Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanoporebased sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing lowcomplexity microbial communities. Background Metagenomic sequencing has revolutionized the way we study and characterize microbial communities. This culture-independent technique based on shotgun sequencing has been applied in a broad range of biological fields, ranging from microbial ecology 1 to evolution 2 , or even clinical microbiology 3. In recent years, metagenomics has also become a powerful tool for recovering individual genomes directly from complex microbiomes 2,4,5 , leading to the identification and description of new-and mostly unculturable-taxa with meaningful implications 6. Illumina has been the most widely used platform for metagenomic studies. Illumina reads are characterized by their short length (75-300 bp) and high accuracy (~ 0.1% of basecalling errors) 7. When performing de novo assemblies, Illumina sequences often result in highly fragmented genomes, even when sequencing pure cultures 8,9. This is a consequence of the inability to correctly assemble genomic regions containing repetitive elements that are longer than the read length 9. This fragmentation problem is magnified when handling metagenomic sequences due to the existence of intergenomic repeats that are shared by more than one taxon present in the microbial community 10. It has to be noted that microbial communities often contain related species or sub-species in different-and unknown-abundances, resulting in extensive intergenomic overlaps that can hinder the assembly process 11,12. Third generation sequencing platforms have recently emerged as a solution to resolve ambiguous repetitive regions and to improve genome contiguity. Despite the considerable error associated to these te...

No abstract

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high-throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long-term study of the colonization process of solar panels has been performed, and our results reveal that species richness and biodiversity exhibit seasonal fluctuations and that there is a trend towards an increase or decrease of specialist (solar panel-adapted) and generalist taxa, respectively. On the former, extremophilic bacterial genera Deinococcus, Hymenobacter and Roseomonas and fungal Neocatenulostroma, Symmetrospora and Sporobolomyces tended to dominate the biocenosis; whereas Lactobacillus sp or Stemphyllium exhibited a decreasing trend. This profile was deeply altered by washing the panels with chemical agents (Virkon), but this did not lead to an increase of the solar panels efficiency. Our results show that solar panels are extreme environments that force the selection of a particular microbial community.

Ocean pollution is a worldwide environmental challenge that could be partially tackled through microbial applications. To shed light on the diversity and applications of the bacterial communities that inhabit the sediments trapped in artificial containers, we analyzed residues (polyethylene terephthalate [PET] bottles and aluminum cans) collected from the Mediterranean Sea by scanning electron microscopy and next generation sequencing. Moreover, we set a collection of culturable bacteria from the plastisphere that were screened for their ability to use PET as a carbon source. Our results reveal that Proteobacteria are the predominant phylum in all the samples and that Rhodobacteraceae, Woeseia, Actinomarinales, or Vibrio are also abundant in these residues. Moreover, we identified marine isolates with enhanced growth in the presence of PET: Aquimarina intermedia, Citricoccus spp., and Micrococcus spp. Our results suggest that the marine environment is a source of biotechnologically promising bacterial isolates that may use PET or PET additives as carbon sources.

Despite the increasing evidence of links between human gut and health, the number of gut microbiomes that have been studied to date at a country level are surprisingly low. Mediterranean countries, including some of the most long-lived and healthy countries in the world, have not been considered so far in those studies at a large scale. The main objective of this work is to characterize the gut microbiome of a healthy adult population of a Mediterranean, paradigmatically healthy country: Spain. Stool samples from 530 healthy volunteers were collected, total metagenomic DNA extracted, and the microbial profiles determined through 16S rRNA metataxonomic sequencing. Our results confirm the associations between several microbial markers and different variables, including sex, age, BMI and diet choices, and bring new insights into the relationship between microbiome and diet in the Spanish population. Remarkably, some of the associations found, such as the decrease of Faecalibacterium with age or the link of Flavonifractor with less healthy dietary habits, have been barely noticed in other large-scale cohorts. On the other hand, a range of links between microorganisms, diet, and lifestyle coincide with those reported in other populations, thus increasing the robustness of such associations and confirming the importance of these microbial markers across different countries. Overall, this study describes the Spanish “normal” microbiome, providing a solid baseline for future studies investigating the effects of gut microbiome composition and deviations in the adherence to the Mediterranean diet.