Biology subjects

Selem-Mojica, N.

Publications and source records attributed to Selem-Mojica, N..

8 recordsLinked to original sources

bioRxiv2026

Global biogeography of mangrove sediment microbiomes is structured by a conserved core and environmental selection

Mangrove sediments are globally important biogeochemical hotspots, yet the large-scale organization and assembly of their microbiomes remain poorly resolved. Here, we compiled and analysed 390 shotgun metagenomes from mangrove sediments across 43 sites worldwide to quantify how diversity, spatial turnover, and ecological processes structure microbial communities across environmental and geographic gradients. We identify a striking dual architecture in mangrove sediment microbiomes. A remarkably small and ubiquitous taxonomic core, representing a minor fraction of total richness but dominating community abundance, persists across continents, climatic regimes, and marine realms. This core is composed primarily of anaerobic microbial lineages associated with carbon, nitrogen, and sulfur cycling and shows limited spatial and environmental turnover. In contrast, the non-core fraction is highly diverse, responds strongly to climatic and edaphic gradients, and drives most biogeographic differentiation. Assembly-process modelling reveals that deterministic selection dominates global taxonomic turnover, with homogeneous selection stabilizing shared community components and heterogeneous selection promoting regional differentiation, while dispersal limitation plays a secondary role. Network analyses further show that core taxa occupy structurally central positions in microbial co-occurrence networks, supporting overall connectivity despite pronounced regional variation in peripheral community composition. Together, these results demonstrate that mangrove sediment microbiomes combine a conserved functional backbone with an environmentally responsive periphery. This organization reconciles global functional continuity with strong regional differentiation and provides a basis for anticipating microbiome responses to environmental change in mangrove ecosystems.

ecology↗

bioRxiv2025

Uncharacterized Acetilactobacillus-like genera represent the most abundant microorganisms in honeys produced by native stingless bee

Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing[≤] 81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI > 99%, interclade ANI[≤] 81%), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.

ecology↗

bioRxiv2024

CAMDA 2023: finding patterns in urban microbiomes

The Critical Assessment of Massive Data Analysis (CAMDA) addresses the challenge of effectively utilizing Big Data in life science. Serving as both a conference and a catalyst for research groups, CAMDA annually presents challenges that foster innovative solutions. For the Forensics CAMDA 2023 challenge, we analyzed 365 metagenomic samples from 16 cities worldwide to characterize their origin. The forensic challenge was addressed from two perspectives: using the reduced abundance OTU tables and employing functional annotations. To identify the most informative Operational Taxonomic Units, we fit negative binomial models ultimately reducing variables to 294. After OTU selection, we implemented supervised models and conducted 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio in each scenario. Support vector classification (SVC) achieved the highest F1 score (0.96) for the abundance tables, accurately classifying most cities, although New York City (NYC) posed a challenge. Via functional profiles with Mifaser at level 4, we achieved the best functional classification using the Neural Network (NN) model. Additionally, to gain insight into further associations between bacterial distribution with other covariates, we applied Dirichlet regression over Escherichia, Enterobacter, and Klebsiella bacteria abundances. We considered climatic and demographic variables of the cities, observing that population increase is indeed associated with a rise in the mean of Escherichia while decreasing temperature is linked to higher proportions of Klebsiella. For replicability of the scripts, a Docker container and a Conda environment are available at the repository: GitHub:github.com/ccm-bioinfo/cambda2023.

bioinformatics↗

bioRxiv2023

A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis

Clavibacter, a plant endophytic actinobacterial genus, includes phytopathogens with devasting effects on several crops. C. michiganensis, the seed-borne and causal agent of bacterial canker in tomato, is arguably the most notorious species of the genus. Yet, its origin and natural reservoirs remain elusive. Moreover, C. michiganensis populations show different genetic pathogenicity profiles with equally unpredictable plant disease outcomes. To tackle these uncertainties, here we analyze genomic data generated during a decade-long survey of Clavibacter in wild and commercial tomato cultivars, providing evolutionary insights that informed on the pathogenicity of this phytopathogen. Unexpectedly, our phylogeny situate the last common ancestor of C. michiganensis next to Clavibacter isolates from grasses rather than to the sole strain we could isolate from wild tomato, which is closer to C. capsici associated with pepper. Pathogenicity profiling of selected C. michiganensis isolates, together with C. phaseoli and C. californiensis as sister taxa of the grass clade, and the newly isolated C. capsici from wild tomato, was found to be congruent with the proposed phylogenetic relationships. Furthermore, we identified gene enrichment after an evolutionary bottleneck leading to the appearance of C. michiganesis, including known pathogenicity factors but also hitherto unnoticed genes with such potential, i.e., nutrient acquisition and specialized metabolite metabolic gene clusters. The holistic perspective provided by our long-term and in-depth analyses hints towards a host shift event as the origin of the causative agent of bacterial canker in tomato, leading to a complex of C. michiganensis with pathogenicity factors that remain to be characterized.

