Biology subjects

Delogu, F.

Publications and source records attributed to Delogu, F..

11 recordsLinked to original sources

bioRxiv2026

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

Plasmids are important agents of prokaryotic evolution and yet existing reference databases remain biased towards cultivable species, limiting our knowledge of their function and ecology in the environment. Here we present a major expansion of known plasmid diversity, through curation and annotation of 8,744 topologically complete plasmids from 9,972 short- and 154 long-read metagenomes as part of the Microflora Danica project. These were found to increase plasmid taxonomic unit diversity by 15% and 99% relative to all and environmental plasmids, respectively, from public sources. In particular, we identify a novel lineage of plasmids in the genus Methanosarcina, encoding genes associated with methanogenesis and cell surface properties, expanding our understanding of chromosome-plasmid complementarity and its potential contribution to host biology. Combining our plasmids with public sources, we curated a set of 17 replication-associated proteins that could be found in 82% of known plasmids and can serve as hallmarks for future detection of plasmids. We present this resource, and a tool for confirming topological completeness of plasmid assemblies, as a toolkit for future plasmid discovery.

microbiology↗

bioRxiv2026

From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments

Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.

ecology↗

bioRxiv2026

A national baseline for methane sink habitats and methanotroph diversity

Methane emissions account for nearly a third of the Earths effective radiative forcing, with methanotrophs playing a critical role in mitigating emissions by oxidising methane in diverse environments1. Despite their ecological importance, methanotrophic diversity and environmental distribution remain incompletely characterised due to cultivation challenges, incomplete or low-quality metagenome-assembled genomes, and limited taxonomic resolution in marker gene surveys. Here, we present a national study of the biogeography of novel and known methanotrophs across Denmarks major natural, urban and agricultural habitats, using genome-resolved classification of 10,683 metagenomes2 and 102 new methanotrophic species3. By linking metabolic potential to habitat-specific distributions, we reveal uncharacterised methanotrophs as dominant in natural ecosystems. These findings provide a comprehensive baseline of methanotroph diversity, reveal clear contrasts between natural and disturbed habitats, and highlight candidate species and habitats for future methane-mitigation strategies.

microbiology↗

bioRxiv2024

Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities

Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the microbial genome catalogue of soils and sediments has been challenging due to the enormous complexity of these environments. Here, we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected across Denmark and through an optimised bioinformatics pipeline, we recovered genomes of 15,314 novel microbial species, including 4,757 high-quality genomes. The recovered microbial genomes span 1,086 novel genera and provide the first high-quality reference genomes for 612 previously known genera, expanding the phylogenetic diversity of the prokaryotic tree of life by 8 %. The long-read assemblies also enabled the recovery of thousands of complete rRNA operons, biosynthetic gene clusters and CRISPR-Cas systems, all of which were underrepresented and highly fragmented in previous terrestrial genome catalogues. Furthermore, the incorporation of the recovered MAGs into public genome databases significantly improved species-level classification rates for soil and sediment metagenomic datasets, thereby enhancing terrestrial microbiome characterization. With this study, we demonstrate that long-read sequencing and optimised bioinformatics, allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain the largest untapped source of biodiversity for expanding genome databases and filling in the gaps of the tree of life.

bioinformatics↗

bioRxiv2024

Microflora Danica: the atlas of Danish environmental microbiomes

The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes in natural and human associated environments. Recent large-scale metagenome surveys record the variety of microbial life in the oceans1, wastewater2, human gut3,4, and earth5,6, with compilations encompassing thousands of public datasets7-13. So far, large-scale microbiome studies either miss functional information or consistency in sample processing, and although they may cover thousands of locations, these are missing resolution, sparsely located, or lacking metadata. Here, we present Microflora Danica, an atlas of Danish environmental microbiomes, encompassing 10,686 shotgun metagenomes and 449 full-length 16S and 18S rRNA datasets linked to a detailed 5 level habitat classification scheme. We determine that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

microbiology↗

bioRxiv2022

Forecasting of a complex microbial community using meta-omics

Microbial communities are complex assemblages whose dynamics are shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in the future. In this context, communities in biological wastewater treatment plants (BWWTPs) represent excellent model systems, because forecasting them is required to ultimately control and operate the plants in a sustainable manner. Here, we forecast the microbial community from the water-air interface of the anaerobic tank of a BWWTP via longitudinal meta-omics (metagenomics, metatranscriptomics and metaproteomics) data covering 14 months at weekly intervals. We extracted all the available time-dependent information, summarised it in 17 temporal signals (explaining 91.1% of the temporal variance) and linked them over time to rebuild the sequence of ecological phenomena behind the community dynamics. We forecasted the signals over the following five years and tested the predictions with 21 extra samples. We were able to correctly forecast five signals accounting for 22.5% of the time-dependent information in the system and generate mechanistic predictions on the ecological events in the community (e.g. a predation cycle involving bacteria, viruses and amoebas). Through the forecasting of the 17 signals and the environmental variables readings we reconstructed the gene abundance and expression for the following 5 years, showing a nearly perfect trend prediction (coefficient of determination [≥] 0.97) for the first 2 years. The study demonstrates the maturity of microbial ecology to forecast composition and gene expression of open microbial ecosystems using year-spanning interactions between community cycles and environmental parameters.

