldos TMK42 e RV foram superiores ao TMK37. O desempenho destes influenciou diretamente a capacidade seletiva e indicadora dos meios sólidos seletivos. No presente estudo, a associação TMK42/XLT4 demonstrou ser mais sensível, e a RV/XLT4 mais específica. O ágar VB também é recomendado para aumentar a probabilidade de detecção do patógeno. Desta forma os caldos RV e TMK42 e o ágar XLT4 e o VB foram considerados os mais indicados para a implantação de protocolos de detecção de Salmonella sp. em fezes suínas.