Biology subjects

Rodrigues, R. R.

Publications and source records attributed to Rodrigues, R. R..

9 recordsLinked to original sources

bioRxiv2025

Connectivity of restored Atlantic Forest fragments drives composition and functionality of the fungal community in the leaf litter layer

The restoration of biodiversity and functional tropical forests is critical to mitigating global biodiversity losses. Aboveground, increasing the connectivity of regenerating forests fragments facilitates the recolonization of tropical forest biodiversity. However, restoring functional ecosystems also requires the recovery of decomposition processes as these are essential in shaping aboveground biodiversity. Therefore, we investigate the role of forest connectivity on restoring the composition and functioning of fungal communities in the leaf litter layer during a chronosequence of forest restoration. In the Brazilian Atlantic Forest, we studied secondary forests regrown between 18 to 55 years after deforestation and different levels of forest connectivity and compared their litter to recently abandoned pastures and undisturbed primary forests. We quantified how forest age and connectivity between fragments influenced the litter fungi composition in relation to tree diversity, litter chemistry, and litter isotopes. We show that fungal composition was highly heterogeneous in forest litter, whereas pasture litter exhibited a more homogeneous community. Moreover, forest connectivity had stronger effects on litter fungal composition compared to forest age. Connectivity promoted wood saprotrophs and endophytes, while suppressed soil saprotrophs, with its effects being more evident during later stages of restoration. Fungal guilds such as endophytes and saprophytes, were primarily influenced by tree diversity and leaf litter chemistry. We conclude that forest connectivity promotes the re-establishment of saprophytic fungi capable of decomposing recalcitrant litter substrates, driven mainly by enhancing tree diversity and litter quality. Practical implications of increasing connectivity may relate to forest resilience on front of future climate change scenarios.

microbiology↗

bioRxiv2025

Gut microbiota of dogs with cancer receiving anti-EGFR/HER2 immunization reveals potential biomarkers of patient survival

BackgroundCanine cancer remains a leading cause of death in dogs, yet advances in veterinary oncology lag behind human medicine, particularly in immunotherapy. While immune checkpoint inhibitors are just entering clinical trials in dogs, other immunotherapies, such as anti-EGFR/HER2 vaccines, have shown promise. In parallel, mounting evidence in human oncology links gut microbiota composition to immunotherapy response. However, this relationship remains unexplored in canine patients. In this pilot study, we analyzed the gut microbiome of dogs enrolled in a clinical trial of anti-EGFR/HER2 immunotherapy to identify microbial biomarkers associated with survival outcomes. MethodsRectal swab samples of 51 dogs were collected at the time of first vaccine administration (baseline microbiota) and underwent 16S rRNA gene sequencing according to standard protocols. ResultsMicrobiome composition showed no significant differences by cancer type, sex, or breed, suggesting no inherent microbiome bias in the cohort. However, Cox regression analysis revealed 11 bacterial taxa whose abundances were significantly associated with overall survival (FDR < 0.1), independently of cancer type. Seven taxa were linked to increased mortality risk, while four were associated with prolonged survival. These associations remained significant after adjusting for confounders such as hemangiosarcoma diagnosis and advanced age. ConclusionsTo our knowledge, this is the first study to identify gut microbial signatures associated with survival in dogs undergoing cancer immunotherapy. These findings suggest that specific bacterial taxa may serve as prognostic biomarkers for immunotherapy outcomes in canine cancer, laying the groundwork for microbiota-targeted strategies to improve therapeutic efficacy in veterinary oncology.

cancer biology↗

bioRxiv2023

JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data

Shotgun microbiome sequencing analysis presents several challenges to accurately and consistently depict sample composition and functional potential. Here we present a two-part framework - JAMS (Just a Microbiology System) - whereby with raw fastq files and metadata as input, meaningful analysis within a sample and between a sample can be performed with ease for either shotgun or 16S sequences. JAMS is the first package to provide seamless deconvolution of functions into their taxonomic contributors. We validated our JAMS framework on two human gut shotgun metagenome test datasets against the popular tool MetaPhlAn 4. We further demonstrate the application of the JAMS package, particularly the plotting functions, on a mouse shotgun dataset.

bioinformatics↗

bioRxiv2023

Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions.

