Publications by authors named "Ulisses Nunes Da Rocha"
Article Synopsis
- - This text discusses the strain LABIM41 (CMRP6330) as a biological solution for crop disease management.
- - The strain's genome consists of nearly 4 million base pairs and features a complex metabolic system.
- - It produces various molecules that play important roles in its beneficial interactions with plants.
Article Synopsis
- - This study analyzed the microbial communities (bacteria, methanogenic archaea, and eukaryotes) in the guts of Pachnoda marginata larvae, specifically comparing the midgut and hindgut using sequencing methods.
- - The composition of these microbial communities varied significantly between gut sections and was influenced by the larvae's diet, with different bacterial families dominating in the midgut depending on whether they fed on leaves or straw.
- - Methanogenic communities also differed between gut compartments, showing higher diversity in the midgut compared to the hindgut, which was more specialized to the host; midgut communities resembled those found in the surrounding soil.
Article Synopsis
- The study investigates the complex interactions between two bacterial species commonly found together in severe, difficult-to-treat infections.
- Researchers used both laboratory experiments and modeling to reveal how one species can partially inhibit the other and how they engage in a cross-feeding relationship, where one provides nutrients to support the other's growth.
- The findings enhance understanding of how these bacteria coexist and interact in polymicrobial infections, which could lead to new treatment strategies.
Article Synopsis
- The ecological role of viral communities in anaerobic digestion (AD) regarding antibiotic resistance genes (ARGs) is still uncertain, but metagenomic analyses suggest that viruses like Siphoviridae and Podoviridae are prevalent in the system.
- A small fraction of viral operational taxonomic units (vOTUs) carries ARGs (only 0.57%), whereas ARGs on plasmids and other elements dominate the resistome, indicating significant potential for the horizontal transfer of these genes.
- Experimental results imply that while there is a possibility for ARG dissemination via phage transduction, the majority of lytic phages interact with antibiotic-resistant bacteria (pARBs) in a way that likely reduces their overall numbers rather than spreading
Article Synopsis
- Metagenomics allows scientists to analyze environmental DNA for insights into microbiomes, but eukaryotic organisms like fungi are often underrepresented due to challenges with intron-rich genes.
- Researchers developed a machine learning algorithm, SVMmycointron, to accurately predict fungal introns, improving gene annotations in metagenomic datasets by up to 9.1%.
- This tool enhances understanding of the role of fungi and other eukaryotes in microbiome function and is accessible for researchers working with metagenomics data.
Article Synopsis
- Genome annotation tools help standardize outputs but limit user customization, which affects their flexibility in further analysis.
- StandEnA is a new command-line tool for Linux that allows users to create custom databases by pulling protein sequences from various sources, using a defined list of standard names.
- StandEnA is open-source and can be accessed online, with supplementary data available for further research.
Article Synopsis
- Recent advancements in sequencing technology have led to an explosion of biological data, creating new challenges for analysis that necessitate the use of machine learning (ML) algorithms.
- This study introduces a novel feature extractor based on Tsallis entropy to enhance the classification of biological sequences and evaluates its effectiveness through five case studies.
- Results indicate that the Tsallis entropy method outperforms traditional Shannon entropy, demonstrating robust generalization and efficiency in dimensionality reduction compared to other techniques.
Article 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 investigates how changes in pH affect microbial communities involved in chain elongation processes in anaerobic bioreactors, focusing on their composition and performance in producing medium-chain carboxylates.
- Results show that increasing pH from 5.5 to 6.5 significantly alters community structure but does not permanently affect product yields, indicating a capacity for recovery following environmental shifts.
- Analyses revealed distinct pH preferences among key microbial species, revealing complex interactions within the community and highlighting the resilience and adaptability of these mixed cultures in fermentation pathways despite environmental changes.
Article Synopsis
- Most eukaryotic genomes are still unsequenced, limiting our understanding of their roles in ecosystems, while efforts to recover prokaryotic genomes are more common.* -
- This study utilized the EukRep pipeline to analyze 6000 metagenomes, successfully obtaining 447 eukaryotic bins, predominantly from streptophytes and fungi, with many coming from diverse environments.* -
- The research highlights gaps in existing genome completeness assessments and suggests improvements through long-read sequencing and better reference databases to enhance eukaryotic genome recovery.*
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.
Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa.
Stefanía Magnúsdóttir Joao Pedro Saraiva Alexander Bartholomäus Majid Soheili Rodolfo Brizola Toscan Ulisses Nunes da Rocha
Front Microbiol
January 2023
Article Synopsis
- Every year, antimicrobial resistance genes (ARGs) in bacteria lead to millions of deaths, especially as urbanization increases and compounds the problem in cities.
- This study analyzed over a thousand urban metagenomes to explore the presence and behavior of ARGs in urban bacteria, focusing on their distribution and whether they were found on plasmids.
- Findings revealed that while multidrug and glycopeptide ARGs are common in urban bacteria, they are not primarily transferred via plasmids and the strains studied showed limited virulence, indicating a need for further research on the prevalence and spread of these resistance genes.
Article Synopsis
- Beneficial microorganisms for corals (BMCs) are effective probiotics that help reduce coral bleaching and mortality, which is critical for their survival as they face extinction.
- Traditional methods for selecting BMCs rely on manual biochemical tests, but this study introduces a genome-based framework to identify new BMC traits and mechanisms, enhancing selection processes.
