Microbiology (medical), Medicine, Statistics, Probability and Uncertainty
31
Scopus Publications
Scopus Publications
Identification of taxonomic changes in the fecal bacteriome associated with colorectal polyps and cancer: potential biomarkers for early diagnosis Beatriz Alessandra Rudi Grion, Paula Luize Camargos Fonseca, Rodrigo Bentes Kato, Glen Jasper Yupanqui García, Aline Bruna Martins Vaz, Beatriz Nafría Jiménez, Ainhoa Lapitz Dambolenea, Koldo Garcia-Etxebarria, Bertram Brenig, Vasco Azevedo, Luis Bujanda, Jesus M. Banales, Aristóteles Góes-Neto Frontiers in Microbiology, 2023 Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota. Host-related factors and inherent characteristics of polyps and tumors may contribute to microbiome variability, potentially acting as confounding factors in the discovery of taxonomic biomarkers for both conditions. In this study we employed shotgun metagenomics to analyze the taxonomic diversity of bacteria present in fecal samples of 90 clinical subjects (comprising 30 CRC patients, 30 with polyps and 30 controls). Our findings revealed a decrease in taxonomic richness among individuals with polyps and CRC, with significant dissimilarities observed among the study groups. We identified significant alterations in the abundance of specific taxa associated with polyps (Streptococcaceae, Lachnoclostridium, and Ralstonia) and CRC (Lactobacillales, Clostridiaceae, Desulfovibrio, SFB, Ruminococcus, and Faecalibacterium). Clostridiaceae exhibited significantly lower abundance in the early stages of CRC. Additionally, our study revealed a positive co-occurrence among underrepresented genera in CRC, while demonstrating a negative co-occurrence between Faecalibacterium and Desulfovibrio, suggesting potential antagonistic relationships. Moreover, we observed variations in taxonomic richness and/or abundance within the polyp and CRC bacteriome linked to polyp size, tumor stage, dyslipidemia, diabetes with metformin use, sex, age, and family history of CRC. These findings provide potential new biomarkers to enhance early CRC diagnosis while also demonstrating how intrinsic host factors contribute to establishing a heterogeneous microbiome in patients with CRC and polyps.
Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics Carolina O. de C. Lima, Giovanni M. De Castro, Ricardo Solar, Aline B. M. Vaz, Francisco Lobo, Gilberto Pereira, Cristine Rodrigues, Luciana Vandenberghe, Luiz Roberto Martins Pinto, Andréa Miura da Costa, Maria Gabriela Bello Koblitz, Raquel Guimarães Benevides, Vasco Azevedo, Ana Paula Trovatti Uetanabaro, Carlos Ricardo Soccol, Aristóteles Góes-Neto Frontiers in Microbiology, 2022 Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24–144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24–48 h (T1), 72–96 h (T2), and 120–144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.
An Integrative View of the Phyllosphere Mycobiome of Native Rubber Trees in the Brazilian Amazon Paula Luize Camargos Fonseca, Demetra Skaltsas, Felipe Ferreira da Silva, Rodrigo Bentes Kato, Giovanni Marques de Castro, Glen Jasper Yupanqui García, Gabriel Quintanilha-Peixoto, Thairine Mendes-Pereira, Anderson Oliveira do Carmo, Eric Roberto Guimarães Rocha Aguiar, Daniel Santana de Carvalho, Diogo Henrique Costa-Rezende, Elisandro Ricardo Drechsler-Santos, Fernanda Badotti, Alice Ferreira-Silva, Guilherme Oliveira, Priscila Chaverri, Aline Bruna Martins Vaz, Aristóteles Góes-Neto Journal of Fungi, 2022 The rubber tree, Hevea brasiliensis, is a neotropical Amazonian species. Despite its high economic value and fungi associated with native individuals, in its original area in Brazil, it has been scarcely investigated and only using culture-dependent methods. Herein, we integrated in silico approaches with novel field/experimental approaches and a case study of shotgun metagenomics and small RNA metatranscriptomics of an adult individual. Scientific literature, host fungus, and DNA databases are biased to fungal taxa, and are mainly related to rubber tree diseases and in non-native ecosystems. Metabarcoding retrieved specific phyllospheric core fungal communities of all individuals, adults, plantlets, and leaves of the same plant, unravelling hierarchical structured core mycobiomes. Basidiomycotan yeast-like fungi that display the potential to produce antifungal compounds and a complex of non-invasive ectophytic parasites (Sooty Blotch and Flyspeck fungi) co-occurred in all samples, encompassing the strictest core mycobiome. The case study of the same adult tree (previously studied using culture-dependent approach) analyzed by amplicon, shotgun metagenomics, and small RNA transcriptomics revealed a high relative abundance of insect parasite-pathogens, anaerobic fungi and a high expression of Trichoderma (a fungal genus long reported as dominant in healthy wild rubber trees), respectively. Altogether, our study unravels new and intriguing information/hypotheses of the foliar mycobiome of native H. brasiliensis, which may also occur in other native Amazonian trees.
Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs Aline Bruna M. Vaz, Paula Luize C. Fonseca, Felipe F. Silva, Gabriel Quintanilha-Peixoto, Inmaculada Sampedro, Jose A. Siles, Anderson Carmo, Rodrigo B. Kato, Vasco Azevedo, Fernanda Badotti, Juan A. Ocampo, Carlos A. Rosa, Aristóteles Góes-Neto Peerj, 2020 The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera Demetra N. Skaltsas, Fernanda Badotti, Aline Bruna Martins Vaz, Felipe Ferreira da Silva, Romina Gazis, Kenneth Wurdack, Lisa Castlebury, Aristóteles Góes-Neto, Priscila Chaverri Scientific Reports, 2019 Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.
16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages Madangchanok Imchen, Ranjith Kumavath, Aline B. M. Vaz, Aristóteles Góes-Neto, Debmalya Barh, Preetam Ghosh, Natalia Kozyrovska, Olga Podolich, Vasco Azevedo Frontiers in Microbiology, 2019 Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.
Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems Madangchanok Imchen, Ranjith Kumavath, Debmalya Barh, Aline Vaz, Aristóteles Góes-Neto, Sandeep Tiwari, Preetam Ghosh, Alice R. Wattam, Vasco Azevedo Scientific Reports, 2018 The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.
Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP Rodrigo Carvalho, Aline Vaz, Felipe Luiz Pereira, Fernanda Dorella, Eric Aguiar, Jean-Marc Chatel, Luis Bermudez, Philippe Langella, Gabriel Fernandes, Henrique Figueiredo, Aristóteles Goes-Neto, Vasco Azevedo Scientific Reports, 2018 Mucositis is an inflammatory condition of the gut, caused by an adverse effect of chemotherapy drugs, such as 5-fluorouracil (5-FU). In an attempt to develop alternative treatments for the disease, several research groups have proposed the use of probiotics, in particular, Lactic Acid Bacteria (LAB). In this context, the use of recombinant LAB, for delivering anti-inflammatory compounds has also been explored. In previous work, we demonstrated that eitherLactococcus lactisNZ9000 or a recombinant strain expressing an antimicrobial peptide involved in human gut homeostasis, the Pancreatitis-associated Protein (PAP), could ameliorate 5-FU-induced mucositis in mice. However, the impact of these strains on the gut microbiota still needs to be elucidated. Therefore, in the present study, we aimed to characterize the effects of bothLactococcistrains in the gut microbiome of mice through a 16 S rRNA gene sequencing metagenomic approach. Our data show 5-FU caused a significant decrease in protective bacteria and increase of several bacteria associated with pro-inflammatory traits. TheLactococcistrains were shown to reduce several potential opportunistic microbes, while PAP delivery was able to suppress the growth ofEnterobacteriaceaeduring inflammation. We conclude the strain secreting antimicrobial PAP was more effective in the control of 5-FU-dysbiosis.
A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon Aline B. M. Vaz, Paula L. C. Fonseca, Fernanda Badotti, Demetra Skaltsas, Luiz M. R. Tomé, Allefi C. Silva, Mayara C. Cunha, Marco A. Soares, Vera L. Santos, Guilherme Oliveira, Priscilla Chaverri, Aristóteles Góes-Neto Scientific Reports, 2018 Hevea brasiliensis is a native hyperdiverse tree species in the Amazon basin with great economic importance since it produces the highest quality natural rubber. H. brasiliensis, in its natural habitat, may harbor fungal endophytes that help defend against phytopathogenic fungi. In this work, we investigated the fungal endophytic communities in two pristine areas in Eastern Amazon (Anavilhanas National Park – ANP and Caxiuanã National Forest – CNF) at different spatial scales: regional, local, individual (tree), and intra-individual (leaflet). Using a culture-based approach, 210 fungal endophytes were isolated from 240 sampling units and assigned to 46 distinct MOTUs based on sequencing of the nrITS DNA. The community compositions of the endophytomes are different at both regional and local scales, dominated by very few taxa and highly skewed toward rare taxa, with many endophytes infrequently isolated across hosts in sampled space. Colletotrichum sp. 1, a probably latent pathogen, was the most abundant endophytic putative species and was obtained from all individual host trees in both study areas. Although the second most abundant putative species differed between the two collection sites, Clonostachys sp. 1 and Trichoderma sp. 1, they are phylogenetically related (Hypocreales) mycoparasites. Thus, they probably exhibit the same ecological function in the foliar endosphere of rubber tree as antagonists of its fungal pathogens.
Endophytic fungal compounds active against Cryptococcus neoformans and C. gattii Cristiane B Pereira, Djalma M de Oliveira, Alice FS Hughes, Markus Kohlhoff, Mariana LA Vieira, Aline B Martins Vaz, Mariana C Ferreira, Camila R Carvalho, Luiz H Rosa, Carlos A Rosa, Tânia MA Alves, Carlos L Zani, Susana Johann, Betania B Cota Journal of Antibiotics, 2015