microbiology↗

bioRxiv2021

Longitudinal analysis of the faecal microbiome in pigs fed Cyberlindnera jadinii yeast as a protein source during the weanling period followed by a rapeseed- and faba bean-based grower-finisher diet

The porcine gut microbiome is closely connected to diet and is central to animal health and growth. The gut microbiota composition in relation to Cyberlindnera jadinii yeast as a protein source in a weanling diet was studied previously. Also, there is a mounting body of knowledge regarding the porcine gut microbiome composition in response to the use of rapeseed (Brassica napus subsp. napus) meal, and faba beans (Vicia faba) as protein sources during the growing/finishing period. However, there is limited data on how the porcine gut microbiome respond to a combination of C. jadinii yeast in the weanling phase and rapeseed meal and faba beans in the growing/finishing phase. This work investigated how the porcine faecal microbiome was changing in response to a novel yeast diet with a high inclusion of yeast proteins (40% of crude protein) in a weanling diet followed by a diet based on rapeseed meal and faba beans during the growing/finishing period. The feacal microbiomes of the weanling pigs fed yeast were more diverse with higher relative abundance of Firmicutes over Bacteroidetes compared with those of soybean meal-based diet fed weanlings. Reduced numbers of Prevotella in the yeast fed faecal microbiomes remained a microbiome characteristic up until two weeks after the yeast diet was changed to the rapeseed/faba bean growing finishing diet. A number of differentially abundant bacterial phylotypes along with distinct co-occurrence patterns observed during the growing/finishing period indicated the presence of a "carry-over" effect of the yeast weanling diet onto the faecal microbiomes of the grower/finisher pigs.

microbiology↗

bioRxiv2020

Mantis: flexible and consensus-driven genome annotation

BackgroundThe past decades have seen a rapid development of the (meta-)omics fields, producing an unprecedented amount of data. Through the use of well-characterized datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation allows the identification of regions of interest (i.e. domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, some challenges remain, specifically in terms of speed, flexibility, and reproducibility. In the era of big data it also becomes increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, thus overcoming some limitations in overly relying on computationally generated data. ResultsWe implemented a protein annotation tool - Mantis, which uses text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for total customization of the reference data used, adaptable, and reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which led to an average 0.038 increase in precision when compared to sequence-wide annotation. Mantis is fast, annotating an average genome in 25-40 minutes, whilst also outputting high-quality annotations (average coverage 81.4%, average precision 0.892). ConclusionsMantis is a protein function annotation tool that produces high-quality consensusdriven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license available at https://github.com/PedroMTQ/mantis.

bioinformatics↗

bioRxiv2019

Integration of absolute multi-omics reveals translational and metabolic interplay in mixed-kingdom microbiomes.

Microbiology is founded on well-known model organisms. For example, the majority of our fundamental knowledge regarding the quantitative levels of DNA, RNA, and protein backdates to keystone pure culture-based studies. Nowadays, meta-omic approaches allow us to directly access the molecules that constitute microbes and microbial communities, however due to a lack of absolute measurements, many original culture-derived "microbiology statutes" have not been updated or adapted to more complex microbiome settings. Within a cellulose-degrading and methanogenic consortium, we temporally measured genome-centric absolute RNA and protein levels per gene, and obtained a protein-to-RNA ratio of 102-104 for bacterial populations, whereas Archaeal RNA/protein dynamics (103-105: Methanothermobacter thermoautotrophicus) were more comparable to Eukaryotic representatives humans and yeast. The linearity between transcriptome and proteome had a population-specific change over time, highlighting a minimal subset of four functional carriers (cellulose degrader, fermenter, syntrophic acetate-oxidizer and methanogen) that coordinated their respective metabolisms, cumulating in the overarching community phenotype of converting polysaccharides to methane. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.

microbiology↗

bioRxiv2018

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.

Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum- and multiple heterogenic strains affiliated to C. proteolyticus. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whilst in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of various carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving C. thermocellum- or Thermotogae-affiliated populations that are historically co-located. HGT material included whole saccharolytic operons and dockerin-encoding enzymatic subunits that are synonymous with cellulosomes. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life-stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated towards co-degradation of cellulose and hemicellulose. We show that C. proteolyticus, a ubiquitous keystone population, consists of closely related strains that have adapted via HGT to degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.

microbiology↗

bioRxiv2017

Comparative Genomic Evidence For Self-Domestication In Homo sapiens

This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-) genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the \"domestication syndrome\" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.

genomics↗