Henrique Machado - Academia.edu (original) (raw)

Papers by Henrique Machado

Current Opinion in Microbiology, 2017

Genome sequencing and the application of omic techniques are driving many important advances in t... more Genome sequencing and the application of omic techniques are driving many important advances in the field of microbial natural products research. Despite these gains, there remain aspects of the natural product discovery pipeline where our knowledge remains poor. These include the extent to which biosynthetic gene clusters are transcriptionally active in native microbes, the temporal dynamics of transcription, translation, and natural product assembly, as well as the relationships between small molecule production and detection. Here we touch on a number of these concepts in the context of continuing efforts to unlock the natural product potential revealed in genome sequence data and discuss nomenclatural issues that warrant consideration as the field moves forward.

Journal of the American Chemical Society, Jan 29, 2018

The microbial metabolites known as the macrolides are some of the most successful natural product... more The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, deri...

Marine Drugs, 2016

Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited f... more Chitinolytic microorganisms secrete a range of chitin modifying enzymes, which can be exploited for production of chitin derived products or as fungal or pest control agents. Here, we explored the potential of 11 marine bacteria (Pseudoalteromonadaceae, Vibrionaceae) for chitin degradation using in silico and phenotypic assays. Of 10 chitinolytic strains, three strains, Photobacterium galatheae S2753, Pseudoalteromonas piscicida S2040 and S2724, produced large clearing zones on chitin plates. All strains were antifungal, but against different fungal targets. One strain, Pseudoalteromonas piscicida S2040, had a pronounced antifungal activity against all seven fungal strains. There was no correlation between the number of chitin modifying enzymes as found by genome mining and the chitin degrading activity as measured by size of clearing zones on chitin agar. Based on in silico and in vitro analyses, we cloned and expressed two ChiA-like chitinases from the two most potent candidates to exemplify the industrial potential.

European Microscopy Congress 2016: Proceedings, 2016

 Users may download and print one copy of any publication from the public portal for the purpose... more  Users may download and print one copy of any publication from the public portal for the purpose of private study or research.  You may not further distribute the material or use it for any profit-making activity or commercial gain  You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

International Journal of Systematic and Evolutionary Microbiology, 2015

A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, S... more A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photoba...

Applied and Environmental Microbiology, 2015

Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is ... more Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae , where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermo...

Microbial Physiology, 2013

Listeria monocytogenes, a foodborne pathogenic bacterium, remains a serious public health concern... more Listeria monocytogenes, a foodborne pathogenic bacterium, remains a serious public health concern due to its frequent occurrence in food products coupled with a high mortality rate. Bacterial pathogenicity depends greatly on the ability to secrete virulence factors to or beyond the bacterial cell surface. The Tat pathway, one of the secretion systems present in L. monocytogenes, was until now only investigated in silico. In L. monocytogenes strain EGDe two genes constitute this pathway, tatC(lmo0361) and tatA(lmo0362). Here we show that tatC and tatA are cotranscribed in a bicistronic- and growth-phase-dependent manner, being downregulated in the stationary phase. An EGDe tatAC mutant strain (EGDe ΔtatAC) was constructed, confirming that the Tat pathway is not essential for L.monocytogenes survival or biofilm-forming ability. When compared to the wild-type EGDe, deletion of tatAC did not decrease the virulence potential of EGDe ΔtatAC in HT-29 human epithelial cell line and even inc...

Journal of Food Science, 2011

The biofilm-forming ability of 21 Listeria monocytogenes isolates, previously pulsotyped and corr... more The biofilm-forming ability of 21 Listeria monocytogenes isolates, previously pulsotyped and corresponding to 16 strains, from different origins was evaluated using the Calgary Biofilm Device R , at 37 • C. Biofilms of 4 selected strains were also produced either on pure cultures or on co-cultures with Pseudomonas aeruginosa (PAO1), at 12 • C and at 37 • C. For these biofilms, the minimum biofilm eradication concentrations (MBECs) of 4 commercial dairy sanitizers (1 alkyl amine acetate based-T99, 2 chlorine based-T66 and DD, and 1 phosphoric acid based-BP) were determined. Listeria monocytogenes biofilms grown, either at 37 • C or 12 • C, were able to achieve similar cell densities by using different incubation periods (24 h and 7 d, respectively). In co-culture biofilms, P. aeruginosa was the dominant species, either at 37 • C or at 12 • C, representing 99% of a total biofilm population of 6 to 7 log CFU/peg. Co-culture biofilms were generally less susceptible than L. monocytogenes pure cultures. More interestingly, the biofilms produced at 12 • C were usually less susceptible to the sanitizers than when produced at 37 • C. Single or co-culture biofilms of L. monocytogenes and PAO1, particularly produced at 12 • C, retrieved MBEC values for agents T99 and BP that were, at times, above the maximum in-use recommended concentrations for these agents. The results presented here reinforce the importance of the temperature used for biofilm formation, when susceptibility to sanitizers is being assessed.

Foodborne Pathogens and Disease, 2013

This article presents the major differences in the exoproteomes of Listeria monocytogenes strains... more This article presents the major differences in the exoproteomes of Listeria monocytogenes strains grown at 11°C and 20°C, and their comparison to 37°C, the optimal temperature of growth of this foodborne pathogenic bacteria. A set of four strains previously characterized and representing the genetic diversity of the species was used. Two were virulent, of which one was persistent, and two were low virulent strains. The proteins secreted by the strains grown in minimal medium were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified by liquid chromatography tandem mass spectrometry. The heterogeneity among the four strains concerning the 15 major proteins detected was noticed. No clear association of exoproteome with virulence or genotype was found. Cluster analysis of the protein patterns of the strains suggests an increasing differentiation of strain response with low temperatures, highlighting the importance of the study of the exoproteomes. The main finding was the lack of some proteins in the exoproteome of the persistent strain, namely, flagellin (FlaA) and of OppA/oligopeptide ABC transporter, when compared to the other strains. In fact, these two proteins differ in abundance between strains grown at low temperature. Moreover, FlaA was the only glycoprotein identified in the exoproteomes. An attempt is made here to assess the relevance of the major exoproteins differentially detected. The investigation of the exoproteomes of other persistent and sporadic strains will allow identification of proteins involved in adaptation of particular L. monocytogenes strains to low temperatures in use throughout the food chain.