Publications by authors named "Daniel Morais"

30 Publications

  • Page 1 of 1

Database limitations for studying the human gut microbiome.

PeerJ Comput Sci 2020 17;6:e289. Epub 2020 Aug 17.

Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.

Background: In the last twenty years, new methodologies have made possible the gathering of large amounts of data concerning the genetic information and metabolic functions associated to the human gut microbiome. In spite of that, processing all this data available might not be the simplest of tasks, which could result in an excess of information awaiting proper annotation. This assessment intended on evaluating how well respected databases could describe a mock human gut microbiome.

Methods: In this work, we critically evaluate the output of the cross-reference between the Uniprot Knowledge Base (Uniprot KB) and the Kyoto Encyclopedia of Genes and Genomes Orthologs (KEGG Orthologs) or the evolutionary genealogy of genes: Non-supervised Orthologous groups (EggNOG) databases regarding a list of species that were previously found in the human gut microbiome.

Results: From a list which contemplates 131 species and 52 genera, 53 species and 40 genera had corresponding entries for KEGG Database and 82 species and 47 genera had corresponding entries for EggNOG Database. Moreover, we present the KEGG Orthologs (KOs) and EggNOG Orthologs (NOGs) entries associated to the search as their distribution over species and genera and lists of functions that appeared in many species or genera, the "core" functions of the human gut microbiome. We also present the relative abundance of KOs and NOGs throughout phyla and genera. Lastly, we expose a variance found between searches with different arguments on the database entries. Inferring functionality based on cross-referencing UniProt and KEGG or EggNOG can be lackluster due to the low number of annotated species in Uniprot and due to the lower number of functions affiliated to the majority of these species. Additionally, the EggNOG database showed greater performance for a cross-search with Uniprot about a mock human gut microbiome. Notwithstanding, efforts targeting cultivation, single-cell sequencing or the reconstruction of high-quality metagenome-assembled genomes (MAG) and their annotation are needed to allow the use of these databases for inferring functionality in human gut microbiome studies.
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http://dx.doi.org/10.7717/peerj-cs.289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924478PMC
August 2020

Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity.

Braz J Microbiol 2021 Jun 4;52(2):787-800. Epub 2021 Apr 4.

Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.

Crude oil extracted from oilfield reservoirs brings together hypersaline produced water. Failure in pipelines transporting this mixture causes contamination of the soil with oil and hypersaline water. Soil salinization is harmful to biological populations, impairing the biodegradation of contaminants. We simulated the contamination of a soil from an oilfield with produced water containing different concentrations of NaCl and crude oil, in order to evaluate the effect of salinity and hydrocarbon concentration on prokaryote community structure and biodegradation activity. Microcosms were incubated in CO-measuring respirometer. After the incubation, residual aliphatic hydrocarbons were quantified and were performed 16S rRNA gene sequencing. An increase in CO emission and hydrocarbon biodegradation was observed with increasing oil concentration up to 100 g kg. Alpha diversity decreased in oil-contaminated soils with an increase in the relative abundance of Actinobacteria and reduction of Bacteroidetes with increasing oil concentration. In the NaCl-contaminated soils, alpha diversity, CO emission, and hydrocarbon biodegradation decreased with increasing NaCl concentration. There was an increase in the relative abundance of Firmicutes and Proteobacteria and a reduction of Actinobacteria with increasing salt concentration. Our results highlight the need to adopt specific bioremediation strategies in soils impacted by mixtures of crude oil and hypersaline produced water.
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http://dx.doi.org/10.1007/s42770-021-00476-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105486PMC
June 2021

Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality.

Microorganisms 2021 Feb 13;9(2). Epub 2021 Feb 13.

Molecular Systems Biology, Helmholtz-Center for Environmental Research, UFZ, 04318 Leipzig, Germany.

