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Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.

The pks island is one of the most prevalent pathogenicity islands among the Escherichia coli strains that colonize the colon of colorectal carcinoma (CRC) patients. This pathogenic island encodes the production of a nonribosomal polyketide-peptide named colibactin, which induces double-strand breaks in DNA molecules. Detection or even depletion of this pks -producing bacteria could help to understand the role of these strains in the context of CRC. In this work, we performed a large-scale in silico screening of the pks cluster in more than 6,000 isolates of E. coli . The results obtained reveal that not all the pks -detected strains could produce a functional genotoxin and, using antibodies against pks -specific peptides from surface cell proteins, a methodology for detection and depletion of pks + bacteria in gut microbiotas was proposed. With our method, we were able to deplete a human gut microbiota of this pks + strains, opening the door to strain-directed microbiota modification and intervention studies that allow us to understand the relation between these genotoxic strains and some gastrointestinal diseases. IMPORTANCE The human gut microbiome has also been hypothesized to play a crucial role in the development and progression of colorectal carcinoma (CRC). Between the microorganisms of this community, the Escherichia coli strains carrying the pks genomic island were shown to be capable of promoting colon tumorigenesis in a colorectal cancer mouse model, and their presence seems to be directly related to a distinct mutational signature in patients suffering CRC. This work proposes a novel method for the detection and depletion of pks -carrying bacteria in human gut microbiotas. In contrast to methods based on probes, this methodology allows the depletion of low-abundance bacterial strains maintaining the viability of both targeted and non-targeted fractions of the microbiota, allowing the study of the contribution of these pks -carrying strains to different diseases, such as CRC, and their role in other physiological, metabolic or immune processes.

There is increasing interest in deciphering the contribution of gut microbiota species to health and disease amelioration. The approach proposed herein provides a novel and affordable strategy to probe deeply into microbiota-host interactions by strategically modifying the relative abundance of specific gut microbes, hence facilitating the study of their contribution to a given trait of the microbiota.

The Spanish Parliament seems to play a secondary role in “risk management”, contrary to an overarching and scarcely controlled Executive Power. This trend can be observed in rules regulating emergency powers, but also in ordinary rules related to risk. It can be explained to a great extent by the current interpretation and legal foundation given to the so-called “precautionary principle”, a norm that inspires and gives coherence to ordinary and extraordinary rules regulating uncertain risks. In this paper, we briefly analyze its origins, its implementation in Spain and the most widely accepted definition given by scholars and the Courts to the precautionary principle. We also analyze potential objections to the current version of the principle, which has led to an improper subordination of the Parliament in this field. Considering those objections and the inaccurate legal foundation hitherto given to precautionary norms, we try to reformulate said foundation to make the Parliament regain a leading role in “risk management”, which in fact amounts to much more than just “managing risks” (i.e. risks shall not only be managed, but also “institutionally channeled” or negotiated). The institutional architecture designed by the Spanish Constitution imposes it. We will also derive from it some practical consequences and potential improvements for the Parliament, related to legislative technique in rules regulating uncertain risks and integration of technical and scientific risk assessment into legislative procedures.

Glycoside hydrolases are responsible for the enzymatic deconstruction of complex carbohydrates. Most of the families are known to conserve the catalytic machinery and molecular mechanisms. This work introduces a new method to predict glycolytic abilities in sequenced genomes and thus, gain a better understanding of how to target specific carbohydrates and identify potentially interesting sources of specialised enzymes. Genome sequences are aligned to those of organisms with expertly curated glycolytic abilities. Clustering of homology scores helps identify organisms that share common abilities and the most promising organisms regarding specific glycolytic abilities. The method has been applied to members of the bacterial families Ruminococcaceae (39 genera), Eubacteriaceae (11 genera) and Lachnospiraceae (59 genera), which hold major representatives of the human gut microbiota. The method predicted the potential presence of glycoside hydrolases in 1701 species of these genera. Here, the validity and practical usefulness of the method is discussed based on the predictions obtained for members of the genus Ruminococcus. Results were consistent with existing literature and offer useful, complementary insights to comparative genomics and physiological testing. The implementation of the Gleukos web portal (http://sing-group.org/gleukos) offers a public service to those interested in targeting microbial carbohydrate metabolism for biotechnological and health applications., SING group thanks CITI (Centro de Investigacion, Transferencia e Innovacion) from the University of Vigo for hosting its IT infrastructure. Funding: This work was funded by the Spanish “Ministerio de Economıa y Competitividad—Agencia Estatal de Investigacion” (grant AGL2016-78311-R; AEI/ FEDER, UE) and by the grant IDI/2018/000236 from the Government of the Principality of Asturias. This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and the Consellerıa de Educacion, Universidades e Formacion Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group. Conflict of interest: Abelardo Margolles and Borja Sanchez are scientific founders of Microviable Therapeutics SL. The rest of the authors have no conflicts of interest to declare, info:eu-repo/semantics/publishedVersion

A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002, belonging to the family Ruminococcaceae, was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002, though with average nucleotide identity values below 90%. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002 is phylogenetically distinct from other species within the genus Ruminococcus. Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002 strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae. Strain IPLA60002 (=DSM 110008=LMG 31505) is proposed as the type strain of Ruminococcoides bili., This study was supported by the: Tenovus (GB) Principle Award Recipient: ElenaConti Rural and Environment Science and Analytical Services Division (GB) (Award SG-RESAS) Principle Award Recipient: SylviaH. Duncan Fundación para el Fomento en Asturias de la Investigación Científica Aplicada y la Tecnología (Award IDI/2018/000236) Principle Award Recipient: NotApplicable Ministerio de Economía y Competitividad (Award Ramón y Cajal” program (RYC-2016-19726)) Principle Award Recipient: SusanaDelgado Ministerio de Economía y Competitividad (Award FPI Predoctoral Grant BES-2014-068736) Principle Award Recipient: NataliaMolinero Ministerio de Economía y Competitividad (Award AGL2013-44761-P) Principle Award Recipient: AbelardoMargolles

[en]Convergence of a stochastic process is an intrinsic property quite relevant for its successful practical for example for the function optimization problem. Lyapunov functions are widely used as tools to prove convergence of optimization procedures. However, identifying a Lyapunov function for a specific stochastic process is a difficult and creative task. This work aims to provide a geometric explanation to convergence results and to state and identify conditions for the convergence of not exclusively optimization methods but any stochastic process. Basically, we relate the expected directions set of a stochastic process with the half-space of a conservative vector field, concepts defined along the text. After some reasonable conditions, it is possible to assure convergence when the expected direction resembles enough to some vector field. We translate two existent and useful convergence results into convergence of processes that resemble to particular conservative vector fields. This geometric point of view could make it easier to identify Lyapunov functions for new stochastic processes which we would like to prove its convergence, This work is partially supported by the projects Crowd4SDG and Humane-AI-net, which have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreements No. 872944 and No. 952026, respectively. This work is also partially supported by the project CI-SUSTAIN funded by the Spanish Ministry of Science and Innovation (PID2019-104156GB-I00).

