Biology subjects

Espinoza, J. L.

Publications and source records attributed to Espinoza, J. L..

9 recordsLinked to original sources

bioRxiv2026

Upper respiratory tract bacterial microbiome features associated with Streptococcus pneumoniae colonisation, environmental and demographic factors among older children in a rural setting in The Gambia

Abstract The upper respiratory tract (URT) microbiome plays a vital role in respiratory health, with older children (5-14 years old) serving as key reservoirs for the transmission of bacteria to younger individuals (< 5 years old). However, the URT microbiome in this age group remains poorly characterised, particularly in relation to colonisation by the pathobiont Streptococcus pneumoniae. To address this gap, we analysed URT samples collected over eight visits from 134 healthy children aged 5-14 years in The Gambia, using culture-dependent methods to detect S. pneumoniae and culture-independent 16S rRNA sequencing to characterise the microbiome in parallel. 16S rRNA sequencing identified Streptococcus and Prevotella as the dominant microbiome constituents. When integrating longitudinal sampling data, we observed temporal instability with frequent switches in microbiome profiles over time. URT samples colonised with S. pneumoniae were associated with increased abundance of Moraxella, Streptococcus and Haemophilus, whereas non-colonised URT samples were enriched with Granulicatella and Filifactor. S. pneumoniae colonisation was also associated with lower Shannon diversity compared with non-colonised samples. Age and season were the strongest determinants of microbiome composition; increasing age was associated with decreasing prevalence and abundance of taxa including Haemophilus and Moraxella, while gram-positive taxa were predominantly enriched in the dry season. These findings provide new insight into the URT microbiome of older children in The Gambia and highlight Granulicatella and Filifactor as potential contributors to colonisation resistance against S. pneumoniae.

microbiology↗

bioRxiv2026

Complex microbial consortia improve yield and physiological performance of leafy greens under deficit irrigation

O_LIWater scarcity is an increasing constraint on agricultural productivity, particularly for high-value vegetable crops. Deficit irrigation strategies can reduce water use but frequently compromise yield and crop physiological status. Scalable, biologically based tools are needed to sustain crop performance under reduced water input without reliance on additional agrochemical inputs. C_LIO_LIFive functionally diverse microbial consortia were assembled from taxa selected to support rhizosphere colonization, soil structural stabilization, and fungal-mediated nutrient and water foraging. Consortia were evaluated in greenhouse trials with lettuce (Lactuca sativa) and spinach (Spinacia oleracea) grown under full irrigation or a 30% deficit irrigation regime (70% of crop water requirement). Crop responses were assessed using yield, harvest delay, root length, wilting incidence, chlorophyll content, and Water Band Index. C_LIO_LIAcross both crops, microbial consortium treatments improved performance under deficit irrigation relative to untreated water-stressed controls. In lettuce, yield increased by 3-9%; in spinach, yield increased by 4-13%, with several treatments restoring performance to levels not significantly different from fully irrigated controls. C_LIO_LIMicrobial treatments reduced harvest delay by an average of three to four days, improved root length, lowered wilting incidence, and reduced WBI, indicating attenuation of plant water stress. In several cases, physiological responses under deficit irrigation approached those observed under full irrigation despite 30% lower water input. Higher application rates generally produced stronger responses, though this trend was not always statistically significant. C_LIO_LISynthesis and applications. Complex microbial consortia can buffer the physiological and yield penalties of deficit irrigation in leafy green crops. These findings demonstrate the potential of soil microbiome-based inoculants as scalable, biologically derived tools to improve agricultural water-use efficiency and resilience under increasing water scarcity. Practical adoption of such consortia could reduce irrigation demand in intensive vegetable production systems without proportional yield loss, supporting both economic and environmental sustainability goals in water-limited agricultural contexts. C_LI

microbiology↗

bioRxiv2026

Multi-omics Analyses of Facial Skin in Acne Identify Distinct Microbial and Metabolic Features at Lesional and Non-lesional Sites

The microbial and biochemical landscape of clinically normal-appearing skin in individuals with acne remains uncharacterized. Here, we performed longitudinal multi-omics profiling of facial skin from 10 individuals with moderate acne and 10 healthy controls, integrating 16S rRNA gene sequencing, shotgun metagenomics, and untargeted metabolomics across lesional and non-lesional sites. Compositional tensor factorization revealed that non-lesional acne skin occupies a distinct intermediate state between healthy and lesional skin in both the microbiome and the metabolome. Machine learning models distinguished healthy from non-lesional acne skin with 70% accuracy, demonstrating that molecular dysbiosis occurs in areas of the skin without visible lesions. Non-lesional sites exhibited reduced microbial diversity, strain-level shifts in Corynebacterium and Lawsonella correlating with disease severity, and metabolic alterations, including elevated lipids and perturbed amino acid and dipeptide profiles. Microbe-metabolite co-occurrence network analyses revealed that healthy skin is enriched for protective metabolites such as urocanic acid, while acne-associated skin shows distinct co-occurrence patterns. These findings establish that acne represents a field effect disorder, with molecular alterations extending beyond visible lesions to encompass the entire facial skin ecosystem. This molecular signature of pre-lesional skin provides potential biomarkers for early intervention and suggests that effective acne treatment may require holistic approaches targeting the broader skin environment rather than individual lesions alone.

