Biology subjects

Caraballo-Rodriguez, A. M.

Publications and source records attributed to Caraballo-Rodriguez, A. M..

18 recordsLinked to original sources

bioRxiv2026

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

Domoic acid (DA) production by diatom genus Pseudo-nitzschia causes recurrent harmful algal blooms with major consequences for marine ecosystems, fisheries, and human health. Predicting DA risk remains challenging because toxin production varies across morphologically similar and cryptic lineages. Consequently, morphology or single marker genes often fail to resolve toxigenic potential. Here, we expand genomic resources for Pseudo-nitzschia by generating and compiling high-quality genomes spanning diverse species and biogeographic origins, establishing a genus-wide phylogenomic framework to investigate the distribution and evolution of the DA biosynthesis (dab) gene cluster. Among chemically characterized strains, the dab pathway was detected in species only with confirmed DA production. While the cluster exhibits a conserved core structure, several lineages display signatures of ongoing evolution, including intronization, locus rearrangement, and pseudogenization. One striking example of dab variation occurs in toxigenic P. australis strains, in which its biochemically validated isodomoic acid A synthase-encoding gene dabC is located outside the dab locus. Metatranscriptomic surveys reveal widespread environmental dab expression across size classes and species, implicating taxa not typically associated with environmental DA events, such as P. cf. obtusa and P. cf. plurisecta. To connect dab expression with chemical output, nutrient limitation experiments in the historically inconsistent DA producer P. pseudodelicatissima combined transcriptional profiling and nontargeted metabolomics demonstrating coordinated dab expression across distinct co-expression modules and DA accumulation in response to silicon limitation. Together, these results refine the phylogenetic scope of DA production and provide a genome-resolved basis for improved molecular monitoring of toxigenic diversity.

genetics↗

bioRxiv2026

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.

bioinformatics↗

bioRxiv2026

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.

bioinformatics↗

bioRxiv2025

Charting the Undiscovered Metabolome with Synthetic Multiplexing

Most molecular features detected in untargeted metabolomics remain uncharacterized due to the limited scope of existing spectral reference libraries. We synthesized >100,000 biologically inspired compounds using multiplexed reactions, of which 91% were absent from existing structural databases, and searched the resulting MS/MS library across >1.7 billion public spectra, increasing annotation rates by 17.4%. This approach revealed previously undescribed exposure-derived metabolites, including ibuprofen-carnitine. Because ibuprofen has been linked to rhabdomyolysis, reduced mitochondrial function, and impaired muscle recovery in carnitine-limited contexts, we investigated the functional relevance of this conjugate. Ibuprofen-carnitine reduced carnitine transport via the OCTN2 transporter, and in a postpartum mouse muscle injury model, ibuprofen delayed muscle repair that could be rescued by carnitine supplementation, with urinary ibuprofen-carnitine:carnitine ratios tracking this effect. These findings support a hypothesis whereby NSAID-carnitine conjugates compete for carnitine transport, impairing energy metabolism and muscle recovery in susceptible individuals. Synthetic multiplexing thus provides a scalable route to annotate the dark metabolome and generate experimentally testable biological hypotheses.

biochemistry↗

bioRxiv2025

Maternal transmission of a plastid structure enhances offspring fitness

Development in the sea has long been thought to be a nutritional gamble that disproportionately ends in starvation. Here, we unexpectedly show that components of plastids are incorporated into sea urchin eggs and that these, in turn, benefit developmental fitness. We find chromoplast-derived carotenoid crystals and chromoplast-specific metabolites inside of sea urchin eggs. The light-dependent activity of these chromoplast components influence the subsequent abundance of phytohormones that, in turn, regulate the use of energetic lipids that promote development and survival. Offspring that benefit from these chromoplast components are predicted to disperse further, over larger geographic areas, and use a wider range of currents, including those that cross ocean basins. Data presented here challenge the long-held assumption that components of non-metazoan organelles are unable to enter the germline and be passed between generations. We hypothesize that sea urchins manipulate plastids solely for their self-interest by a process that we term machioplasty, with the result of this process being a novel and adaptive form of maternal provisioning. SIGNIFICANCEMaking a fertilizable egg is a complex and carefully regulated process. One long-held assumption is that any component of non-animal organelles are unable to cross the evolutionary valley between non-reproductive and reproductive cells. Here, we unexpectedly show that components of plastids are incorporated into sea urchin eggs and that these, in turn, benefit developmental fitness. Offspring benefit from these plastid components by developing more quickly into larvae and having higher survival due to ability to use phytohormones that influence energetic lipids. This allows offspring to use a wider range of ocean currents, including those that cross entire basins. This challenge the long-held assumption that components of non-metazoan organelles are unable to be passed between generations.