30 Páginas.-- 6 Figuras.-- 1 Tabla, In this work, we have used a metataxonomic analysis to study the bacterial biodiversity in three types of commercial dressing and ingredients habitually used in table olive packaging. The bioinformatics analysis showed that salt samples (marine and spring) had the highest biodiversity indexes, followed by the aromatic herbs (thyme, oregano, and fennel) and finally by fermented dressing samples (garlic, pepper, and pepper paste). In salt samples, a significant high presence of Cytophagia, Sphingobacteria, Deltaproteobacteria and Halobacteria classes was observed. On the contrary, the presence of Bacilli class in fermented dressing samples was significantly higher compared to the other samples. Finally, the abundance of Gammaproteobacteria was statistically higher in the samples of herbs. At genus or family taxonomic level, Pseudomonas and diverse non-assigned genus of the Enterobacteriaceae family predominated in many samples of herbs. In fermented dressing samples, diverse genus belonging to the Enterobacteriaceae family appeared in a high relative abundance in pepper paste and garlic, and presence of Vibrio sp. was detected in pepper. However, Lactobacillus, Weisella, and Pediococcus were the predominant genera found in many of these fermented samples. Salinibacter was the most representative genus in both types of salt samples. Multivariate analysis (PCA) of the metataxonomic data sets discriminated well the samples belonging to the three different groups, showing a high proportion of sequences shared by samples-group. This survey reports for the first time the presence of new bacterial species not previously related with table olive processing, as well as the presence of others which could compromise the stability of olive packaging., The research was funded by the Spanish Government (Project OliFilm AGL-2013-48300-R: www.olifilm.science.com.es) AB-C and JB-G thanks the Spanish Ministry of Economy and Competitiveness for their FPI grant and JDC-Incorp. contract, respectively. BC-D thanks the Andalusian Ministry of Economy, Science and Innovation by her pre-doctoral contract.

Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity., Tis work was funded by the project IDE/2016/000282 from IDEPA (“Instituto de Desarrollo Empresarial of the Principality of Asturias”), which is partially supported by FEDER funds, SME-2017-0946-10 from MEIC (Ministry of Economy, Industry and competitiveness), SNEO 20171062 from CDTI (Centre for the Development of Industrial Technology) and a collaboration contract between Microviable Terapeutics SL. and the Consejo Superior de Investigaciones Científcas (Spanish National Research Council - CSIC).

Peptides encrypted in the intestinal microbial-exoproteome mediate the host-microbiota crosstalk, which is disrupted in inflammatory bowel disease (IBD). Here, the MAHMI database was used for the identification of 20 novel intestinal bacterial peptides. Our results revealed that serum IgA levels directed towards the peptides, but not IgG, discriminated healthy controls from IBD patients. Indeed, they also differentiated patients with ulcerative colitis from Crohńs disease and, within them, patients with and without intestinal inflammation. All peptides were immunomodulatory as they changed the intestinal cytokine milieu following human lamina propria mononuclear cells culture (with/out LPS), revealing a Bifidobacterium longum subsp. longum peptide with the highest tolerogenic properties. Therefore, bacterial peptides encrypted in the human gut metaproteome may have utility as non-invasive biomarkers to aid on IBD diagnosis and monitoring. These peptides also display immunomodulatory effects on the intestinal mucosa revealing them as novel functional compounds for non-drug therapeutic strategies in IBD., This research was funded by the Spanish Ministry of Economy (SAF2014-56642-JIN), the Spanish Ministry of Health (PIE13/00041), ACAD (Asociación Castellana de Aparato Digestivo), GETECCU (Grupo Español de Trabajo en Enfermedad de Crohn y Colitis Ulcerosa) and the Community of Madrid (Consejería de Educación, Juventud y Deporte, Programa de Garantía Juvenil 2015 y 2016). SFT acknowledges the “Instituto de Salud Carlos III” for his “Sara Borrell” fellowship (CD17/00014). BS acknowledges the support of the “Programa Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad” (AGL2013-44039R) for implementing the MAHMI database.

Bile salt hydrolase (BSH) activity is a desirable trait in putative probiotic bacteria, such as those belonging to the Bifidobacterium genus. On the one hand, bile salt hydrolysis is considered to represent a bile detoxification mechanism for gut commensal bacteria and thus the presence of this activity was believed to be a predictor of bile tolerance of putative probiotic strains. On the other hand, it has recently been revealed that chemical modifications of the bile acid pool performed by the gut microbiota strongly impact on host health. This explains the increasing interest to investigate the role played by bile-modifying enzymes of gut commensals on lowering cholesterol levels, on modulating gut inflammation or on influencing the development of cancer or metabolic disorders. This chapter compiles qualitative and quantitative methods to analyse BSH activity in bifidobacteria, though they could be adapted to other bacterial groups of interest.

Dihydrochalcones, phlorizin (PZ) and its aglycone phloretin (PT), have evidenced immunomodulatory effects through several mechanisms. However, the differential metabolic signatures that lead to these properties are largely unknown. Since macrophages play an important role in the immune response, our study aimed to characterise human THP-1 macrophages under PZ and PT exposure. A multiplatform-based untargeted metabolomics approach was used to reveal metabolites associated with the anti-inflammatory mechanisms triggered by the dihydrochalcones in LPS-stimulated macrophages, for the first time. Results showed differential phenotypic response in macrophages for all treatments. Dihydrochalcone treatment in LPS-stimulated macrophages mimics the response under normal conditions, suggesting inhibition of LPS response. Antagonistic effects of dihydrochalcones against LPS was mainly observed in glycerophospholipid and sphingolipid metabolism besides promoting amino acid biosynthesis. Moreover, PT showed greater metabolic activity than PZ. Overall, the findings of this study yielded knowledge about the mechanisms of action PZ and PT at metabolic level in modulating inflammatory response in human cells., This research was funded by EU FEDER funds, Interreg España-Portugal Programme, under the framework of the Project: ref. 0377_IBERPHENOL_6_E; by Xunta de Galicia funds, Spain (CITACA Strategic Partnership, Reference: ED431E 2018/07) and also supported by UIDB/50006/2020 and PTDC/SAU-NUT/30448/2017 with funding from FCT/MCTES through national funds. I. F. acknowledge her Fundação para a Ciência e Tecnologia (FCT) research contract (SFRH/BPD/86173/2012).

