Publications by authors named "Jonas Coelho Kasmanas"
Article Synopsis
- The study investigates how factors like species abundance, sequencing depth, and taxonomic relationships affect the recovery of metagenome-assembled genomes (MAGs) in microbial communities.
- Different recovery pipelines were tested, revealing that the DT pipeline offered the most accurate results, whereas the 8K pipeline produced the most MAGs but with lower accuracy.
- Findings indicate that simply having more MAGs doesn't reflect true community composition, emphasizing the importance of sequencing depth and caution in interpreting MAG recovery data for biological conclusions.
Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination.
View Article and Find Full Text PDFThe AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.
Anim Microbiome
October 2023
Background: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward.
View Article and Find Full Text PDFArticle Synopsis
- The text refers to a correction issued for a previously published academic article.
- It specifies the DOI (Digital Object Identifier) for the original article, which enables readers to locate it easily.
- Corrections like this usually address errors or updates to ensure the accuracy of scientific information.
Article Synopsis
- - The study highlights the lack of regulations on antibiotic discharges from wastewater treatment plants (WWTP) into rivers, which allows for the persistence of antibiotic resistance genes (ARGs) in surface waters.
- - Using advanced techniques like quantitative PCR and nanopore sequencing, the researchers tracked the levels of specific ARGs and sulfonamides in river water, noting that WWTP effluent was the main source of these contaminants.
- - The findings indicated that downstream from the WWTP, water quality improved with decreasing concentrations of sulfonamides and ARGs, but an unexpected increase in the relative abundance of certain genes suggested potential gene multiplication in the river system.
Article Synopsis
- Metagenomics is a rapidly growing field focused on studying microbial communities, but challenges arise from poorly classified data in existing databases like SRA and MG-RAST.
- The Marine Metagenome Metadata Database (MarineMetagenomeDB) was created to provide a better way for researchers to find and analyze marine metagenomes, featuring curated metadata for thousands of samples.
- The database includes detailed information on 11,449 marine metagenomes, allowing users to filter samples using a web app with search functionalities and a map to visualize sample locations, plus a tool for downloading raw sequence data easily.
Background: The ability to quantitatively predict ecophysiological functions of microbial communities provides an important step to engineer microbiota for desired functions related to specific biochemical conversions. Here, we present the quantitative prediction of medium-chain carboxylate production in two continuous anaerobic bioreactors from 16S rRNA gene dynamics in enriched communities.
Results: By progressively shortening the hydraulic retention time (HRT) from 8 to 2 days with different temporal schemes in two bioreactors operated for 211 days, we achieved higher productivities and yields of the target products n-caproate and n-caprylate.
The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands.
View Article and Find Full Text PDFMetagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data.
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