microbiology↗

bioRxiv2020

ActDES- a Curated Actinobacterial Database for Evolutionary Studies

Actinobacteria are a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic. These are made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last twenty years, the large size and complexity of many Actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large scale comparative genomics and evolutionary studies. To enable greater understanding and exploitation of Actinobacterial genomes, specialist genomic databases must be linked to high-quality genome sequences. Here we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome reannotation. Utilising this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. Significance as a bioresource to the communityThe Actinobacteria are a large diverse phylum of bacteria, often with large, complex genomes with a high G+C content. Sequence databases have great variation in the quality of sequences, equivalence of annotation and phylogenetic representation, which makes it challenging to undertake evolutionary and phylogenetic studies. To address this, we have assembled a curated, taxa-specific, non-redundant database to aid detailed comparative analysis of Actinobacteria. ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies - facilitated by reliable identification of orthologs across a set of defined, phylogenetically-representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These analyses can then act as a springboard for the studies of the evolution of virulence genes, the evolution of metabolism and identification of targets for metabolic engineering. Data summaryAll genome sequences used in this study can be found in the NCBI taxonomy browser https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/www.tax.cgi and are summarised along with Accession numbers in Table S1 All other data are available on Figshare https://doi.org/10.6084/m9.figshare.12167529 and https://doi.org/10.5281/zenodo.3830391 O_LIPerl script files available on GitHub https://github.com/nselem/ActDES including details of how to batch annotate genomes in RAST from the terminal https://github.com/nselem/myrast C_LIO_LISupp. Table S1 List of genomes from NCBI (Actinobacteria database.xlsx) https://doi.org/10.6084/m9.figshare.12167529 C_LIO_LICVS genome annotation files including the FASTA files of nucleotide and amino acids sequences (individual .cvs files) https://doi.org/10.6084/m9.figshare.12167880 C_LIO_LIBLAST nucleotide database (.fasta file) https://doi.org/10.6084/m9.figshare.12167724 C_LIO_LIBLAST protein database (.fasta file) https://doi.org/10.6084/m9.figshare.12167724 C_LIO_LISupp. Table S2 Expansion table genus level (Expansion table.xlsx Tab Genus level) https://doi.org/10.6084/m9.figshare.12167529 C_LIO_LISupp. Table S2 Expansion table species level (Expansion table.xlsx Tab species level) https://doi.org/10.6084/m9.figshare.12167529 C_LIO_LIAll GlcP and Glk data - blast hits from ActDES database, MUSCLE Alignment files and .nwk tree files can be found at https://doi.org/10.6084/m9.figshare.12167529 C_LIO_LIInteractive trees in Microreact for Glk tree https://microreact.org/project/w_KDfn1xA/90e6759e and associated files can be found at https://doi.org/10.6084/m9.figshare.12326441.v1 C_LIO_LIInteractive trees in Microreact for GlcP tree https://microreact.org/project/VBUdiQ5_k/0fc4622b and associated files can be found at https://doi.org/10.6084/m9.figshare.12326441.v1 C_LI