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life.
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http://dx.doi.org/10.3390/microorganisms9020381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918521PMC
February 2021

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood.

mSystems 2021 Jan 5;6(1). Epub 2021 Jan 5.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.

Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
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http://dx.doi.org/10.1128/mSystems.01017-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786133PMC
January 2021

16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.

Microb Ecol 2021 Feb 29;81(2):535-539. Epub 2020 Aug 29.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic.

Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.
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http://dx.doi.org/10.1007/s00248-020-01586-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7835310PMC
February 2021

Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass.

Environ Microbiol 2020 11 31;22(11):4604-4619. Epub 2020 Aug 31.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic.

Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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http://dx.doi.org/10.1111/1462-2920.15183DOI Listing
November 2020

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Sci Data 2020 07 13;7(1):228. Epub 2020 Jul 13.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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http://dx.doi.org/10.1038/s41597-020-0567-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359306PMC
July 2020

Proposal of the CAD System for Melanoma Detection Using Reconfigurable Computing.

Sensors (Basel) 2020 Jun 3;20(11). Epub 2020 Jun 3.

Laboratory of Machine Learning and Intelligent Instrumentation, Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil.

This work proposes dedicated hardware to real-time cancer detection using Field-Programmable Gate Arrays (FPGA). The presented hardware combines a Multilayer Perceptron (MLP) Artificial Neural Networks (ANN) with Digital Image Processing (DIP) techniques. The DIP techniques are used to extract the features from the analyzed skin, and the MLP classifies the lesion into melanoma or non-melanoma. The classification results are validated with an open-access database. Finally, analysis regarding execution time, hardware resources usage, and power consumption are performed. The results obtained through this analysis are then compared to an equivalent software implementation embedded in an ARM A9 microprocessor.
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http://dx.doi.org/10.3390/s20113168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313700PMC
June 2020

Explorative Meta-Analysis of 377 Extant Fungal Genomes Predicted a Total Mycobiome Functionality of 42.4 Million KEGG Functions.

Front Microbiol 2020 6;11:143. Epub 2020 Feb 6.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia.

Unveiling the relationship between taxonomy and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial taxonomic diversity, our understanding of its relationship to functional diversity is still scarce. Here, we used a meta-analysis of completely annotated extant genomes of 377 taxonomically distinct fungal species to predict the total fungal microbiome functionality on Earth with accumulation curves (ACs) of all known functions from the level 3 of KEGG Orthology using both parametric and non-parametric estimates in an explorative data-mining approach. The unsaturated model extrapolating functional diversity as a function of species richness described the ACs significantly better than the saturated model that assumed a limited total number of functions, which suggested the presence of widespread and rare functions. Based on previous estimates of 3.8 million fungal species on Earth, we propagated the unsaturated model to predict a total of 42.4 ± 0.5 million KEGG level 3 functions of which only 0.06% are known today. Our approach not only highlights the presence of widespread and rare functions but points toward the necessity of novel and more sophisticated methods to unveil the entirety of functions to fully understand the involvement of the fungal microbiome in ecosystem functioning.
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http://dx.doi.org/10.3389/fmicb.2020.00143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015973PMC
February 2020

The total microbiome functions in bacteria and fungi.

J Proteomics 2020 02 19;213:103623. Epub 2019 Dec 19.

Molecular Systems Biology, Helmholtz-Center for Environmental Research, UFZ, Leipzig, Germany.