- The research outlines exclusive probiotic traits and proposes new mechanisms like synthesizing glycine betaine and ectoines, providing a roadmap for future selections of coral probiotics that could help save these vital marine ecosystems.
Article Synopsis
- * Researchers combined flow cytometry cell sorting with bioinformatics to classify cells from a wastewater microbial community into different abundance groups and sequenced their genomes.
- * Results showed a significant increase in species identification (two-fold improvement), revealing that sorting allows the recovery of genomes that are otherwise undetected in unsorted samples.
Article Synopsis
- Cyanobacteria are gaining attention in biotechnology, particularly for genetic engineering and innovative reactor designs like capillary biofilm reactors (CBRs), which enhance cell growth.
- Strain PCC 7712 has been identified as ideal for CBRs due to its excellent biofilm attachment and high biomass yield, prompting the complete genome sequencing of both PCC 7712 and a related strain, PCC 7601.
- Despite their nearly identical genomes, differences in protein-coding sequences and nitrogen fixation abilities were observed between the two strains, indicating potential for targeted strain engineering.
Article Synopsis
- * This study examined the carbohydrate utilization abilities of over 7000 bacterial and archaeal taxa using the Genomes from Earth's Microbiomes (GEM) catalog, revealing significant variation in enzyme production among different microbial groups and habitats.
- * The research highlighted that specific habitats, like plant-associated environments, harbor diverse carbohydrate-active enzymes, which could help predict microbial functions and identify important carbohydrate resources in various ecosystems.
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.
Article Synopsis
- - The study investigates the biocontrol potential of a bacterial strain, B.BV10, through three methods: testing its antifungal properties in the lab, evaluating its effectiveness on strawberry plants in a greenhouse, and analyzing its genome for relevant genetic features regarding its activity.
- - Results showed that B.BV10 effectively inhibited the growth of various harmful fungi and significantly reduced gray mold on strawberry plants while increasing fruit biomass.
- - Genome analysis of B.BV10 revealed it has nearly 3.9 million base pairs, with genes linked to antifungal compounds, biofilm formation, and root colonization, providing insights that could help in developing this strain for agricultural applications in the future.
Article Synopsis
- The study investigates the roles of bacterial symbionts in octocorals by analyzing 66 metagenome-assembled genomes from 30 prokaryotic species found in three octocoral species and seawater.
- The findings identify unique symbiotic bacteria, particularly from the novel genus Ca. Gorgonimonas, which have specific adaptations to thrive in suboxic environments and possess genes that aid in colonizing and persisting within their octocoral hosts.
- Additionally, the research highlights potential substrate interactions, such as chitin turnover, and suggests that some symbiotic lineages may specialize in chemical defense, indicating a complex interplay between the coral microbiome and its bacterial residents.
Article Synopsis
- Electrified biotrickling filters are a sustainable technology for treating water contaminated with ammonium and low in organic carbon, but little is known about the microbiome in their conductive granule beds.
- Researchers used minimally invasive sampling methods to collect granules during reactor operation and analyzed them for electrochemical activity and microbial composition.
- The study found significant redox sites associated with bioelectrochemical denitrification and identified a complex nitrogen food web with denitrifying species, emphasizing the potential of these systems for environmental cleanup.
Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.
Júnia Schultz Isabella Campelo Vilardi Argentino René Kallies Ulisses Nunes da Rocha Alexandre Soares Rosado
Front Microbiol
May 2022
Article Synopsis
- Extreme temperature gradients in polar volcanoes help select various extremophiles, particularly in areas like Deception Island, which exhibits temperature variations from 100°C to subzero.
- A study focused on isolating thermophilic bacteria from geothermal sediments showed that 126 bacterial strains were identified, with 76 capable of growing on crude oil and 30 demonstrating effective hydrocarbon degradation.
- Four strains showed excellent crude oil degradation capabilities, with one strain identified as having significant potential for biotechnological applications, including bioremediation and microbial enhanced oil recovery in extreme environments.
Article Synopsis
- The study focuses on the microbial communities found in deep-sea iron-manganese (Fe-Mn) deposits, which are being impacted by mining activities.
- Researchers analyzed samples from two Atlantic Ocean locations, discovering unique microbial taxa and lower diversity compared to Pacific deposits.
- The findings emphasize the role of microbes in biogeochemical processes and highlight the need for understanding these communities before deep-sea mining occurs.
Article Synopsis
- * Two inoculation procedures were tested: one under oxic conditions with lower inoculum (P1) and another under anoxic conditions with higher inoculum (P2), resulting in P2 producing more methane, while P1 had higher acetic acid levels.
- * The study found varying bacterial families and methanogenic genera in the enrichment cultures, highlighting that the choice of inoculum preparation significantly affects the efficiency of converting biomass to methane and managing byproducts like acetic acid.
Article Synopsis
- Building stable and controllable microbiomes over long periods has been difficult due to their susceptibility to random fluctuations and complexity.
- The study introduced a looped mass transfer design, which connected five local microbiomes to a regional pool, allowing for continuous growth and monitoring over 114 generations.
- This mass transfer effectively reduced variations in microbiome assembly, increased constancy and resistance, and helped to sustain certain cell types at risk of extinction, demonstrating a stabilizing effect through the rescue of subcommunities.