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This work reports on the first described aerotolerant Bifidobacterium bifidum strain, Bifidobacterium bifidum IPLA60003, which has the ability to form colonies on the surface of agar plates under aerobic conditions, a weird phenotype that to our knowledge has never been observed in B. bifidum. The strain IPLA60003 was generated after random UV mutagenesis from an intestinal isolate. It incorporates 26 single nucleotide polymorphisms that activate the expression of native oxidative-defense mechanisms such as the alkyl hydroxyperoxide reductase, the glycolytic pathway and several genes coding for enzymes involved in redox reactions. In the present work, we discuss the molecular mechanisms underlying the aerotolerance phenotype of B. bifidum IPLA60003, which will open new strategies for the selection and inclusion of probiotic gut strains and next generation probiotics into functional foods.

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

This work reports on the first described aerotolerant Bifidobacterium bifidum strain. One of the main challenges for exploiting the therapeutic potential of next generation probiotics is their inclusion into functional foods, which is hampered by extreme oxygen sensitivity. This is indeed an unmet technological problem of human gut bifidobacteria. Aerobic conditions are present during the processes of producing, handling, manufacturing and storing probiotics. B. bifidum species includes several probiotic strains of invaluable therapeutic potential, but they also exhibit one of the lowest resistance to oxygen among human bifidobacteria. In this work, we present strain Bifidobacterium bifidum IPLA60003, which has the ability to form colonies on the surface of agar plates under aerobic conditions, a weird phenotype that to our knowledge has never been observed in B. bifidum. The strain IPLA60003 was generated after random UV mutagenesis from an intestinal isolate. It incorporates 26 single nucleotide polymorphisms that activate the expression of native oxidative defense mechanisms such as the alkyl hydroxyperoxide reductase, the glycolytic pathway and several genes coding for enzymes involved in redox reactions. In the present work, we discuss the molecular mechanisms underlying the aerotolerance phenotype of B. bifidum IPLA60003, which will open new strategies for the selection and inclusion of probiotic gut strains and next generation probiotics into functional foods. Further, we addressed the technological application of IPLA60003 evaluating its survival and metabolic activity in milk for 28 days. Besides, we studied the survival of the strains in fresh cultures, after freezing at -80ºC and after lyophilization by plate counts incubated in anaerobiosis and in the presence of O2. Globally, technological performance of strain IPLA60003 was better than other two non-aerotolerant B. bifidum strains.

[ES] La presente invención se relaciona con un microorganismo del género Bifidobacterium spp. que comprende un promotor que comprende la secuencia GAAAGGA (SEQ ID NO: 1) a una distancia de entre 12 y 31 nucleótidos del codón de inicio responsable de la transcripción de un gen, en donde dicho microorganismo es aerotolerante y pertenece a la especie B. bifidum. La presente invención también se relaciona con la composición que comprende dicho microorganismo y los usos del mismo tanto en salud debido a sus propiedades beneficiosas para la salud como en la fabricación de productos lácteos fermentados., [EN] The present invention is related to a microorganism of the genus Bifidobacterium spp. which includes a promoter that comprises the Gaaagga sequence (SEQ ID no: 1) at a distance between 12 and 31 nucleotides of the start -up codon responsible for the transcription of a gene, where said microorganism is aerotolerant and belongs to species B. bifidum. The present invention is also related to the composition that includes this microorganism and the uses of the same in health due to its beneficial health properties and in the manufacture of fermented dairy products.

