Publications by authors named "Milkha M Leimena"
Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters.
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- Next generation sequencing (NGS) technologies, specifically RNA sequencing (RNA-seq), are utilized to analyze the metatranscriptome of microbial ecosystems, with a focus on developing a bioinformatic pipeline.
- The newly developed pipeline efficiently removes unwanted rRNA sequences and accurately identifies the function and taxonomic origin of mRNA reads, showing strong congruity with community composition data from previous studies.
- The pipeline is validated through reproducible experiments and comparison of sequencing methods, demonstrating its potential to analyze microbial activity and interactions in diverse environments, particularly in the human small intestine microbiota.
RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase the relative abundance of mRNA and cannot employ the poly(T)-primed approach in cDNA synthesis. In this study, we aimed to validate the use of RNA sequencing (direct cDNA sequencing and 3'-untranslated region [UTR] sequencing) using Lactobacillus plantarum WCFS1 as a model organism, employing its established microarray platform as a reference.
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