Endophytic microbial diversity in coffee cherries of Coffea arabica from southeastern Brazil.

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction - denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer.

The gastrointestinal tracts (GIT) of herbivores harbor dense and diverse microbiota that has beneficial interactions with the host, particularly for agriculturally relevant animals like ruminants such as cattle. When assessing ruminant health, microbiological indicators are often derived from the rumen or feces. However, it is probable that ruminal and fecal microbiota do not reflect the microbial communities within the GIT of ruminants. To test this, we investigated the compartments of the GIT from a Brazilian Nelore steer and performed a 16S rRNA pyrosequencing analysis on the collected samples. Our results showed high intra-individual variation, with samples clustering according to their location in the GIT including the forestomach, small intestine, and large intestine. Although sequences related to the phyla Firmicutes and Bacteroidetes predominated all samples, there was a remarkable variation at the family level. Comparisons between the microbiota in the rumen, feces, and other GIT components showed distinct differences in microbial community. This work is the first intensive non-culture based GIT microbiota analysis for any ruminant and provides a framework for understanding how host microbiota impact the health of bovines.

Multidrug efflux systems in Escherichia coli and Enterobacter cloacae obtained from wholesome broiler carcasses / Sistemas de efluxo multidroga em Escherichia coli e Enterobacter cloacae obtidas de carcaças de frangos sadios

Members of the Enterobacteriaceae family are present in the intestines of man and animals as commensals or are important disease causing agents. Bacteria bearing multidrug efflux systems (MDR) are able to survive adverse ecological niches. Multiresistant Escherichia coli and Enterobacter cloacae isolates from wholesome broiler carcasses were investigated for the presence of MDR. Lowering of Minimal Inhibitory Concentration for antimicrobials in the presence of a proton-motive force (PMF) uncoupler was tested as a potential display of the MDR phenotype. PCR amplification of the genes encoding AcrA and AcrB, components of a MDR system was performed. Diversity of each species was ascertained by Pulsed-Field Gel Electrophoresis (PFGE) of DNA digested with endonuclease XbaI. For all the isolates, except E. coli 1 and E. cloacae 9, lowering of MIC or of the growth rate in the presence of antimicrobials was observed, indicating a PMF dependent resistance mechanism. Expected products of DNA amplification with acrAB derived primers was obtained with all E. coli strains and with two of the five E. cloacae strains. Dendrogram generated shows diverse pulsetypes, confirming the genetic diversity among the strains. An important issue and related public health is the fact that different models and mechanisms of antimicrobial resistance are present in a small number of non-pathogenic strains and isolated from the same origin. These may be sources of resistance genes to others microorganisms, among them, pathogenic strains.

Os membros da família Enterobacteriaceae estão presentes no intestino do homem e dos animais como comensais ou agentes causadores de doença importantes. Bactérias multirresistentes podem possuir sistemas de efluxo multidrogas (MDR) sendo capazes de sobreviver em nichos ecológicos adversos. Escherichia coli e Enterobacter cloacae, multirresistentes, isoladas de frangos sadios foram investigadas quanto à presença de MDR. A diminuição da concentração inibitória mínima de antimicrobianos, na presença de um desacoplador da força próton motora (PMF), foi usada para detectar o fenótipo MDR. Foi realizada PCR dos genes codificadores de AcrA e AcrB, componentes de um sistema MDR. A diversidade de cada isolado foi confirmada por eletroforese em gel de campo pulsado (PFGE) usando a endonuclease XbaI. Observou-se em todos os isolados, exceto E. coli 1 e E. cloacae 9, uma diminuição das MICs ou das curvas de crescimento na presença dos antimicrobianos, indicando um mecanismo de resistência dependente da PMF. Os produtos amplificados esperados derivados de acrAB foram obtidos em todos os isolados de E. coli e em dois, dos cinco, de E. cloacae. O dendrograma gerado mostra diferentes perfis de bandas (pulsetypes), confirmando a diversidade genética entre os isolados. Uma questão importante e relacionada à saúde publica é o fato de que diferentes modelos e mecanismos de resistência aos antimicrobianos estão presentes em um número reduzidos de isolados não patogênicos e obtidos de uma mesma origem. Esses podem ser fontes de genes de resistência para outros microorganismos, entre eles, cepas patogênicas.

Multidrug efflux systems in Escherichia coli and Enterobacter cloacae obtained from wholesome broiler carcasses.

Members of the Enterobacteriaceae family are present in the intestines of man and animals as commensals or are important disease causing agents. Bacteria bearing multidrug efflux systems (MDR) are able to survive adverse ecological niches. Multiresistant Escherichia coli and Enterobacter cloacae isolates from wholesome broiler carcasses were investigated for the presence of MDR. Lowering of Minimal Inhibitory Concentration for antimicrobials in the presence of a proton-motive force (PMF) uncoupler was tested as a potential display of the MDR phenotype. PCR amplification of the genes encoding AcrA and AcrB, components of a MDR system was performed. Diversity of each species was ascertained by Pulsed-Field Gel Electrophoresis (PFGE) of DNA digested with endonuclease XbaI. For all the isolates, except E. coli 1 and E. cloacae 9, lowering of MIC or of the growth rate in the presence of antimicrobials was observed, indicating a PMF dependent resistance mechanism. Expected products of DNA amplification with acrAB derived primers was obtained with all E. coli strains and with two of the five E. cloacae strains. Dendrogram generated shows diverse pulsetypes, confirming the genetic diversity among the strains. An important issue and related public health is the fact that different models and mechanisms of antimicrobial resistance are present in a small number of non-pathogenic strains and isolated from the same origin. These may be sources of resistance genes to others microorganisms, among them, pathogenic strains.

Detection of the apr gene in proteolytic psychrotrophic bacteria isolated from refrigerated raw milk.

Bacteria of the genus Pseudomonas have been associated with the spoilage of raw milk and dairy products due to the production of thermostable proteolytic enzymes. The apr gene encodes for alkaline metalloprotease in Pseudomonas and other related bacteria. Its presence in psychrotrophic proteolytic bacteria isolated from raw milk collected from cooling tanks was verified. A polymerase chain reaction (PCR) technique was used with degenerate primers. Total DNA from 112 isolates was pooled in different groups and then used as template for the amplification reactions. Controls consisted of DNA extracted from 26 cultures. An expected DNA fragment of 194 bp was detected in groups that contained bacteria identified as Pseudomonas. The PCR product was observed only when DNA from control cultures of Pseudomonas aeruginosa, Pseudomonas fluorescens, Serratia marcescens and Aeromonas hydrophila were used. A detection limit assay indicated that the apr gene could be directly amplified from pasteurized milk inoculated with 10(8) CFU/ml of P. fluorescens. With this method it was possible to detect proteolytic bacteria at 10(5) CFU/ml in reconstituted skim milk powder if cells were recovered for DNA extraction before amplification.