Technological advances have generated tremendous amounts of high-throughput omics data. Integrating data from multiple cohorts and diverse omics types from new and previously published studies can offer a holistic view of a biological system and aid in deciphering its critical players and key mechanisms. In this protocol, we describe how to use Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that can perform meta-analysis of cohorts and detect master regulators among measured parameters that govern pathological or physiological responses of host-microbiota (or any multi-omic data) interactions in a particular condition or disease. TkNA first reconstructs the network that represents a statistical model capturing the complex relationships between the different omics of the biological system. Here, it selects differential features and their per-group correlations by identifying robust and reproducible patterns of fold change direction and sign of correlation across several cohorts. Next, a causality-sensitive metric, statistical thresholds, and a set of topological criteria are used to select the final edges that form the transkingdom network. The second part of the analysis involves interrogating the network. Using the networks local and global topology metrics, it detects nodes that are responsible for control of given subnetwork or control of communication between kingdoms and/or subnetworks. The underlying basis of the TkNA approach involves fundamental principles including laws of causality, graph theory and information theory. Hence, TkNA can be used for causal inference via network analysis of any host and/or microbiota multi-omics data. This quick and easy-to-run protocol requires very basic familiarity with the Unix command-line environment.

systems biology↗

bioRxiv2020

Host response to cholestyramine can be mediated by the gut microbiota

The gut microbiome has been implicated as a major factor contributing to metabolic diseases as well as being contributors to the response to drugs used for the treatment of such diseases. In this study, using a diet-induced obesity mouse model, we tested the effect of cholestyramine, a bile acid sequestrant, on the murine gut microbiome and mammalian metabolism. We also explored the hypothesis that some beneficial effects of this drug on systemic metabolism can be attributed to alterations in gut microbiota. First, we demonstrated that cholestyramine can decrease glucose and epidydimal fat levels. Next, while investigating gut microbiota we found increased alpha diversity of the gut microbiome of cholestyramine-treated mice, with fourteen taxa showing restoration of abundance to levels resembling those in mice fed with a control diet. Analyzing expression of genes known to be regulated by cholestyramine (including Cyp7a1), we confirmed the expected effect of this drug in the liver and ileum. Finally, using a transkingdom network analysis we inferred Acetatifactor muris and Muribaculum intestinale as potential mediators/modifiers of cholestyramine effects on the mammalian host. In addition, A. muris correlated positively with glucagon (Gcg) expression in the ileum and negatively correlated with small heterodimer partner (Shp) expression in the liver. Interestingly, A. muris also correlated negatively with glucose levels, further indicating the potential probiotic role for A. muris. In conclusion, our results indicate the gut microbiome has a role in the beneficial effects of cholestyramine and suggest specific microbes as targets of future investigations.

pharmacology and toxicology↗

bioRxiv2020

Disentangling the effects of sampling scale and size on the shape of species abundance distributions

Many authors have tried to explain the shape of the species abundance distribution (SAD). Some of them have suggested that sampling scale is an important factor shaping SADs. These suggestions, however, did not consider the indirect and well-known effect of sample size, which increases as samples are combined to generate SADs at larger scales. Here, we separate the effects of sample size and sampling scale on the shape of the SAD for three groups of organisms (trees, beetles and birds) sampled in the Brazilian Atlantic Forest. We compared the observed SADs at different sampling scales with simulated SADs having the same richness, relative abundances but comparable sample sizes, to show that the main effect shaping SADs is sample size and not sampling scale. The effect of scale was minor and deviations between observed and simulated SADs were present only for beetles. For trees, the match between observed and simulated SADs was improved at all scales when we accounted for conspecific aggregation, which was even more important than the sampling scale effect. We build on these results to propose a conceptual framework where observed SADs are shaped by three main factors, in decreasing order of importance: sample size, conspecific aggregation and beta diversity. Therefore, studies comparing SADs across sites or scales should use sampling and/or statistical approaches capable of disentangling these three effects on the shape of SADs.

