Limitations of the use of the mtp40 fragment as a marker of differentiation between Mycobacterium tuberculosis and M. bovis

UNIFESP-EPM Departamento de Microbiologia, Imunologia e ParasitologiaUNIFESP, EPM, Depto. de Microbiologia, Imunologia e ParasitologiaSciEL

Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms.

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the Sao Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.FAPESP 2009/52030-5RCNPqCAPE

Detection of Cyanotoxin-Producing Genes in a Eutrophic Reservoir (Billings Reservoir, São Paulo, Brazil)

CyanoHABs (cyanobacterial harmful algal blooms) are blooms of cyanobacteria capable of producing cyanotoxins, a large group of secondary metabolites that are toxic to most eukaryotes. In this work, the main aim was to evaluate the presence of multiple genes from each of the clusters responsible for biosynthesis of cyanotoxins (cylindrospermopsin, microcystin and saxitoxin) in total DNA obtained from sixteen environmental water samples by PCR. Microcystin gene mcyE was amplified in all analyzed samples. Among the cylindrospermopsin genes analyzed, only the cyrC gene was amplified from DNA obtained from three of sixteen samples. Of the three different saxitoxin genes analyzed, sxtB and sxtI were present in four and three of the sixteen samples studied, respectively, and sxtA did not show any positive result. Based on our results, we suggest caution when using only one gene from the full clusters responsible for biosynthesis of cyanotoxins, given that it may not be sufficient to confirm or exclude the toxigenic potential of a sample

Diversity of Mycobacteriaceae from aquatic environment at the São Paulo Zoological Park Foundation in Brazil.

We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and eighty isolates were cultivated and identified by phenotypic characteristics (growth rate and pigmentation) and sequencing of hsp65, rpoB and 16S rRNA genes. The results revealed that almost 48% of the isolates could be identified at the species level; about 50% were classified at the genus level, and only less than 2% of the isolates showed an inconclusive identification. The isolates classified at the genus level and not identified were then evaluated by phylogenetic analyses using the same three concatenated target genes. The results allowed us to identify at the genus level some isolates that previously had inconclusive identification, and they also suggested the presence of putative candidate species within the sample, demonstrating that this zoological park is an important source of diversity