This work describes a new procedure that allows the targeted modification of the human gut microbiota by using antibodies raised against bacterial surface-associated proteins specific to the microorganism of interest. To this end, a polyclonal antibody recognising the surface-associated protein Surface Layer Protein A of Lactobacillus acidophilus DSM20079 was developed. By conjugating this antibody with fluorescent probes and magnetic particles, we were able to specifically identify this bacterium both in a synthetic, and in real gut microbiotas by means of a flow cytometry approach. Further, we demonstrated the applicability of this antibody to deplete complex human gut microbiotas from L. acidophilus in a single step. L. acidophilus was found to interact with other bacteria both in synthetic and in real microbiotas, as reflected by its concomitant depletion together with other species. Further optimization of the procedure including a trypsin step enabled to achieve the selective and complete isolation of this species. Depleting a single species from a gut microbiota, using antibodies recognizing specific cell surface elements of the target organism, will open up novel ways to tackle research on the specific immunomodulatory and metabolic contributions of a bacterium of interest in the context of a complex human gut microbiota, including the investigation into therapeutic applications by adding/depleting a key bacterium. This represents the first work in which an antibody/flow-cytometry based application enabled the targeted edition of human gut microbiotas, and represents the basis for the design of precision microbiome-based therapies., Our work is supported by the Spanish "Programa Estatal de Investigacian, Desarrollo e Inovacion Orientada a los Retos de la Sociedad" (grant AGL2016-78311-R and contract BES-2017-080978, funded by AEI/FEDER, UE), the Asociación Española Contra el Cáncer (AECC; Grant PS-2016) and by the Asturias Regional Plan I + D + i for research groups (FICYT-IDI/2018/000236, funded by PCTI Gobierno del Principado de Asturias/FEDER, UE).

Bile salt hydrolase (BSH) activity is a desirable trait in putative probiotic bacteria, such as those belonging to the Bifidobacterium genus. On the one hand, bile salt hydrolysis is considered to represent a bile detoxification mechanism for gut commensal bacteria and thus the presence of this activity was believed to be a predictor of bile tolerance of putative probiotic strains. On the other hand, it has recently been revealed that chemical modifications of the bile acid pool performed by the gut microbiota strongly impact on host health. This explains the increasing interest to investigate the role played by bile-modifying enzymes of gut commensals on lowering cholesterol levels, on modulating gut inflammation or on influencing the development of cancer or metabolic disorders. This chapter compiles qualitative and quantitative methods to analyse BSH activity in bifidobacteria, though they could be adapted to other bacterial groups of interest.

In recent years the role of extracellular vesicles (EVs) of Gram-positive bacteria in host-microbe cross-talk has become increasingly appreciated, although the knowledge of their biogenesis, release and host-uptake is still limited. The aim of this study was to characterize the EVs released by the dairy isolate Lactiplantibacillus plantarum BGAN8 and to gain an insight into the putative mechanism of EVs uptake by intestinal epithelial cells. The cryo-TEM observation undoubtedly demonstrated the release of EVs (20 to 140 nm) from the surface of BGAN8, with exopolysaccharides seems to be part of EVs surface. The proteomic analysis revealed that the EVs are enriched in enzymes involved in central metabolic pathways, such as glycolysis, and in membrane components with the most abundant proteins belonging to amino acid/peptide ABC transporters. Putative internalization pathways were evaluated in time-course internalization experiments with non-polarized HT29 cells in the presence of inhibitors of endocytic pathways: chlorpromazine and dynasore (inhibitors of clathrin-mediated endocytosis—CME) and filipin III and nystatin (disrupting lipid rafts). For the first time, our results revealed that the internalization was specifically inhibited by dynasore and chlorpromazine but not by filipin III and nystatin implying that one of the entries of L. plantarum vesicles was through CME pathway., Te work carried bout at IPLA-CSIC was funded by the Project IDI_2018_000236 (PCTI Govern of Principado de Asturias / FEDER,, UE). Work performed at the University of Barcelona was fnanced by the Project AGL2016-79113-R (AEI/FEDER, UE). S. Sokovic Bajic acknowledges her FEMS and IUBMB Grants for funding two (3-months) stays at IPLA-CSIC.

Apples represent a significant source of dietary phenolic compounds with evidenced anti-inflammatory and immunomodulatory activities. Nevertheless, the effect of the whole apple matrix on human macrophages is unknown. In this context, our study attempts to evaluate the effect of apple-derived phenolic compounds-rich extracts (pulp, peel and leaf) on IL-1β production in THP-1-differentiated macrophages and derived metabolic alterations through untargeted metabolomics. Our results have showed that apple pulp treatment inhibited the release of the pro-inflammatory cytokine IL-1β induced by LPS in THP-1 macrophages by ELISA analysis. Metabolomics demonstrate that different proportions of phenolic compounds led to differential alterations in the metabolism of THP-1 macrophages. Indeed, apple extracts promoted alterations in lipid, carbohydrate, amino acid and vitamins as well as cofactors metabolism. Specifically, leaf extracts were characterized by alteration of galactose metabolism while the extracts derived from the fruit showed predominant alterations in lipids metabolism. All extracts mimicked the response observed under normal conditions in LPS-stimulated macrophages, inhibiting LPS response. Thus, the phenolic enriched extracts from apples will be a good source of natural compounds with a beneficial effect against inflammation, and they may be applied as a food supplement and/or functional ingredient for the treatment of inflammatory diseases., This research was funded by EU FEDER funds, Interreg España-Portugal Programme, under the framework of the Project: ref. 0377_IBERPHENOL_6_E and also supported by UIDB/50006/2020 and PTDC/SAU-NUT/30448/2017 with funding from FCT/MCTES through national funds. I. F. ac- knowledge her Fundação para a Ciência e Tecnologia (FCT) research contract (SFRH/BPD/86173/2012).

Describir e​l se​ntido de vida de siete habitantes de calle de la ciudad de Medellín, en el 2020-2. La presente investigación pretende describir el sentido de vida de siete habitantes de calle de laciudad de Medellín, en el 2020-2, para este propósito se utilizó una encuesta semiestructurada lacual se aplicó a siete participantes con la cual se preguntó por el sentido de sus vidas, así como siconsideraban que la vida tiene uno. Esta investigación es de enfoque cualitativo, diseñodescriptivo y cuenta con metodología fenomenológica hermenéutica.Los resultados que surgieron tras realizar el análisis, es que hay diferentes factores queinfluyen en el sentido de vida del habitante de calle, así como también se pueden presentar variosal mismo tiempo, tales como la religión, que se presenta como un paliativo a los sufrimientos quepadecen y los ayuda a pensar en un futuro mejor y alejado de las calles. El progreso personal,económico y material. El bienestar, como gozar de buena salud, alimentación, amistades. Lafamilia, como sustento psicológico y moral. Y las drogas, que se presenta como un impedimentopara abandonar la vida en las calles, pero a la vez, a raíz de la adicción es el motivo de despertar.De estos diversos factores, principalmente fueron la religión, el progreso y la familia los que sepresentaron como el sentido de vida de los habitantes de calle participantes de esta investigación.