[ES] La presente invención se relaciona con un microorganismo del género Bifidobacterium spp. que comprende un promotor que comprende la secuencia GAAAGGA (SEQ ID NO: 1) a una distancia de entre 12 y 31 nucleótidos del codón de inicio responsable de la transcripción de un gen, en donde dicho microorganismo es aerotolerante y pertenecea la especie B. bifidum. La presente invención también se relaciona con la composición que comprende dicho microorganismo y los usos del mismo tanto en salud debido a sus propiedades beneficiosas para la salud como en la fabricación de productos lácteos fermentados., [EN] The present invention relates to a microorganism of the genus Bifidobacterium spp. comprising a promoter comprising the sequence GAAAGGA (SEQ ID NO: 1) at a distance of between 12 and 31 nucleotides from the start codon responsible for the transcription of a gene, wherein the microorganism is aerotolerant and belongs to the species B. bifidum. The present invention also relates to the composition comprising said microorganism and the uses thereof both in health due to its health-promoting properties and in the manufacture of fermented milk products., [FR] La présente invention concerne un micro-organisme du genre Bifidobacterium spp. qui comprend un promoteur comprenant la séquence GAAAGGA (SEQ ID NO: 1) à une distance comprise entre 12 et 31 nucléotides du codon de départ responsable de la transcription d'un gène, ledit micro-organisme étant aérotolérant et appartenant à l'espèce B. bifidum. La présente invention concerne également la composition comprenant ledit micro-organisme et les utilisations de celui-ci aussi bien dans la santé du fait de ses propriétés bénéfiques pour la santé que dans la fabrication de produits lactés fermentés.

[EN] The consumption of fermented vegetables is widespread throughout the world and represents an important component of the human diet with considerable contribution to the food supply for a world popula-tion in continuous growth. Many of the fermented vegetables share a general process which requires salting and acidification steps. Among the microorganisms responsible for fermentation, lactic acid bacteria are the most relevant with important organoleptic, quality and safety benefits. This review deals with the microbial ecology of fermented vegetables focusing on the biodiversity of lactic acid bacteria, the most important molecular tech-niques used for their identification and genotyping, their importance for the formation of biofilms as well as their use as starter cultures for obtaining high-quality and safe vegetable products, [ES] El consumo de vegetales fermenta-dos está muy extendido en el mundo y representa un componente importante de la dieta humana con un apoyo considerable a la cadena alimentaria para una población mundial en continuo crecimiento. Muchos de los vege-tales fermentados comparten un proceso general, que requiere una puesta en salmuera y acidificación. Entre los microorganismos responsables de la fermentación, las bacterias del ácido láctico son las más relevantes con una importante influencia sobre aspectos organolépticos, de calidad y seguridad del producto final. Esta revisión trata sobre la ecología microbiana de los vegetales fermentados, prestando especial atención a la biodiversidad de las bacterias del ácido láctico, las técnicas moleculares más importantes utilizadas para su identificación y genotipado, su importancia para la formación de biofilms y su uso como cultivos iniciadores multifuncionales para la obtención de productos vegetales de alta calidad y seguridad.

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 Crohn’s 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.

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.

[Background] Several independent studies have addressed the beneficial role of lactic acid bacteria over different cancer types, both in vitro and in vivo. However, and to our knowledge, no molecular study has been performed to understand how this inhibitory effect may take place. [Methods] Different fractions from several lactic acid bacteria and bifidobacteria were obtained in order to test their effect over two well-known epithelial cell lines, Caco-2 and Ht29, using the RTCA device. Effect of this extract over cell cycle and the process of necrosis/apoptosis was checked by flow cytometry. Molecular mechanism of action was elucidated by RNASeq. Results: The most active fraction was obtained from Lactobacillus acidophilus, and RNASeq analysis revealed an activation of several detoxification/xenobiotic pathways in epithelial cells. Nuclear magnetic resonance revealed a quite complex extract with the presence of alanine and lactic acid. Alanine had no effect over proliferation but buffering of the extract suggested that some of the observed inhibitory effect was due to lactic acid. The antiproliferative effect was visible from 300 mg/L lactic acid, and 2,7 g/L were enough to induce complete culture death in Ht29 an Caco-2. [Conclusion] Although it remains to known the role of other compounds in the anti-proliferative effect of the L. acidophilus extract, we have shown for the first time that CaCo-2 and Ht29 cell lines are sensible to lactic acid concentrations lower than those observed for instance in yoghourt (9 g/L), suggesting that carcinogenic cells may be more sensitive to lactic acid than normal cells. Production of lactic acid in the colon is therefore a molecular mechanism of action by which lactic acid bacteria exert their beneficial role in the colon.