developmental biology↗

bioRxiv2025

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer's Disease

The etiology of Alzheimers Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) generated from five tissue types in two genetic AD mouse models under colonized or germ-free conditions, complemented by shotgun metagenomics sequencing data (666 samples). Systems-level analyses of 3xTg and 5xFAD mice reveal clusters of dysregulated molecular classes across tissues including carnitines, bile acids, B vitamins, and neurotransmitters. This signature, coupled with microbiome profiles, suggests increased oxidative stress via mitochondrial dysfunction. Molecular feature tracking via tissueMASST, a mass spectrometry search tool we developed to bridge animal model findings with human data, identifies microbially-modulated phenylacetyl-carnitine as positively associated with aging and cognitive impairment across human AD studies. With hundreds of yet-to-be-characterized metabolites, this public resource and its associated tools will aid future research in the pathophysiology of AD.

microbiology↗

bioRxiv2024

Empirically establishing drug exposure records directly from untargeted metabolomics data

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N-acyl lipid changes in a cohort with human immunodeficiency virus. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.

bioinformatics↗

bioRxiv2024

plantMASST - Community-driven chemotaxonomic digitization of plants

Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.

plant biology↗

bioRxiv2024

Urinary Metabolomic Profile is Minimally Impacted by Common Storage Conditions and Additives

Metabolomics reflects the molecular communications within a biological system. Urine can be obtained non-invasively and is rich in metabolites that are potential biomarkers for human health and disease. The optimal urine storage conditions for metabolomic analysis are unknown. We measured the impact of common storage conditions and the presence of a DNA-stabilizer, AssayAssure(R) (Thermo Scientific), on metabolite content of voided human urine. Urinary metabolite composition was not altered across storage conditions. Although addition of AssayAssure(R) significantly alters metabolic profile by adduct addition, this does not preclude the identification of parent metabolites or overshadow biological differences. These data suggest biobanked urine stored in any of the tested conditions for metabolomic studies may be considered for metabolomic analysis.

molecular biology↗

bioRxiv2023

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health.

microbiology↗

bioRxiv2021

Mutualistic interactions between B. subtilis and seeds dictate plant development

A tightly coordinated developmental program controls precise genetic and metabolic reprogramming that dictates efficient transition of the seeds from dormancy to metabolically active seedlings. Beneficial microbes are known to stimulate the germination of the seeds or adaptation of the seedlings; however, investigations of exact mechanisms mediating these interactions and the resulting physiological responses of the plants are only beginning. Bacillus subtilis is commonly detected in the plant holobiont and belongs to the group of microbes that provide multifaceted contribution to the health of the plants. The present study demonstrated that B. subtilis triggered genetic and physiological responses in the seeds that determined subsequent metabolic and developmental status of adult plants. Chemically diverse extracellular matrix of Bacillus was demonstrated to structurally cooperate in bacterial colonization of the seed storage tissues. Additionally, an amyloid protein and fengycin, which are two components of the extracellular matrix, targeted the oil bodies of the seed endosperm, provoking changes in lipid metabolism or accumulation of glutathione-related molecules that stimulated two different plant growth programs: the development of seed radicles or overgrowth and immunization of adult plants. We propose this mutualistic interaction is conserved in Bacilli and plant seeds containing storage oil bodies.

microbiology↗

bioRxiv2021

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence

Bacterial communities are in a continuous adaptive and evolutionary race for survival. A myriad of molecules that kill, defend, or mediate communication between bacterial cells of different lineages shape the final structure of the microbial community. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked mainly by a decrease of Bacillus cell membrane permeability among other pleiotropic cellular responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial evolutive and adaptive strategies that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication.