Unveiling the relationship between phylogeny and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial phylogenetic diversity, our understanding of its relationship to functional diversity is still scarce. Here we predicted the total microbiome functions of bacteria and fungi on Earth using the total known functions from level 3 of KEGG Orthology by modelling the increase of functions with increasing diversity of bacteria or fungi. For bacteria and fungi, the unsaturated model described the data significantly better (for both P <2.2e-16), suggesting the presence of two types of functions. Widespread functions ubiquitous in every living organism that make up two thirds of our current knowledge of microbiome functions are separated from rare functions from specialised enzymes present in only a few species. Given previous estimates on species richness, we predicted a global total of 35.5 million functions in bacteria and 3.2 million in fungi; of which only 0.02% and 0.14% are known today. Our approach highlights the necessity of novel and more sophisticated methods to unveil the entirety of rare functions to fully understand the involvement of the microbiome in ecosystem functioning. SIGNIFICANCE: The functionality of and within a microbial community is generally inferred based on the taxonomic annotation of the organism. However, our understanding of functional diversity and how it relates to taxonomy is still limited. Here we predict the total microbiome functionality in bacteria and fungi on Earth using known and annotated protein-coding sequences in species accumulation curves. Our estimates reveal that the majority of functionality (>99%) could be assigned to yet unknown and rare functions, highlighting that our current knowledge is incomplete and functional inference is thus lackluster.
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http://dx.doi.org/10.1016/j.jprot.2019.103623DOI Listing
February 2020

A meta-analysis of global fungal distribution reveals climate-driven patterns.

Nat Commun 2019 11 13;10(1):5142. Epub 2019 Nov 13.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.
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http://dx.doi.org/10.1038/s41467-019-13164-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853883PMC
November 2019

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation.

Sci Rep 2019 08 13;9(1):11731. Epub 2019 Aug 13.

Laboratory of Applied Microbiology, Microbiology Department, Institute of Biological Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.

Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.
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http://dx.doi.org/10.1038/s41598-019-47921-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692397PMC
August 2019

Comparison of enzymatic activities and proteomic profiles of grown on different carbon sources.

Proteome Sci 2019 1;17. Epub 2019 Jun 1.

1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.

Background: The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose and hemicelluloses. The most important hemicellulose decomposers are clustered with the genus . As the related species differ in their range of hydrolytic activities and substrate preferences, was selected as one of the most effective isolates and thus suitable for proteomic studies on substrate comparisons in the extracellular fraction. The genome is the biggest in the butyrivibria cluster and is focused on "environmental information processing" and "carbohydrate metabolism".

Methods: The study of the effect of carbon source on 3071 was based on cultures grown on four substrates: xylose, glucose, xylan, xylan with 25% glucose. The enzymatic activities were studied by spectrophotometric and zymogram methods. Proteomic study was based on genomics, 2D electrophoresis and nLC/MS (Bruker Daltonics) analysis.

Results: Extracellular β-endoxylanase as well as xylan β-xylosidase activities were induced with xylan. The presence of the xylan polymer induced hemicellulolytic enzymes and increased the protein fraction in the interval from 40 to 80 kDa. 2D electrophoresis with nLC/MS analysis of extracellular 3071 proteins found 14 diverse proteins with significantly different expression on the tested substrates.

Conclusion: The comparison of four carbon sources resulted in the main significant changes in proteome occurring outside the fibrolytic cluster of proteins. The affected proteins mainly belonged to the glycolysis and protein synthesis cluster.
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http://dx.doi.org/10.1186/s12953-019-0150-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545216PMC
June 2019

Antioxidant, photoprotective and inhibitory activity of tyrosinase in extracts of Dalbergia ecastaphyllum.

PLoS One 2018 30;13(11):e0207510. Epub 2018 Nov 30.

Centre for Agricultural, Environmental and Biological Sciences, Federal University of Recôncavo of Bahia/UFRB, University Campus, Cruz das Almas, Bahia, Brazil.