[Aim] The aim of this work was to evidence that the use of different stool collection strategies has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory, notably if oxygen toxicity is not considered. This is particularly critical if the purpose of the sample is to envisage personalized biotherapeutic purposes, such as autologous fecal microbiota transplant or designing personalized biotherapeutics. [Methods] In order to analyze differences in the viability of fecal microbial populations during the whole delivery procedure, the same fecal specimens were sampled in conventional stool containers and GutAlive® devices, which minimize exposure of fecal microbiota to oxygen. Samples from five healthy donors were used and 150 differential colonies between the two devices were recovered. Differences included those associated to the two collection devices and individuals. All colonies were identified by 16S rRNA gene sequencing. Complete genomes of two extremely oxygen sensitive (EOS) bacteria recovered were sequenced with the Illumina MiSeq Sequencing System. [Results] Microbial diversity obtained was notably higher using GutAlive®. This device was able to maintain the viability of EOS species such as Akkermansia muciniphila, Faecalibacterium prausnitzii and a possible new member of the Clostridiales order. These obligate anaerobes were not recovered using the conventional stool container. Remarkably, GutAlive® allowed culturing and identifying an anaerobic isolate which may represent a new lineage within Clostridiales. This shows the importance of a personalized approach in microbiota-based therapies, as this novel isolate was recovered only from feces of one of the donors. [Conclusion] Using GutAlive® for stool sampling and transport allowed higher recovery of viable EOS bacteria by limiting oxygen exposure during the whole process. By standardizing the sampling and transport of the fecal specimens to the lab, GutAlive®

Durante los últimos diez años ha habido avances en la compresión de cómo la microbiota intestinal humana contribuye a nuestra salud y enfermedad. La microbiota humana, especialmente la microbiota intestinal, es considerada un “órgano esencial” debido a que las comunidades microbianas que colonizan todas las superficies de nuestro cuerpo nos proporcionan funciones metabólicas, inmunológicas y fisiológicas esenciales. Tras el nacimiento, nuestra microbiota intestinal alcanza su configuración final a la edad de 2 a 3 años con la introducción de alimentos sólidos, estableciéndose una comunidad de microorganismos dominada por anaerobios obligados. Después del nacimiento, alrededor de 100 especies bacterianas colonizan el intestino, aumentando hasta 103 en la edad adulta. Su composición evoluciona constantemente, dependiendo de factores internos y externos como la edad, la raza, la dieta, la colonización materna, así como la exposición a antibióticos y xenobióticos. Además, otros factores como el estrés o los tratamientos farmacológicos conducen a rápidos cambios en la composición de nuestra microbiota. La complejidad de la microbiota intestinal hace difícil deducir la contribución individual de una especie/cepa a un fenotipo, enfermedad o condición. Por ello, el desarrollo de métodos para la modificación dirigida de una microbiota, especialmente enfocada en eliminar de una comunidad microbiana una bacteria específica, podría ser útil para descifrar como una especie contribuye a una enfermedad o a un proceso fisiológico, inmunológico o metabólico. En este estudio presentamos una tecnología que, si bien no es desconocida, sí que es pionera en cuanto a su aplicación. Hemos utilizado un anticuerpo policlonal dirigido a la proteína A de la capa S de Lactobacillus acidophilus DSM20079T para conseguir detectarlo en un consorcio bacteriano compuesto de 8 especies representativas de la microbiota intestinal humana. Además, se ha realizado una depleción y enriquecimiento positivo

This work presents a novel in silico approach to the prediction and characterization 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 uncharacterized activities, such as several hexosyltransferases and some hydrolases. Gene neighborhood 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.