Bacteria-host interactions are mediated by different microbial associated molecular patterns which are most often surface structures such as, among others, exopolysaccharides (EPSs). In this work, the capability of two isogenic EPS-producing Bifidobacterium animalis subsp. lactis strains to modulate the gut microbiota of healthy mice, was assessed. Each strain produces a different type of polymer; the ropy strain S89L synthesized a rhamnose-rich, high-molecular weight EPS in highest abundance than the non-ropy DMS10140 one. BALB/c mice were orally fed for 10 days with milk-bifidobacterial suspensions and followed afterward for 7 post-intervention days (wash-out period). The colonic content of mice was collected in several sampling points to perform a metataxonomic analysis. In addition, the influence of specific microbial clades, apparently stimulated by the ropy and non-ropy strains, on mouse plasmatic cytokine levels was investigated through hierarchical association testing. Analysis of 16S rRNA gene sequences showed that the abundance of Firmicutes phylum significantly increased 7 days after cessing the treatment with both strains. The relative abundance of Alloprevotella genus also rose, but after shorter post-treatment times (3 days for both DMS10140 and S89L strains). Some bacterial clades were specifically modulated by one or another strain. As such, the non-ropy DMS10140 strain exerted a significant influence on Intestinomonas genus, which increased after 4 post-administration days. On the other hand, feeding with the ropy strain S89L led to an increase in sequences of Faecalibaculum genus at 4 post-treatment days, while the abundance of Erysipelotrichaceae and Lactobacillaceae families increased for prolonged times. Association testing revealed that several lactobacilli and bifidobacterial significantly stimulated by ropy S89L strain were positively associated with the levels of certain cytokines, including IL-5 and IL-27. These results highlight relevant changes in mice gut microbiota produced after administration of the ropy S89L strain that were associated to a potential immune modulation effect.

Supplementary data to this article can be found online at https:// doi.org/10.1016/j.jff.2020.103969., This work supports the massive presence of potential immunomodulatory peptides in the human gut metaproteome. These peptides were identified through the MAHMI database as potentially anti-inflammatory, and sixteen of them synthesized for characterize their mechanism of action. From them, peptide HM14 was encrypted in an extracellular protein produced by Bifidobacterium longum, a common member of the human microbiota, and displayed the highest anti-inflammatory capability. Molecular mechanism of action of HM14 pointed to a specific interaction between this immunomodulatory peptide and antigen presenting cells, which resulted in a higher formation of iTreg cells. Moreover, HM14 was effective in decreasing pro-inflammatory parameters in PBMCs isolated from a cohort of Crohns patients. Finally, non-targeted metabolomics confirmed the ability of HM14 to modulate the metabolic activity of PBMCs to fulfil its energy and biosynthetic requirements. Overall, our combined in silico/multiomics approach supports the human gut metaproteome as a source for immunomodulatory peptides., Our work is supported by the Spanish “Programa Estatal de Investigación. Desarrollo e Innovación Orientada a los Retos de la Sociedad” (grants AGL2013-44761-P and AGL2016-78311-R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales”, Grant PS-2016), by the Asturias Regional Plan I + D + i for research groups (FYCYT-IDI/2018/000236) and by the Autonomic “Investigadores Emerxentes do Sistema Universitario de Galicia” (Grant EM2014/046). This work was partially supported by the Consellería de Educación. Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group. Finally, the authors wish to thank Jaume Morales and Rubén García form Agilent Technologies for technical support., info:eu-repo/semantics/publishedVersion

© 2020 by the authors., Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest., The research included in the present work was funded by the grants AGL2016-78311-R (funded by AEI/FEDER, UE), RTI2018-095021-J-I00 (funded by MCIU/AEI/FEDER, UE), and IDI/2018/000236 (funded by PCTI Gobierno del Principado de Asturias/FEDER, UE). This study was supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group, the “Centro singular de investigación de Galicia” (accreditation 2019-2022) and the European Union (European Regional Development Fund—ERDF)-Ref. ED431G2019/06, and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte.

COVID-2019 has progressed in around 10-15% of patients to an acute respiratory distress syndrome characterized by extensive pulmonary inflammation and elevated production of pro-inflammatory cytokines. Neutrophil activation seems to be crucial in the initiation and perpetuation of this exacerbated lung inflammation. However, the precise mechanisms by which this activation occurs remain yet elusive. To this end, this in silico study tried to identify potential proinflammatory inducing peptides (PIPs) produced by the action of the elastase released in neutrophil-extracellular traps over SARS-CoV-2 particles. We found nine potential PIPs exclusive from the SARS-CoV-2, showing homology against T cell recognition epitopes. Moreover, 78 percent of these exclusive PIPs were found produced by the enzymatic cleavage on the spike glycoproteins, suggesting that high PIP concentrations might be released following SARS-CoV-2 huge replication rate. Therefore, these PIPs might play a role in the exacerbated inflammatory response observed in some patients.

Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

Lactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus acidophilus DSM20079T (DSM20079) to healthy piglets resulted in plasmatic increases of the anti-inflammatory IL10, whilst IL12 and the pro-inflammatory ratio IL12+TNF/IL10 decreased. The extracellular protein fraction of DSM20079 was identified as the responsible for the crosstalk interaction that elicited these tolerogenic effects. This strain was able to activate innate immune pathways in dendritic cells and to decrease the production of pro-inflammatory cytokines in both CD4+/CD8+ T cell subsets in healthy donors and in Crohns Disease patients. The tolerogenic effect exerted by the extracellular proteins of this strain suggests their potential use as coadjutant for therapeutic applications targeting chronic inflammatory illnesses., Our work is supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (grant AGL2016-78311-R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer ColoRectal a partir de secuencias genéticas de microbiomas intestinales”, Grant PS-2016) and by the Asturias Regional Plan I+D+i for research groups (FYCYT-IDI/2018/000236). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. LJR was supported by the Principado de Asturias, PCTI 2018–2020 (GRUPIN: IDI2018-000237) and FEDER. This work was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group., info:eu-repo/semantics/publishedVersion

