CIBERER : Spanish national network for research on rare diseases: A highly productive collaborative initiative

Altres ajuts: Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia e Innovación.CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on rare diseases (RDs) currently consists of 75 research groups belonging to universities, research centers, and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical, and cellular research of RDs. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this article, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions toward the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to RD research

Supplementary Material: Maritalea mediterranea sp. nov., isolated from marine plastic residues from Valencia, Spain

The 16S rRNA gene sequence of strain P4.10XT have been deposited in GenBank under the accession number MZ994596. The genomic assembly of strain P4.10XT has been deposited under the GenBank accession number ASM2156869v1.Peer reviewe

The wasted chewing gum bacteriome

Here we show the bacteriome of wasted chewing gums from five different countries and the microbial successions on wasted gums during three months of outdoors exposure. In addition, a collection of bacterial strains from wasted gums was set, and the biodegradation capability of different gum ingredients by the isolates was tested. Our results reveal that the oral microbiota present in gums after being chewed, characterised by the presence of species such as Streptococcus spp. or Corynebacterium spp., evolves in a few weeks to an environmental bacteriome characterised by the presence of Acinetobacter spp., Sphingomonas spp. and Pseudomonas spp. Wasted chewing gums collected worldwide contain a typical sub-aerial biofilm bacteriome, characterised by species such as Sphingomonas spp., Kocuria spp., Deinococcus spp. and Blastococcus spp. Our findings have implications for a wide range of disciplines, including forensics, contagious disease control, or bioremediation of wasted chewing gum residues.Financial support from the Spanish Government on SETH Project (Reference: RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the European CSA on biological standardization BIOROBOOST (EU Grant number 820699) are acknowledged. LS is funded by European project BIOROBOOST. ÀVV is funded with a FPU (Formación de Profesorado Universitario) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578.Peer reviewe

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition

Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture‐dependent approach yielded a 100‐isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash‐zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential.Financial support from the Spanish Government (Grant Helios, Reference: BIO2015‐66960‐C3‐1‐R co‐financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the European CSA on biological standardization BIOROBOOST (EU grant number 820699) is acknowledged. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐16‐08976. ÀVV is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578.Peer reviewe

Gillisia lutea sp. nov., isolated from marine aluminium residues from the Mediterranean sea

A novel Gram-reaction-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore forming, orange-pigmented bacterium identified as M10.2AT, was isolated from marine residues submerged on the Malva-rosa beach (València, Spain), on the western coast of the Mediterranean Sea. This strain was catalase-positive and oxidase-negative and grew under mesophilic, neutrophilic and halophilic conditions. With respect to the 16S rRNA gene sequences, M10.2AT showed similarities with Gillisia mitskevichiae DSM 19839T and Gillisia hiemivida IC154T (97.57 and 97.50 % gene sequence similarity, respectively). The genome of M10.2AT was sequenced and has been deposited in the DDBJ/ENA/GenBank databases under the accession code JAKGTH000000000. The genomic DNA G+C content was 36.13 %. Its adscription to a novel species of the genus Gillisia was confirmed by the genomic indexes average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridisation (dDDH). The major fatty acids were iso-C15 : 0, iso-C15 : 1G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to the results of this polyphasic study, strain M10.2AT represents a novel species of the genus Gillisia, for which name Gillisia lutea sp. nov. (type strain M10.2AT = CECT 30308T = DSM 112385T) is proposed.Financial support from Spanish Government (Grant SETH with reference RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia e Innovación) and European Union (MICRO4BIOGAS project with reference ID101000470 funded by European Union’s Horizon 2020 research and innovation programme) is acknowledged. E.M.M. and À.V.V. are recipients of a Formación del Profesorado Universitario (FPU) grant with references FPU17/04184 and FPU18/02578, respectively, from the Spanish Government (Ministerio de Ciencia e Innovación, Spain).Peer reviewe

A 3D printed plastic frame deeply impacts yeast cell growth

Solid State Fermentation (SSF) processes have been explored for yeast growth and protein and metabolites production. However, most of these processes lack standardization. In this work, we present a polylactic acid (PLA) 3D printed matrix that dramatically enhances yeast growth when embedded in liquid media compared to equivalent static cultures, and changes yeast expression patterns at the proteome level (data are available via ProteomeXchange with identifier PXD043759). Moreover, differences in sugar assimilation and ethanol production, as the main product of alcoholic fermentation, are observed. Our results suggest that these matrixes may be useful for a vast range of biotechnological applications based on yeast fermentation.Financial support from the Spanish Government (Grant SETH, Reference: RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades), the European CSA on biological standardization BIOROBOOST (EU grant number 820699) and Micro4Biogas (European Commission H2020 Program Ref. Grant Agreement ID 101000470) is acknowledged. EM-M and ÀV-V are funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with references FPU17/04184 and FPU18/02578, respectively.Peer reviewe

The car tank lid bacteriome: a reservoir of bacteria with potential in bioremediation of fuel