Dalbergia ecastaphyllum is a native Brazil plant with importance for beekeeping, and widely used in folk medicine. For the first time, the extracts of this plant were assessed for the presence of hydrophilic and lipophilic antioxidants, as well as inhibition of tyrosinase, free radicals scavenging and sunscreen protection. The antioxidant activity was evaluated by free radical scavenging (DPPH) and β-carotene bleaching assay. The tyrosinase inhibitory activity was evaluated and calculated the EC50. The photoprotective activity was measured using different concentrations of D. ecastaphyllum extracts. The Sun Protection Factor (SPF) of the samples was higher than 6, and the sample from Ilhéus showed the most pronounced photoprotective effect. Sample from Canavieiras presented the highest antioxidant activity by free radical scavenging DPPH and β-carotene bleaching method, with 92.41% and 48.34%, respectively. All samples inhibited the tyrosinase, especially the sample from Prado that was most effective (124.62 μg.mL-1). Significant negative correlation was found between flavonoid contents and inhibition of tyrosinase. The overall results provide relevant information about the Dalbergia ecastaphyllum species, indicating as potential material to cosmetic and pharmaceutical industry.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207510PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269094PMC
April 2019

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum".

Microb Ecol 2019 Apr 7;77(3):664-675. Epub 2018 Sep 7.

Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic.

"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.
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http://dx.doi.org/10.1007/s00248-018-1250-9DOI Listing
April 2019

BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data.

PeerJ 2018 30;6:e5299. Epub 2018 Jul 30.

Soil Department, "Luiz de Queiroz" College of Agriculture - ESALQ/USP, Piracicaba, São Paulo, Brazil.

Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation to process these huge datasets. The demand on system resources usually requires migrating from Windows to Linux-based operating systems and prior familiarity with command-line interfaces. To overcome this barrier, we developed a fully automated and easy-to-install package as well as a complete, easy-to-follow pipeline for microbial metataxonomic analysis operating in the Windows Subsystem for Linux (WSL)-Bioinformatics Through Windows (BTW). BTW combines several open-access tools for processing marker gene data, including 16S rRNA, bringing the user from raw sequencing reads to diversity-related conclusions. It includes data quality filtering, clustering, taxonomic assignment and further statistical analyses, directly in WSL, avoiding the prior need of migrating from Windows to Linux. BTW is expected to boost the use of NGS amplicon data by facilitating rapid access to a set of bioinformatics tools for Windows users. Moreover, several Linux command line tools became more reachable, which will enhance bioinformatics accessibility to a wider range of researchers and practitioners in the life sciences and medicine. BTW is available in GitHub (https://github.com/vpylro/BTW). The package is freely available for noncommercial users.
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http://dx.doi.org/10.7717/peerj.5299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6074753PMC
July 2018

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

Bioinformatics 2018 07;34(13):2292-2294

Institute of Microbiology of the CAS, 14220 Prague 4, Czech Republic.

Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems.

Results: SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data.

Availability And Implementation: SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022770PMC
July 2018

Closed Genome Sequence of Phytopathogen Biocontrol Agent Strain AGVL-005, Isolated from Soybean.

Genome Announc 2018 Feb 15;6(7). Epub 2018 Feb 15.

Agrivalle Brasil Indústria e Comércio de Produtos Agrícolas Ltda., Salto, Sao Paulo, Brazil

We report here the closed and near-complete genome sequence and annotation of strain AGVL-005, a bacterium isolated from soybean seeds in Brazil and used for phytopathogen biocontrol.
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http://dx.doi.org/10.1128/genomeA.00057-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814484PMC
February 2018

Differences in bacterial composition between men's and women's restrooms and other common areas within a public building.

Antonie Van Leeuwenhoek 2018 Apr 10;111(4):551-561. Epub 2017 Nov 10.

Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil.