microbiology↗

bioRxiv2025

Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for next generation sequencing (pan)genome-resolved metagenomics and metatranscriptomics

Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing computational runtime and memory requirements, while translated searches in protein-space lose classification resolution from ambiguous mapping events. Leviathans utility is demonstrated through two case studies: a marine plastisphere metagenomics dataset analyzing metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan. ImportanceUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy with substantially lower runtime and memory requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.

bioinformatics↗

bioRxiv2024

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBAs versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.

bioinformatics↗

bioRxiv2023

Host-Microbiome Associations in Saliva Predict COVID-19 Severity

Established evidence indicates that oral microbiota plays a crucial role in modulating host immune responses to viral infection. Following Severe Acute Respiratory Syndrome Coronavirus 2 - SARS-CoV-2 - there are coordinated microbiome and inflammatory responses within the mucosal and systemic compartments that are unknown. The specific roles that the oral microbiota and inflammatory cytokines play in the pathogenesis of COVID-19 are yet to be explored. We evaluated the relationships between the salivary microbiome and host parameters in different groups of COVID-19 severity based on their Oxygen requirement. Saliva and blood samples (n = 80) were collected from COVID-19 and from non-infected individuals. We characterized the oral microbiomes using 16S ribosomal RNA gene sequencing and evaluated saliva and serum cytokines using Luminex multiplex analysis. Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. The hierarchical classification of COVID-19 status and respiratory severity using multiple modalities separately (i.e., microbiome, salivary cytokines, and systemic cytokines) and simultaneously (i.e., multi-modal perturbation analyses) revealed that the microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity, followed by the multi-modal. Our findings suggest that oral microbiome and salivary cytokines may be predictive of COVID-19 status and severity, whereas atypical local mucosal immune suppression and systemic hyperinflammation provide new cues to understand the pathogenesis in immunologically naive populations. Significance StatementThe oral mucosa is one of the first sites encountered by bacterial and viral infections, including SARS-CoV-2. It consists of a primary barrier occupied by a commensal oral microbiome. The primary function of this barrier is to modulate immunity and provide protection against invading infection. The occupying commensal microbiome is an essential component that influences the immune systems function and homeostasis. The present study showed that the host oral immune response performs unique functions in response to SARS-CoV-2 when compared to systemic responses during the acute phase. We also demonstrated that there is a link between oral microbiome diversity and COVID-19 severity. Additionally, the salivary microbiome was predictive of not only disease status but also severity.

immunology↗

bioRxiv2022

Rapid reductions in population size drive evolutionary divergence in diatoms

Unicellular photosynthetic marine microbes, or phytoplankton, make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology and biogeochemistry, we have a limited understanding of how the basic features of their demographics along with dynamic environments affect trait evolution. A key feature of diatom ecology is frequent extreme reductions in population size, both as part of their bloom-and-bust growth dynamics, and as a result of living within ocean currents. Here, we use experimental evolution to understand which metabolic pathways and functions readily diversify in diatom populations following population bottleneck events. We subjected replicate populations of six genetically distinct diatom strains to population bottlenecks and then subsequently allowed them to evolve as large populations in the absence of environmental change. Phylogenies and global expression of orthologs were generally strain-specific, indicating that vertical (inherited) evolutionary constraints largely determine the occupation of specific locations in the transcriptional landscape (i.e. tran-scape). Following bottlenecks and subsequent evolution as large populations, transcriptional networks of most populations returned to those of the ancestral population. However, at least one replicate population per lineage migrated in the tran-scape, demonstrating that evolutionary changes in gene expression patterns and transcriptional relationships can be driven by population bottlenecks even in the absence of environmental change. Importantly, the orthologs dominating transcriptional diversification resided in common, central metabolic pathways. These data advance our understanding of constraints and patterns of transcriptional relationships underlying trait evolution in microbes that drive global food webs and elemental cycles.

evolutionary biology↗

bioRxiv2019

The concentration of heterotrophic growth substrates in culture medium is a crucial determinant of the culturability of subsurface soil microbes

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted extracted cells into one of two custom-designed defined growth media that differed only by a 100-fold difference in the concentration of amino acids and organic carbon. Across both media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria. The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria. We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically-divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic-acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and the concentration of substrates in culture medium influences the culturability of specific microbial lineages. ImportanceIsolating environmental microbes and studying their physiology under controlled conditions is an essential aspect of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities--the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.

microbiology↗

bioRxiv2016

Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene Acquisition

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. Diatom centromere sequences contain low GC content regions and an abundance of long contiguous AT windows, but lack repeats or other conserved sequence features. Native and foreign sequences of similar GC content can maintain episomes and recruit the diatom centromeric histone protein CENP-A, suggesting non-native sequences can also function as diatom centromeres. Thus, simple sequence requirements enable DNA from foreign sources to incorporate into the nuclear genome repertoire as stable extra-chromosomal episomes, revealing a potential mechanism for bacterial and foreign eukaryotic DNA acquisition.

molecular biology↗