The human gut microbiota is composed of the different microorganisms of our intestinal ecosystem. It has an important metabolic and nutritional role, and it is involved in the correct development of the gut and the maturation of our immune system. Currently, the application of fecal microbiota transplantation (FMT) has allowed us to establish causality in microbiome studies, and we know that microbiota can cure diseases or induce the appearance of disease symptoms, or even determine the success of some health treatments. But knowledge of the curative effects of feces has been documented many centuries ago. In the present article we want to make a brief review of the history of FMT, focusing on its effect on the human microbiome and its capacity to act on human physiology. We also want to place special emphasis on aspects that must be taken into account to translate microbiome research to medicine, related to safety, regulation and standardization of methods, as well as the importance of being able to predict the success of FMT.

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.

[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 <.001) and higher than with the nutrient-free control (by 25 ± 19%; P =.05). Patients complaining of abdominal distension after eating lettuce exhibited an increase in girth (35 ± 3 mm larger than basal; P <.001) without significant increase in colonic gas content (39 ± 4 mL increase; P =.071); abdominal distension was related to a descent of the diaphragm (by 7 ± 3 mm; P =.027) with redistribution of normal abdominal contents. [Conclusion and Inferences] Lettuce is a low gas-releasing substrate for microbiota fermentation and lettuce-induced abdominal distension is produced by an uncoordinated activity of the abdominal walls. Correction of the somatic response might be more effective than the current dietary restriction strategy.

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.

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.

[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 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.

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.

Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted “generally recognized as safe” (GRAS) and “qualified presumption of safety” (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.

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.

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.

Introducción/Objetivos Faecalibacterium prausnitzii es un miembro de la familia Ruminococcaceae extremadamente sensible al oxígeno. Es una bacteria abundante en el colon de individuos sanos, pero sus niveles disminuyen drásticamente en la enfermedad de Crohn. Además de la producción de butirato (que reduce la inflamación de la mucosa intestinal y es la principal fuente de energía para los colonocitos), se le han atribuido otras propiedades anti-inflamatorias adicionales asociadas a la producción de proteínas secretadas. El objetivo de este estudio fue estudiar el efecto sobre células del sistema inmunitario de microbiotas de donantes sanos y enfermos de Crohn, con diferentes abundancias relativas de F. prausnitzii. Metodología. Se reclutaron 10 microbiotas intestinales de donantes sanos y 10 de enfermos de Crohn. Las microbiotas de donantes sanos se modificaron siguiendo la metodología de anticuerpos y perlas magnéticas descrita por Marcos y colaboradores (Sci Rep 2021, 11:1270), para deplecionarlas o enriquecerlas en F. prausnitzii. Se seleccionaron las microbiotas de donantes sanos con elevada representación de F. prausnitzii y aquellas microbiotas de pacientes con enfermedad de Crohn donde no se detectó F. prausnitzii y se determinó su actividad inmunomoduladora utilizando modelos celulares. Resultados Los resultados aportan nuevos datos sobre el papel que juega F. prausnitzii en la enfermedad de Crohn. La microbiota de enfermos de Crohn suplementada con F. prausnitzii de donantes sanos disminuye la producción de citocinas proinflamatorias, con respecto a la microbiota original. Conclusiones Nuestro estudio contribuye a comprender las funciones de algunas subpoblaciones de la microbiota intestinal que parecen jugar un papel importante en la fisiopatología de la enfermedad de Crohn, mediante la caracterización de sus interacciones con las células del sistema inmunitario.

The invention relates to the field of medical diagnosis, particularly to methods and antibodies useful for the identification of colibactin producing bacteria (pks+ bacteria). Herein are disclosed peptides and antibodies that allow for the detection and isolation of pks+ bacteria, as well as uses and methods of use of said peptides and antibodies