Bacteria-host interactions are mediated by different microbial associated molecular patterns which are most often surface structures such as, among others, exopolysaccharides (EPSs). In this work, the capability of two isogenic EPS-producing Bifidobacterium animalis subsp. lactis strains to modulate the gut microbiota of healthy mice, was assessed. Each strain produces a different type of polymer; the ropy strain S89L synthesized a rhamnose-rich, high-molecular weight EPS in highest abundance than the non-ropy DMS10140 one. BALB/c mice were orally fed for 10 days with milk-bifidobacterial suspensions and followed afterward for 7 post-intervention days (wash-out period). The colonic content of mice was collected in several sampling points to perform a metataxonomic analysis. In addition, the influence of specific microbial clades, apparently stimulated by the ropy and non-ropy strains, on mouse plasmatic cytokine levels was investigated through hierarchical association testing. Analysis of 16S rRNA gene sequences showed that the abundance of Firmicutes phylum significantly increased 7 days after cessing the treatment with both strains. The relative abundance of Alloprevotella genus also rose, but after shorter post-treatment times (3 days for both DMS10140 and S89L strains). Some bacterial clades were specifically modulated by one or another strain. As such, the non-ropy DMS10140 strain exerted a significant influence on Intestinomonas genus, which increased after 4 post-administration days. On the other hand, feeding with the ropy strain S89L led to an increase in sequences of Faecalibaculum genus at 4 post-treatment days, while the abundance of Erysipelotrichaceae and Lactobacillaceae families increased for prolonged times. Association testing revealed that several lactobacilli and bifidobacterial significantly stimulated by ropy S89L strain were positively associated with the levels of certain cytokines, including IL-5 and IL-27. These results highlight relevant changes in mice gut microbiota produced after administration of the ropy S89L strain that were associated to a potential immune modulation effect., The MicroHealth group acknowledge the projects AGL2015- 64901-R (AEI/FEDER, UE) and RTI2018-096339-B-I00 (MCIU/AEI/FEDER, UE), as well as the grant IDI/2018/000236 from the “Plan for Research, Development and Innovation of the Principado de Asturias 2018–2020” co-financed by the European Regional Development Funds (FEDER). NC-B thanks her FPI fellowship to the MINECO (BES2013-063984). CS acknowledges his Postdoctoral research contract funded by the “Instituto de Investigación Sanitaria del Principado de Asturias” (ISPA). The CIBER-EHD was funded by the Instituto de Salud Carlos III. PDE and LH-G are predoctoral fellows from University of Granada of “Programa de Doctorado: Medicina Clínica y Salud Pública.” We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Certain non-digestible oligosaccharides (NDO) are specifically fermented by bifidobacteria along the human gastrointestinal tract, selectively favoring their growth and the production of health-promoting metabolites. In the present study, the ability of the probiotic strain Bifidobacterium longum subsp. infantis CECT7210 (herein referred to as B. infantis IM-1&reg, ) to utilize a large range of oligosaccharides, or a mixture of oligosaccharides, was investigated. The strain was able to utilize all prebiotics screened. However, galactooligosaccharides (GOS), and GOS-containing mixtures, effectively increased its growth to a higher extent than the other prebiotics. The best synbiotic combination was used to examine the antimicrobial activity against Escherichia coli, Cronobacter sakazakii, Listeria monocytogenes and Clostridium difficile in co-culture experiments. C. difficile was inhibited by the synbiotic, but it failed to inhibit E. coli. Moreover, Cr. sakazakii growth decreased during co-culture with B. infantis IM-1&reg, Furthermore, adhesion experiments using the intestinal cell line HT29 showed that the strain IM-1&reg, was able to displace some pathogens from the enterocyte layer, especially Cr. sakazakii and Salmonella enterica, and prevented the adhesion of Cr. sakazakii and Shigella sonnei. In conclusion, a new synbiotic (probiotic strain B. infantis IM-1&reg, and GOS) appears to be a potential effective supplement for maintaining infant health. However, further studies are needed to go more deeply into the mechanisms that allow B.infantis IM-1&reg, to compete with enteropathogens.

© 2020 by the authors., Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. The probiotic microorganisms most commonly used in the food and pharmacy industry belong to Lactobacillus and Bifidobacterium, and several strains of these genera have demonstrated beneficial attributes. In addition, some other intestinal bacteria inhabiting the human microbiota, such as Faecalibacterium prausnitzii and Akkermansia muciniphila, have recently been discovered and are able to display health-promoting effects in animal and human trials. The beneficial properties of probiotics have been known for a long time, although little is known about the molecular mechanisms and the molecules responsible for their effects. However, in recent years, advances in microbiome studies, and the use of novel analytical and molecular techniques have allowed a deeper insight into their effects at the molecular level. This review summarizes the current knowledge of some of the molecules of probiotics and other intestinal commensal bacteria responsible for their immunomodulatory effect, focusing on those with more solid scientific evidence., Funding in our group is supported by the grants IDI/2018/000236 from the Principality of Asturias, AGL2016-78311-R (AEI/FEDER UE) from the Ministry of Economy and Competitiveness (MINECO), and RTI2018-096339-B-I00 and RTI2018-095021-J-I00 (MCIU/AEI/FEDER, UE).

Background Some patients complain that eating lettuce, gives them gas and abdominal distention. Our aim was to determine to what extent the patients' assertion is sustained by evidence. Methods An in vitro study measured the amount of gas produced during the process of fermentation by a preparation of human colonic microbiota (n = 3) of predigested lettuce, as compared to beans, a high gas‐releasing substrate, to meat, a low gas‐releasing substrate, and to a nutrient‐free negative control. A clinical study in patients complaining of abdominal distention after eating lettuce (n = 12) measured the amount of intestinal gas and the morphometric configuration of the abdominal cavity in abdominal CT scans during an episode of lettuce‐induced distension as compared to basal conditions. Key Results Gas production by microbiota fermentation of lettuce in vitro was similar to that of meat (P = .44), lower than that of beans (by 78 ± 15%; P, In some patients lettuce produces abdominal distension, which is not related to gas, but rather to an uncontrolled reaction of the abdominal muscles and the diaphragm. Hence, learning to control the abdominal muscles may prevent distension with no need of dietary restrictions.