ecology↗

bioRxiv2019

Heterogenization of remaining biodiversity in fragmented tropical forests across agricultural landscapes

The increasing worldwide interest on the conservation of tropical forests reflects the conversion of over 50% of their area into agricultural lands and other uses. Understanding the distribution of remaining biodiversity across agricultural landscapes is an essential task to guide future conservation strategies. To understand the long-term effects of fragmentation on biodiversity, we investigated whether forest fragments in southeastern Brazil are under a taxonomic homogenization or heterogenization process. We estimated pre-deforestation species richness and composition based on a Species Distribution Modelling approach, and compared them to the observed patterns of - and {beta}-diversity. In particular, we asked (i) if changes in {beta}-diversity reveal convergence or divergence on species composition; (ii) if these changes are similar between forest fragments in Strictly Protected Areas (SPAs) (n=20) and within private lands (n=367) and in different regions of the state (West, Center, and Southeast). We detected steep reductions in observed local species richness in relation to our modeled predictions, and this was particularly true among forest fragments in non-protected private lands. The higher observed {beta} diversity indicated an overall biotic heterogenization process, consistent with the idea that the originally diverse vegetation is now reduced to small and isolated patches, with unique disturbance histories and impoverished communities derived from a large regional species pool. Since conservation of biodiversity extends beyond the boundaries of strictly Protected Areas, we advocate forest fragments are valuable for conservation in agricultural landscapes, with particular relevance for private lands, which represent the most exposed and neglected share of what is left.

ecology↗

bioRxiv2019

The restoration species pool for restoring tropical landscapes: assessment of the largest Brazilian supply chain

Brazil has been committed to fulfill international restoration goals and to enforce environmental legislation that will require private landowners to undertake ecological restoration of 21 million hectares of degraded and deforested landscapes. To support a broad range of restoration practices, a consolidated supply chain able to represent regional plant diversity is essential. This study investigated the restoration species pool in native plant nurseries in Sao Paulo state, southeastern Brazil and evaluated their geographic distribution, similarity of their plant stocks and the proportion of species represented from regional floras. Despite the lack of technical assistance and the large presence of non-native species (126 species, average 7.5 species/nursery), we found still more impressive native species richness in plant nurseries (561 species, average 86.4 species/nursery) from both the Atlantic Forest and Cerrado domains, representing 38 to 44% of regional floras. There was a huge bias toward tree and shrub species (96.6%) and absence or underrepresentation of other growth forms, as well as of savanna specialists, animal-dispersed and threatened species. The great dissimilarity of species offered in the nurseries surveyed underscores the importance of regional seed collection practices. Effective assistance and capacitation are essential to address issues related to misidentification of species, underrepresentation of most functional plant groups, and the presence of non-native species, as well as to support the supply chain, currently undergoing market downturn.\n\nAuthor contributions CYV and RRR conceived and designed the research. CYV performed data compilation; CYV and RPN analyzed the data; CYV and RAGV led the writing of the manuscript; all authors contributed to the drafts and gave final approval for publication.\n\nImplications for practiceO_LIPlant nurseries collecting propagules from the surrounding vegetation provide an adequate - but limited - restoration species pool, with very dissimilar plant stocks available among plant nurseries.\nC_LIO_LIPlant nurseries concentrate their production on shrub and tree species and sub-represent other growth forms and some functional groups such as animal-dispersed and threatened species.\nC_LIO_LIThe diversity of the restoration species pool is the basis to support a broad range of restoration practice, being essential to boost restoration initiatives that complement and support the conservation of remaining diversity in human modified landscapes.\nC_LIO_LIEffective assistance and capacity building should be provided to address issues related to misidentification, underrepresentation of functional groups and the presence of exotic and invasive species, as well as to support the supply chain, currently under market downturn\nC_LI

ecology↗

bioRxiv2017

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool \"COREMIC\" meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com), developed using Google App Engine, to help in the process of database mining to identify the \"core microbiome\" associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (5 environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val < 0.05% for Fishers exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

microbiology↗