Bioprospecting of microorganisms suitable for bioremediation of fuel or oil spills is often carried out in contaminated environments such as gas stations or polluted coastal areas. Using next-generation sequencing (NGS) we analyzed the microbiota thriving below the lids of the fuel deposits of diesel and gasoline cars. The microbiome colonizing the tank lids differed from the diversity found in other hydrocarbon-polluted environments, with Proteobacteria being the dominant phylum and without clear differences between gasoline or diesel-fueled vehicles. We observed differential growth when samples were inoculated in cultures with gasoline or diesel as the main carbon source, as well as an increase in the relative abundance of the genus Pseudomonas in diesel. A collection of culturable strains was established, mostly Pseudomonas, Stenotrophomonas, Staphylococcus, and Bacillus genera. Strains belonging to Bacillus, Pseudomonas, Achromobacter, and Isoptericola genera showed a clear diesel degradation pattern when analyzed by GC-MS, suggesting their potential use for bioremediation and a possible new species of Isoptericola was further characterized as hydrocarbon degrader.Financial support from the Spanish Government (Grant SETH, ref. RTI2018-095584-B-C41-42-43-44 co-financed by ERDF and AEI-Ministerio de Ciencia e Innovación MICINN) and European Union H2020 (BioRobooST project ID 210491758; Micro4Biogas project ID101000470; MIPLACE project ref. PCI2019-111845-2, 427 Programación Conjunta Internacional 2019, AEI) are acknowledged. À.V.-V. is a recipient of a Formación de Profesorado Universitario (FPU) grant from the Spanish Ministerio de Universidades, with reference FPU18/02578. A.L.-P. is funded with a Doctorado Industrial fellowship from Ministerio de Ciencia, Innovación y Universidades, with reference DI-17-09613.Peer reviewe

Sagittula salina sp. nov., isolated from marine waste

A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9XT was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9XT were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9XT was closely related to Sagittula stellata E-37T and Sagittula marina F028-2T. The genomic G+C content of strain M10.9XT was 65.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus Sagittula . The major cellular fatty acids were C18 : 1  ω7c/C18 : 1  ω6c and C16 : 0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9XT represents a novel species of the genus Sagittula for which the name Sagittula salina sp. nov. (type strain M10.9XT=DSM 112301T=CECT 30307T) is proposed.This manuscript was financially supported by the EU funded project Micro4Biogas (FNR-12-2020 (RIA), Project ID 101000470) and the Spanish Government on SETH Project (Reference: RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades). LS is funded by European project BIOROBOOST. EMM and ÀVV are recipients of a Formación del Profesorado Universitario (FPU) grant with references FPU17/04184 and FPU18/02578, respectively, from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades, Spain).Peer reviewe

Maritalea mediterranea sp. nov., isolated from marine plastic residues

A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10XT, was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10XT was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10XT was closely related to Maritalea myrionectae DSM 19524T and Maritalea mobilis E6T (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10XT was 53.66 %. The genomic indexes average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus Maritalea. The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C18 : 1 ω7c 11-methyl. The results of this polyphasic study confirm that P4.10XT represents a novel species of the genus Maritalea, for which the name Maritalea mediterranea sp. nov. is proposed (type strain P4.10XT=CECT 30306T = DSM 112386T).Financial support from Spanish Government (SETH Project with reference RTI2018-095584-B-C41-42-43-44 co-financed by European Regional Development Fund - Ministry of Science and Innovation – State Research Agency; MIPLACE Project with reference PCI2019-111845-2 funded by Ministry of Science and Innovation – State Research Agency) and European Union (MICRO4BIOGAS project with reference ID101000470 funded by European Union's Horizon 2020 research and innovation programme) is acknowledged. E.M.M. and À.V.V. are recipients of a University Faculty Training Programme (FPU) grant with references FPU17/04184 and FPU18/02578 respectively, from the Spanish Government (Ministry of Science, Innovation and Universities).Peer reviewe

Living in a bottle: Bacteria from sediment-associated Mediterranean waste and potential growth on polyethylene terephthalate

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.Financial support by Ministerio de Ciencia e Innovación (grant SETH ref. RTI2018‐095584‐B‐C41‐42‐43‐44 co‐financed by FEDER), the European Union H2020 (BIOROBOOST project ID 210491758; Micro4Biogas project ref.101000470), Agencia Estatal de la Innovación AEI (MIPLACE projectref. PCI2019‐111845‐2), and Agència Valenciana de la Innovación AVI (ENTOMOPLAST project ref. INNEST/2021/334) are acknowl-edged. Àngela Vidal‐Verdú and Esther Molina‐Menor are funded with a Formación del Profesorado Universitario grant from the Spanish Ministerio de Ciencia, Innovación y Universidades with references FPU18/02578 and FPU17/04184, respectively. Adriel Latorre‐Pérezis a recipient of a Doctorado Industrial fellowship from the Spanish Ministerio de Ciencia, Innovación y Universidades (reference DI‐17‐09613).Peer reviewe