[EN] The invention relates to the field of medical diagnosis, particularly to methods and antibodies useful for the identification of colibactin producing bacteria (pks+ bacteria). Herein are disclosed peptides and antibodies that allow for the detection and isolation of pks+ bacteria, as well as uses and methods of use of said peptides and antibodies, [FR] L'invention concerne le domaine du diagnostic médical, en particulier des procédés et des anticorps utiles pour l'identification de bactéries productrices de colibactine (bactéries pks+). L'invention concerne des peptides et des anticorps qui permettent la détection et l'isolement de bactéries pks+, ainsi que des utilisations et des procédés d'utilisation desdits peptides et anticorps

Este libro surge como una iniciativa para compilar una serie de artículos alumbrados a partir de la génesis del Grupo CURIE (Científic@s Unid@s por la Reactivación de la Investigación en España), semilla de la Asociación Española para el Avance de la Ciencia (AEAC). Durante meses sus miembros estuvieron intercambiando reflexiones y debatiendo sobre la distancia entre la ciencia y la sociedad, y la necesidad de crear una asociación que llenase ese vacío entre los científicos y los ciudadanos, que apostase por llevar la ciencia y los conocimientos generados por la misma a toda la sociedad, tal y como establecen la Declaración de Derechos Humanos y la Constitución Española, en su artículo 44.

The human gastrointestinal tract (GIT) is a very complex ecosystem involving a continuous interaction between nutrients, host cells and microorganisms. Recently, we have discovered a new family of immunomodulatory peptides that are encrypted within the sequence of a precise extracellular protein, which is secreted by the lactic acid bacterium Lactobacillus plantarum (Patent WO 2013034795 A1) (1). The genetic information about commensal/probiotic bacteria and gut microbiomes that is present in public repositories is huge, with only a list of 10 million unique bacterial proteins available mainly from the METAHIT and HMP projects (http://gigadb.org/dataset/100064). Our aim is to explore these 10 million unique proteins to obtain information on encrypted peptides which might have immunomodulatory bioactivity on host cells. With this in mind we have developed the MAHMI (Mechanism of Action of the Human Microbiome) database, a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Fifteen peptides were chosen by its potential immunomodulatory bioactivity. Selected peptides were assayed in vitro at a final concentration of 10 µg/mL using monocyte derived cells (Mo-DCs). Our bioinformatics/in vitro methodology allowed selection of new inmunomodulatory peptides encrypted in the human intestinal bacteria metaproteome. HM14 signaled through an unknown receptor, and imprinted anti-inflammatory traits in immune cells as evidenced by RNASeq and flow cytometry. The mechanisms used by this kind of peptides may be useful for the treatment of inflammatory diseases

New studies and therapies based on gut microbiota sampling need from protocol normalization and standardization. During this process, keeping microbial viability from the sampling to the delivery, and the manipulation and storage of the faecal samples is crucial. This standardization requires a device/kit to avoid the toxic effect of oxygen on intestinal microbiota. [Objective] To develop and validate an anaerobic stool sample collection device: GutAliveR (PCT/ES2017/070087). [Methods] The efficiency of GutAliveRwas tested and compared with other stool collection systems. Maintenance of the anaerobic conditions was experimentally evaluated by means of total counts of anaerobic microorganisms. For this purpose, autoclaved faecal samples were inoculated with cultures of different anaerobic microorganisms. Also, a biodiversity index was calculated from faecal samples of healthy donors. Recounts were carried out at inoculation time and after 5/24/72 h incubation at room temperature (RT). [Results] In GutAliveR , anaerobic microorganisms inoculated showed a lower loss of viability after 24 and 72 h compared with conventional systems. Bifidobacterium bifidum remained viable and culturable up to 72 h at RT, while using a conventional system the bifidobacterial population was reduced 37% at 24 h and more than 99% at 72 h. The biodiversity index is higher when GutAliveR is used to collect and transport the faecal samples. [Conclusion] GutAliveR ensures an anoxic environment for the stool sampling and transport until processing at the laboratory. This could be critical in some applications, such as standardization and normalization of microbiota-based studies and the isolation of new probiotic strains from faeces.