microbiology↗

bioRxiv2018

EvoMining reveals the origin and fate of naturalproducts biosynthetic enzymes

Natural products, or specialized metabolites, are important for medicine and agriculture alike, as well as for the fitness of the organisms that produce them. Microbial genome mining aims at extracting metabolic information from genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process the likelihood of identifying truly novel biosynthetic systems is low. To overcome this limitation we previously introduced EvoMining, a genome mining approach that incorporates evolutionary principles. Here, we release and use our latest version of EvoMining, which includes novel visualization features and customizable databases, to analyze 42 central metabolic enzyme families conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these enzyme families are lineage specific, opening a new metabolic space related to shell enzymes, which have been overlooked to date. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving microbial adaptive evolution. By defining the origins and fates of metabolic enzymes, EvoMining not only complements traditional genome mining approaches as an unbiased and rule-independent strategy, but it opens the door to gain insights into the evolution of natural products biosynthesis. We anticipate that EvoMining will be broadly used for metabolic evolutionary studies, and to generate genome-mining predictions leading to unprecedented chemical scaffolds and new antibiotics.\n\nDATA SUMMARYDatabases have been deposited at Zenodo; DOI: 10.5281/zenodo.1162336 http://zenodo.org/deposit/1219709\n\nTrees and metadata have been deposited in MicroReact\n\nGDH Actinobacteria https://microreact.org/project/r1IhjVm6X\n\nGDH Cyanobacteria https://microreact.org/project/HyjYUN7pQ)\n\nGDH Pseudomonas https://microreact.org/project/rJPC4EQa7\n\nGDH Archaea https://microreact.org/project/ByUcvNmaX\n\nALS Cyanobacteria https://microreact.org/project/B11HkUtdm\n\nEvoMining code has been deposited in gitHub https://github/nselem/evomining\n\nDocker container in Dockerhub https://hub.docker.com/r/nselem/evomining/\n\nWe confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.\n\nIMPACT STATEMENTEvoMining allows studying expansion-and-recruitment events of enzyme families in prokaryotic lineages, with the goal of providing both evolutionary insights and a genome mining approach for the discovery of truly novel natural products biosynthetic gene clusters. Thus, by better understanding the origin and fate of gene copies within enzyme families, this work contributes towards the identification of lineage-dependent enzymes that we call shell enzymes, which are ideal beacons to unveil chemical dark matter. We show that enzyme functionality is a continuum, including transition enzymes located between central and specialized metabolism. To exemplify these evolutionary dynamics, we focused in the genes directing the synthesis of the sunscreen peptide scytonemin, as the two key enzymes of this biosynthetic pathway behave as shell enzymes and were correctly identified by EvoMining. We also show how evolutionary approaches are better suited to study unexplored lineages, such as those belonging to the Archaea domain, which is systematically mined here for novel natural products for the first time. The release of EvoMining as a stand-alone tool will allow researchers to explore its own enzyme families of interest, within their own genomic lineages of expertise, by taking into account the lessons learned from this work

bioinformatics↗

bioRxiv2018

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

Genome mining has become a key technology to explore and exploit natural product diversity through the identification and analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on a single-genome basis; currently, the process is being scaled up to large-scale mining of pan-genomes of entire genera, complete strain collections and metagenomic datasets from which thousands of bacterial genomes can be extracted at once. However, no bioinformatic framework is currently available for the effective analysis of datasets of this size and complexity. Here, we provide a streamlined computational workflow, tightly integrated with antiSMASH and MIBiG, that consists of two new software tools, BiG-SCAPE and CORASON. BiG-SCAPE facilitates rapid calculation and interactive visual exploration of BGC sequence similarity networks, grouping gene clusters at multiple hierarchical levels, and includes a glocal alignment mode that accurately groups both complete and fragmented BGCs. CORASON employs a phylogenomic approach to elucidate the detailed evolutionary relationships between gene clusters by computing high-resolution multi-locus phylogenies of all BGCs within and across gene cluster families (GCFs), and allows researchers to comprehensively identify all genomic contexts in which particular biosynthetic gene cassettes are found. We validate BiG-SCAPE by correlating its GCF output to metabolomic data across 403 actinobacterial strains. Furthermore, we demonstrate the discovery potential of the platform by using CORASON to comprehensively map the phylogenetic diversity of the large detoxin/rimosamide gene cluster clan, prioritizing three new detoxin families for subsequent characterization of six new analogs using isotopic labeling and analysis of tandem mass spectrometric data.

bioinformatics↗

bioRxiv2017

The cycad coralloid root contains a diverse endophytic bacterial community with novel biosynthetic gene clusters unique to its microbiome

Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Nostoc, and Rhizobium species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities and used for whole-genome inferences that suggest two Dioon-specific monophyletic groups and a level of specialization characteristic of co-evolved symbiotic relationships. In agreement with this, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with metabolite profiling using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.

genomics↗