Humans distribute a wide range of microorganisms around building interiors, and some of these are potentially pathogenic. Recent research established that humans are the main drivers of the indoor microbiome and up to now significant literature has been produced about this topic. Here we analyzed differences in bacterial composition between men's and women's restrooms and other common areas within the same public building. Bacterial DNA samples were collected from restrooms and halls of a three-floor building from the Federal University of Pampa, RS, Brazil. The bacterial community was characterized by amplification of the V4 region of the 16S rRNA gene and sequencing. Throughout all samples, the most abundant phylum was Proteobacteria, followed by Actinobacteria, Bacteroidetes and Firmicutes. Beta diversity metrics showed that the structure of the bacterial communities were different among the areas and floors tested, however, only 6-9% of the variation in bacterial communities was explained by the area and floors sampled. A few microorganisms showed significantly differential abundance between men's and women's restrooms, but in general, the bacterial communities from both places were very similar. Finally, significant differences among the microbial community profile from different floors were reported, suggesting that the type of use and occupant demographic within the building may directly influence bacterial dispersion and establishment.
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http://dx.doi.org/10.1007/s10482-017-0976-6DOI Listing
April 2018

Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater.

Microb Ecol 2018 Apr 3;75(3):688-700. Epub 2017 Oct 3.

Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.
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http://dx.doi.org/10.1007/s00248-017-1078-8DOI Listing
April 2018

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere.

Front Microbiol 2017 11;8:1266. Epub 2017 Jul 11.

Microbiology Department, Universidade Federal de Minas GeraisBelo Horizonte, Brazil.

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the long-term use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly and ) was enriched in the RP-amended soil. was the second most abundant taxon in the RP-treated soil. sp. and sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were and . These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.
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http://dx.doi.org/10.3389/fmicb.2017.01266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504191PMC
July 2017

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil.

Braz J Microbiol 2017 Jul - Sep;48(3):391-392. Epub 2016 Dec 10.

Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. Electronic address:

Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.
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http://dx.doi.org/10.1016/j.bjm.2016.09.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498421PMC
March 2018

ZIKV - CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms.

PLoS Negl Trop Dis 2016 06 22;10(6):e0004817. Epub 2016 Jun 22.

Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.

Background: In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly.

Methodology/principal Findings: Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression.

Conclusions/significance: We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy.
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http://dx.doi.org/10.1371/journal.pntd.0004817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917180PMC
June 2016

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies.

Microb Ecol 2016 08 24;72(2):443-7. Epub 2016 May 24.

Universidade Federal do Pampa - UNIPAMPA, São Gabriel, RS, Brazil.

Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org .
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http://dx.doi.org/10.1007/s00248-016-0785-xDOI Listing
August 2016

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.

J Microbiol Methods 2016 07 22;126:18-23. Epub 2016 Apr 22.

Biology Department, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.

Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.
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http://dx.doi.org/10.1016/j.mimet.2016.04.012DOI Listing
July 2016

Responses of microbial community from tropical pristine coastal soil to crude oil contamination.

PeerJ 2016 18;4:e1733. Epub 2016 Feb 18.

Department of Microbiology, Universidade Federal de Viçosa , Viçosa, Minas Gerais , Brazil.

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.
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http://dx.doi.org/10.7717/peerj.1733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768689PMC
February 2016

Microbiology: Microbiome studies need local leaders.

Nature 2015 Dec;528(7580):39

Federal University of Pampa, Sāo Gabriel, Rio Grande do Sul, Brazil.

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http://dx.doi.org/10.1038/528039eDOI Listing
December 2015

Data analysis for 16S microbial profiling from different benchtop sequencing platforms.

J Microbiol Methods 2014 Dec 3;107:30-7. Epub 2014 Sep 3.

Microbiology Department, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.

Progress in microbial ecology is confounded by problems when evaluating results from different sequencing methodologies. Contrary to existing expectations, here we demonstrate that the same biological conclusion is reached using different NGS technologies when stringent sequence quality filtering and accurate clustering algorithms are applied.
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http://dx.doi.org/10.1016/j.mimet.2014.08.018DOI Listing
December 2014

Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.

Microb Ecol 2014 Feb 31;67(2):237-41. Epub 2013 Oct 31.

Microbiology Department, Federal University of Vicosa, Vicosa, Minas Gerais, 365700-000, Brazil,

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.
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http://dx.doi.org/10.1007/s00248-013-0302-4DOI Listing
February 2014