[Background] The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of adequate methodologies to assess molecular studies. Although a few reports have described the biliary microbiota in some hepatobiliary diseases, the bile microbiota of healthy individuals has not been described. With this in mind, the goal of the present study was to generate fundamental knowledge on the composition and activity of the human bile microbiota, as well as establishing its potential relationship with human bile-related disorders., [Results] Human bile samples from the gallbladder of individuals from a control group, without any record of hepatobiliary disorder, were obtained from liver donors during liver transplantation surgery. A bile DNA extraction method was optimized together with a quantitative PCR (qPCR) assay for determining the bacterial load. This allows the selection of samples to perform functional metagenomic analysis. Bile samples from the gallbladder of individuals suffering from lithiasis were collected during gallbladder resection and the microbial profiles assessed, using a 16S rRNA gene-based sequencing analysis, and compared with those of the control group. Additionally, the metabolic profile of the samples was analyzed by nuclear magnetic resonance (NMR). We detected, for the first time, bacterial communities in gallbladder samples of individuals without any hepatobiliary pathology. In the biliary microecosystem, the main bacterial phyla were represented by Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Significant differences in the relative abundance of different taxa of both groups were found. Sequences belonging to the family Propionibacteriaceae were more abundant in bile samples from control subjects; meanwhile, in patients with cholelithiasis members of the families Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, and Veillonellaceae were more frequently detected. Furthermore, the metabolomics analysis showed that the two study groups have different metabolic profiles., [Conclusions] Our results indicate that the gallbladder of human individuals, without diagnosed hepatobiliary pathology, harbors a microbial ecosystem that is described for the first time in this study. Its bacterial representatives and metabolites are different from those detected in people suffering from cholelithiasis. In this regard, since liver donors have been subjected to the specific conditions of the hospital’s intensive care unit, including an antibiotic treatment, we must be cautious in stating that their bile samples contain a physiologically normal biliary microbiome. In any case, our results open up new possibilities to discover bacterial functions in a microbial ecosystem that has not previously been explored., The study was supported by MINECO under grant number AGL2013-44761-P. Lorena Ruiz is a postdoctoral researcher supported by the Juan de la Cierva Postdoctoral Trainee Program (IJCI-2015-23196), and Natalia Molinero is the recipient of an FPI Predoctoral Grant (BES-2014-068736).

Background Changes produced in the upper airway after rapid maxillary expansion makes this procedure a therapeutic option for treating sleep apnea-hypopnea syndrome (SAHS) in children. The objective of this systematic review and meta-analysis was to analyze the evidence available for the effects of rapid maxillary expansion (RME) on SAHS, analyzing changes produced in oximetric variables: apnea-hypopnea index (AHI); oxygen saturation (SO2); sleep efficiency (SE), total sleep time (TST), percentage of rapid eye movement (REM) phase; and arousal index (AI). Material and Methods An electronic search was conducted in the PubMed, Scopus, Embase, and Cochrane databases, and in grey literature (Opengrey). No limit was placed on publication date or language. Inclusion criteria were: patients in growth with sleep apnea who underwent rapid maxillary expansion with oximetric values registered before and after treatment. Articles with patient sample sizes

This work presents a novel in silico approach to the prediction and characterisation of the glycolytic capacities of the beneficial intestinal bacterium Faecalibacterium prausnitzii. Available F. prausnitzii genomes were explored taking the glycolytic capacities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as reference. The comparison of the generated glycolytic profiles offered insights into the particular capabilities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as well as the potential of the rest of strains. Glycoside hydrolases were mostly detected in the pathways responsible for the starch and sucrose metabolism and the biosynthesis of secondary metabolites, but this analysis also identified some other potentially interesting, but still uncharacterised activities, such as several hexosyltransferases and some hydrolases. Gene neighbourhood maps offered additional understanding of the genes coding for relevant glycoside hydrolases. Although information about the carbohydrate preferences of F. prausnitzii is scarce, the in silico metabolic predictions were consistent with previous knowledge about the impact of fermentable sugars on the growth promotion and metabolism of F. prausnitzii. So, while the predictions still need to be validated using culturing methods, the approach holds the potential to be reproduced and scaled to accommodate the analysis of other strains (or even families and genus) as well as other metabolic activities. This will allow the exploration of novel methodologies to design or obtain targeted probiotics for F. prausnitzii and other strains of interest., This work was supported by the Spanish "Programa Estatal de Investigacion, Desarrollo e Innovacion Orientada a los Retos de la Sociedad" (Grant AGL2016-78311-R); and, the Asociacion Espanola Contra el Cancer (" Obtencion de peptidos bioactivos contra el Cancer Colo-Rectal a partir de secuencias geneticas de microbiomas intestinales," Grant PS-2016). This work was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684). This work was partially supported by the Conselleria de Educacion, Universidades e Formacion Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group., info:eu-repo/semantics/publishedVersion

Background: There is increasing evidence of the key role that the gut microbiota plays in inflammatory diseases. Objectives: To identify differences in the faecal microbial composition of patients with psoriasis compared with healthy individuals in order to unravel the microbiota profiling in this autoimmune disease. Methods: 16S rRNA gene sequencing and bioinformatic analyses were performed with the total DNA extracted from the faecal microbiota of 19 patients with psoriasis and 20 healthy individuals from the same geographic location. Results: Gut microbiota composition of patients with psoriasis displayed a lower diversity and different relative abundance of certain bacterial taxa compared with healthy individuals. Conclusions: The gut microbiota profile of patients with psoriasis displayed a clear dysbiosis that can be targeted for microbiome-based therapeutic approaches., This work was funded by the Spanish ‘Programa Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad’ (Grant AGL2013-44039R) and the ‘Fundación Científica Asociación Española contra el Cáncer’(Grant PS-2016). This work was also partiallyfunded by the grant of the ‘Fondo de Investiga-ciones Sanitarias’ (FIS) PI16/01792.

Bile is a biological fluid synthesized in the liver, mainly constituted by bile acids and cholesterol, which functions as a biological detergent that emulsifies and solubilizes lipids, thereby playing an essential role in fat digestion. Besides, bile acids are important signaling molecules that regulate key functions at intestinal and systemic levels in the human body, affecting glucose and lipid metabolism, and immune homeostasis. Apart from this, due to their amphipathic nature, bile acids are toxic for bacterial cells and, thus, exert a strong selective pressure on the microbial populations inhabiting the human gut, decisively shaping the microbial profiles of our gut microbiota, which has been recognized as a metabolic organ playing a pivotal role in host health. Remarkably, bacteria in our gut also display a range of enzymatic activities capable of acting on bile acids and, to a lesser extent, cholesterol. These activities can have a direct impact on host physiology as they influence the composition of the intestinal and circulating bile acid pool in the host, affecting bile homeostasis. Given that bile acids are important signaling molecules in the human body, changes in the microbiota-residing bile biotransformation ability can significantly impact host physiology and health status. Elucidating ways to fine-tune microbiota-bile acids-host interplay are promising strategies to act on bile and cholesterol-related disorders. This manuscript summarizes the current knowledge on bile and cholesterol metabolism by intestinal bacteria, as well as its influence on host physiology, identifying knowledge gaps and opportunities to guide further advances in the field., This study was supported by MINECO under grant number AGL2013-44761-P. LR is a postdoctoral researcher supported by the Juan de la Cierva Postdoctoral Trainee Program (MINECO, JCI-2015-23196) and NM is the recipient of an FPI Predoctoral Grant (BES-2014-068736).