microbiology↗

bioRxiv2020

The ant fungus garden acts as an external digestive system

Most animals digest their food within their own bodies, but some do not. Many species of ants grow fungus gardens that pre-digest food as an essential step of the ants nutrient uptake. To better understand this digestion process, we generated a 3D molecular map of an Atta texana fungus garden, revealing chemical modifications mediated by the fungus garden as plant material passes through.

systems biology↗

bioRxiv2020

Ion Identity Molecular Networking in the GNPS Environment

Molecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

bioinformatics↗

bioRxiv2019

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

Metabolomics data are difficult to find and reuse, even in public repositories. We, therefore, developed the Reanalysis of Data User (ReDU) interface (https://redu.ucsd.edu/), a community- and data-driven approach that solves this problem at the repository scale. ReDU enables public data discovery and co- or re-analysis via uniformly formatted, publicly available MS/MS data and metadata in the Global Natural Product Social Molecular Networking Platform (GNPS), consistent with findable, accessible, interoperable, and reusable (FAIR) principles.1

bioinformatics↗

bioRxiv2019

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR) and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

biochemistry↗

bioRxiv2018

Extracellular matrix components are required to protect Bacillus subtilis colonies from T6SS-dependent Pseudomonas invasion and modulate co-colonization of plant

Bacteria adapt to environmental changes and interact with other microorganisms using a wide array of molecules, metabolic plasticity, secretion systems and the formation of biofilms. Some research has looked at changes in the expression of biofilm related genes during interactions between different bacterial species, however no studies have directly demonstrated the functional significance of biofilms in modulating such interactions. In this study, we have explored this fundamental question by studying the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We demonstrate the important role of the extracellular matrix in protecting B. subtilis colonies from infiltration by Pseudomonas. Surprisingly, we find that the Pseudomonas type VI secretion system (T6SS) is required in the cell-to-cell contact with matrix-impaired B. subtilis cells, revealing a novel role for T6SS against Gram-positive bacteria. In response to P. chlororaphis infiltration, we find that B. subtilis activates sporulation and expresses motility-related genes. Experiments using plant organs demonstrate the functional importance of these different bacterial strategies in their coexistence as stable bacterial communities. The findings described here further our understanding of the functional role played by biofilms in mediating bacterial social interactions.

microbiology↗

bioRxiv2018

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages

A major aspect of our daily lives is the need to acquire, store and prepare our food. Storage and preparation can have drastic effects on the compositional chemistry of our foods, but we have a limited understanding of the temporal nature of processes such as storage, spoilage, fermentation and brewing on the chemistry of the foods we eat. Here, we performed a temporal analysis of the chemical changes in foods during common household preparations using untargeted mass spectrometry and novel data analysis approaches. Common treatments of foods such as home fermentation of yogurt, brewing of tea, spoilage of meats and ripening of tomatoes altered the chemical makeup through time, through both chemical and biological processes. For example, brewing tea altered its composition by increasing the diversity of molecules, but this change was halted after 4 min of brewing. The results indicate that this is largely due to differential extraction of the material from the tea and not modification of the molecules during the brewing process. This is in contrast to the preparation of yogurt from milk, spoilage of meat and the ripening of tomatoes where biological transformations directly altered the foods molecular composition. Comprehensive assessment of chemical changes using multivariate statistics showed the varied impacts of the different food treatments, while analysis of individual chemical changes show specific alterations of chemical families in the different food types. The methods developed here represent novel approaches to studying the changes in food chemistry that can reveal global alterations in chemical profiles and specific transformations at the chemical level.\n\nO_LSTHighlightsC_LSTO_LIWe created a reference data set for tomato, milk to yogurt, tea, coffee, turkey and beef.\nC_LIO_LIWe show that normal preparation and handling affects the molecular make-up.\nC_LIO_LITea preparation is largely driven by differential extraction.\nC_LIO_LIFormation of yogurt involves chemical transformations.\nC_LIO_LIThe majority of meat molecules are not altered in 5 days at room temperature.\nC_LI

biochemistry↗