[Background] Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but available analysis tools are often hard to install, configure and use by users without advanced bioinformatics skills. [Methods] Within reason, DEWE aims to make RNA-Seq analysis as easy for non-proficient users as for experienced bioinformaticians. DEWE supports two well-established and widely used differential expression analysis workflows: using Bowtie2 or HISAT2 for sequence alignment; and, both applying StringTie for quantification, and Ballgown and edgeR for differential expression analysis. Also, it enables the tailored execution of individual tools as well as helps with the management and visualisation of differential expression results. [Results] DEWE provides a user-friendly interface designed to reduce the learning curve of less knowledgeable users while enabling analysis customisation and software extension by advanced users. Docker technology helps overcome installation and configuration hurdles. In addition, DEWE produces high quality and publication-ready outputs in the form of tab-delimited files and figures, as well as helps researchers with further analyses, such as pathway enrichment analysis. [Conclusions] The abilities of DEWE are exemplified here by practical application to a comparative analysis of monocytes and monocyte-derived dendritic cells, a study of clinical relevance. DEWE installers and documentation are freely available at https://www.sing-group.org/dewe., This work was supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (grant AGL2013-44039R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales”, grant PS-2016); the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group; the Portuguese Foundation for Science and Technology under the scope of the strategic funding of UID/BIO/04469/2019 unit; and the Asturias Regional Plan I + D + i for research groups (FYCYT-IDI/2018/000236). H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0).

Advances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico screening of proteomes and metaproteomes is key to uncover bioactivities of translational, clinical and biotechnological interest, and to help assign functions to certain proteins, such as those predicted as hypothetical. This work introduces a new method for the prediction of the bioactivity potential of proteomes/metaproteomes, supporting the discovery of functionally relevant proteins based on prior knowledge. This methodology complements functional annotation enrichment methods by allowing the assignment of functions to proteins annotated as hypothetical/putative/uncharacterised, as well as and enabling the detection of specific bioactivities and the recovery of proteins from defined taxa. This work shows how the new method can be applied to screen proteome and metaproteome sets to obtain predictions of clinical or biotechnological interest based on reference datasets. Notably, with this methodology, the large information files obtained after DNA sequencing or protein identification experiments can be associated for translational purposes that, in cases such as antibiotic-resistance pathogens or foodborne diseases, may represent changes in how these important and global health burdens are approached in the clinical practice. Finally, the Sequence-based Expert-driven pRoteome bioactivity Prediction EnvironmENT, a public Web service implemented in Scala functional programming style, is introduced as means to ensure broad access to the method as well as to discuss main implementation issues, such as modularity, extensibility and interoperability., This work was supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (grant AGL2013-44039R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales”, grant PS-2016). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure.

Longitudes grandes entre vanos, disminución de peso a través del uso de estructura metálica y falta de control son las causas para que se produzcan vibraciones por efecto de caminado. En esta investigación se analizaron 10 edificios que cumplieron con los requisitos sismorresistentes establecidos en la normativa NEC-SE-DS. En estas modelaciones se realizó un análisis y evaluación de vibraciones mediante software y la aplicación de métodos analíticos como Murray, SCI e Hivoss; resultando el más eficiente aquel que elaboró un proceso minucioso y detallado, siendo así el de Murray. La investigación mostró que, aunque las edificaciones cumplieron con la norma de diseño sismorresistente, estos presentaron vibraciones debido al caminado; a lo cual este documento planteó una alternativa para corregir estos errores usando arriostramientos torsionales, los cuales permitieron reducir entre el 24,19 % y 35,29 % el índice de aceleración por caminado.

Chemoprevention is the use of natural and/or synthetic substances to block, reverse, or retard the process of carcinogenesis. In this field, the use of antitumor peptides is of interest as, (i) these molecules are small in size, (ii) they show good cell diffusion and permeability, (iii) they affect one or more specific molecular pathways involved in carcinogenesis, and (iv) they are not usually genotoxic. We have checked the Web of Science Database (23/11/2015) in order to collect papers reporting on bioactive peptide (1691 registers), which was further filtered searching terms such as "antiproliferative," "antitumoral," or "apoptosis" among others. Works reporting the amino acid sequence of an antiproliferative peptide were kept (60 registers), and this was complemented with the peptides included in CancerPPD, an extensive resource for antiproliferative peptides and proteins. Peptides were grouped according to one of the following mechanism of action: inhibition of cell migration, inhibition of tumor angiogenesis, antioxidative mechanisms, inhibition of gene transcription/cell proliferation, induction of apoptosis, disorganization of tubulin structure, cytotoxicity, or unknown mechanisms. The main mechanisms of action of those antiproliferative peptides with known amino acid sequences are presented and finally, their potential clinical usefulness and future challenges on their application is discussed.

Despite the existing evidence on the impact of olive oil and red wine on the intestinal microbiota, the effect of the global Mediterranean Diet (MD) has not been sufficiently studied. We explored the association between the adherence to a Mediterranean dietary pattern, and its components, with faecal microbiota in a cohort of adults with non-declared pathology. This transversal study involved 31 adults without a previous diagnosis of cancer, autoimmune or digestive diseases. Based on the data obtained by means of an annual food frequency questionnaire (FFQ), and the information existing in the literature, a Mediterranean Diet Score (MDS) was calculated. Dietary fibre was obtained from Marlett et al. tables and Phenol-Explorer Database was used for phenolic compounds intake. Quantification of microbial groups was performed by Ion Torrent 16S rRNA gene-based analysis and quantification of short-chain fatty acids (SCFAs) was performed using gas chromatography-mass spectrometry (MS). MDS was associated with a higher abundance of Bacteroidetes (p = 0.001), Prevotellacea (p = 0.002) and Prevotella (p = 0.003) and a lower concentration of Firmicutes (p = 0.003) and Lachnospiraceae (p = 0.045). Also, in subjects with MDS ≥ 4, higher concentrations of faecal propionate (p = 0.034) and butyrate (p = 0.018) were detected. These results confirm the complexity of the diet-microbiota interrelationship., Supported by a grant AGL2010-14952 from the Spanish Ministry of Science and Innovation and in part by a grant from the European Regional Development Fund (GRUPIN14-043; to I. Gutiérrez-Díaz). B. Sánchez was recipient of a Ramón y Cajal postdoctoral contract from the Spanish Ministry of Economy and Competitiveness.

Flow cytometry (FC) is a very popular technique for to the study of different eukaryotic cell phenotypes. In addition, FC has many applications in the field of food microbiology, although the few number of specific molecules that can be potentially targeted with fluorescence-conjugated antibodies limits its potential applications. The present work represents a step forward in the application of FC for detection of specific foodborne or probiotic bacteria by using fluorescent antibodies binding specific surface-associated protein. To illustrate this novel approach, we have used a monoclonal and polyclonal antibodies targeting cell-wall hydrolase (CWH), one of the major surface-associated proteins of the probiotic Lactobacillus rhamnosus GG. In order to verify the specific union of the antibodies to this surface protein, ten different bacterial strains belonging to different bacteria species taxonomically related and no related to L. rhamnosus, were tested. The optimal conditions for bacteria detection corresponded to a final suspension of 5E107 bacteria in exponential phase of growth using FC buffer, without freezing, without adding extra BSA to the FC buffer and without fixing bacteria. Our results showed that GG strain was detected using the polyclonal anti-CWH serum in a higher extent (91.62%) than the rest of strains (L. casei 393: 64.49%; L. amylovorus: 46.13%, E. coli: 45.13%; L. acidophilus DSM20079T: 35.83%; B. longum NCIMB8809: 33.68%; L. gasseri BM7/10: 32.41%; L. reuteri DSM21016: 29.26%; L. plantarum NCIMB8826: 26.33% and L. delbruekii: 22.52%). The percentage of L. rhamnosus labeled with the monoclonal antibody was 53.06, which contrasted with the 91.62% labeled with the polyclonal antibody. The low affinity of the monoclonal antibody was perhaps due to the lack of immunogenicity of the single epitope chosen for antibody generation (CWHp). The high efficiency observed for the polyclonal anti-CWH serum is maybe a consequence of being constituted by a mixture of antibodies that recognizes different epitopes in the L. rhamnosus GG protein. With this proof of concept, we have shown for the first time that foodborne or probiotic bacteria can be specifically detected using antibodies targeting adequate molecules present on their surface.

There are strong evidences that probiotics influence the immune status of the host, in a strain-specific manner, acting in the gastrointestinal tract. On the hypothesis that certain extracellular proteins and peptides from gut bacteria may mediate part of this immunomodulation and assuming they are able to diffuse through the mucus layer and interact with immune cells we have developed this work. Our study attempts to understand the immunomodulatory mechanisms of (i) Pext, the extracellular protein fraction of Lactobacillus acidophilus DSM20079T, (ii) HM14, a peptide encrypted in an extracellular glycoside hydrolase from Bifidobacterium longum NCIMB 8809 and (iii) Escherichia coli O111:B4 lipopolysaccharide (LPS), a well-known pro-inflammatory molecule, over human peripheral blood mononuclear cells (PBMCs). An untargeted LC-ESI-QTOF-MS metabolomics approach was applied to reveal intracellular changes in treated-PBMCs isolated from healthy donors. Differences in NADH arrest, NAD+ concentration reduction, as well as increases in palmitic acid and methanephrin were observed in HM14 and Pext treated-cells compared to those stimulated with LPS. This would support an anti-inflammatory molecular mechanism of action of such proteinaceous molecules. Moreover, this methodology has confirms the importance of metabolomics approaches to better understanding immune cell responses to gut bacterial-derived molecules., This work was funded by the Autonomic Investigadores Emerxentes do Sistema Universitario de Galicia (Grant EM2014/046) and the Spanish Programa Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad (Grant AGL2013-44039R). This work has received also financial support from the Xunta de Galicia (Plan de mellora do Centro de Investigacións Agroalimentarias CIA3 do Campus de Ourense).

This work reports on a large-scale potential neuropeptide activity screening in human gut microbiomes deposited in public databases. In our experimental approach, the sequences of the bioactive peptides collected in the MAHMI database, mainly predicted as immunomodulatory or antitumoral, were crossed with those of the neuroactive/digestive peptides. From 91,325,790 potential bioactive peptides, only 581 returned a match when crossed against the 5949 neuroactive peptides from the NeuroPep database and the 15 digestive hormones. Relevant bacterial taxa, such as Ruminococcus sp., Clostridium sp. were found among the main producers of the matching sequences, and many of the matches corresponded to adiponectin and the hormone produced by adipocites, which is involved in glucose homeostasis. These results show, for the first time, the presence of potentially bioactive peptides produced by gut microbiota members over the nervous cells, most notably, peptides with already predicted immunomodulatory or anti-inflammatory activity. Classical (Lactobacillus sp.) and next-generation (Faecalibacterium sp.) probiotics are shown to produce these peptides, which are proposed as a potential mechanism of action of psychobiotics. Our previous experimental results showed that many of these peptides were active when incubated with immune cells, such as dendritic cells, so their effect over the nervous system innervating the gut mucosa holds significant potential and should be explored., This work was supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (Grant AGL2016-78311-R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales”, grant PS-2016). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. This work was partially supported by the Asturias Regional Plan I+D+i for research groups (FYCYT-IDI/2018/000236) and by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group.

Introduction: The role of the human intestinal microbiota in the maintenance of a healthy physiological condition, as well as its relation to the development of disease, remains to be clarified. Current evidence suggests that intestinal microbes could be involved in the initiation and amplification of autoimmune diseases, including rheumatoid arthritis and systemic lupus erythematosus (SLE). Despite recent progress in understanding how these microbes influence the pathophysiology of lupus, studies are still limited. Areas covered: In this review, we have tried to summarize the most relevant findings that have contributed to our understanding of the links between the human intestinal microbiota and the development of lupus. We also describe the potential role of individual microbial players in the physiology of lupus, and how they can shape relevant immune responses. Expert commentary: Culture-independent techniques based on massive sequencing represent a powerful tool to unravel the biological activity of gut microbes. Current data demonstrates that, depending on the pattern of intestinal microorganisms or the presence of specific bacteria, different responses related to lupus physiology can be triggered. Fecal microbiota transplantation, live biotherapeutics, or dietary interventions targeting the microbiota will likely become a treatment for SLE.

In a recent excellent Review1 (Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat. Rev. Gastroenterol. Hepatol. 15, 111–128 (2018)), the connection between human and microbial bile acid (BA) metabolism was described. In this Review, the authors identified possible therapeutic targets from data published in the context of gastrointestinal inflammation and carcinogenesis. From the microbial point of view, BAs are one of the main factors determining probiotic survival through the human gastrointestinal tract, which indeed was the focus of my PhD work