[Introduction] Bifidobacteria and lactobacilli include both probiotic strains and representative microorganisms of the human gut microbiota, and their presence has been associated to a proper immune development and maturation. In addition, several independent works report the anti-inflammatory properties of several strains of those groups. However, we are far from understanding the molecular interplay behind/supporting these beneficial interactions. [Objective] To study the effect of different fractions of lactobacilli and bifidobacteria in human peripheral blood mononuclear cells (PBMCs) isolated from healthy donors and patients with Inflammatory Bowel Disease (IBD) at the time of diagnosis. [Methods] The fractions were obtained from strains of Bifidobacterium longum NCIMB 8809, Lactobacillus rhamnosus GG and Lactobacillus acidophilus DSM 20079: DNA, surface-associated proteins, whole cell soluble extract and extracellular proteins. Different concentrations of the fractions were incubated with PBMCs, and key T-cell cytokines, T regulatory cell differentiation and RNASeq of CD4+ cells were performed. [Results] Among the extracts, extracellular proteins from L. acidophilus DSM 20079 increased IL-2 production by PBMCs isolated from healthy donors, and were able to increment the proportion of functional T regulatory cells. Data on the signaling mechanisms involved were obtained by RNASeq of CD4+ Th cell subpopulations. Finally, this fraction decreased drastically the production of the pro-inflammatory mediator TNF-alpha and induced increments of IL-12 in PBMCs isolated from IBD patients at the diagnosis. [Conclusions] Extracellular proteins from strain L. acidophilus DSM 20079 had a positive impact on the immunological status of both healthy donors and IBD patients. This fraction will be on the basis of new clinical studies focused in the immunomodulation of the human host targeting pro-inflammatory effectors and the T-cell regulatory response. This fraction may repres

n los últimos años se está revelando la relación entre el metabolismo de sales biliares y el colesterol, la microbiota intestinal y su implicación en la salud. A diferencia de otras localizaciones, el microbioma del tracto biliar apenas ha sido estudiado. En este trabajo se ha realizado un análisis metagenómico filogenético y funcional de muestras de bilis humana, además de un análisis metabolómico, con el fin de caracterizar el microbioma biliar de donantes de hígado y pacientes con colelitiasis, e identificar posibles disbiosis asociadas a esta patología. Se obtuvieron muestras de bilis de donantes de hígado y pacientes con colelitiasis, de las que se extrajo el ADN biliar siguiendo un protocolo optimizado. Se llevó a cabo la secuenciación masiva de amplicones del ADNr 16S mediante la tecnología Illumina. Además, se realizó secuenciación masiva por shotgun y análisis de metagenómica funcional de tres muestras de bilis de sujetos sanos. El análisis metabolómico se realizó utilizando técnicas de NMR. Los resultados mostraron una gran diversidad microbiana presente en este tipo de muestras, con presencia de 4 filos mayoritarios: Firmicutes, Bacteriodetes, Actinobacteria y Proteobacteria. El análisis estadístico mostró diferencias significativas en la abundancia relativa de diversos taxones presentes en la bilis de ambos grupos. En concreto, secuencias de la familia Propionibacteriaceae fueron más abundantes en la bilis de los donantes de hígado, mientras que en pacientes con colelitiasis fueron más frecuentes las de las familias Bacteroidaceae, Prevotellaceae, Porphyromonadaceae y Veillonellaceae. El análisis funcional mostró que la asignación a las principales categorías funcionales del COG es similar a la del microbioma intestinal humano. Por último, el análisis metabolómico nos permitió asociar diferentes perfiles metabólicos a los grupos de individuos objeto de estudio.

[ES] El estudio de los probióticos ha cobrado una gran importancia en los últimos años debido a su papel en el mantenimiento de una microbiota intestinal equilibrada, así como en el tratamiento de ciertas enfermedades, incluidos ciertos tipos de cáncer. En este trabajo, se ha analizado el efecto anti-proliferativo de un extracto bacteriano obtenido a partir de la cepa probiótica Lactobacillus acidophilus sobre la línea celular HT29. Este efecto se ha detectado con una técnica de impedancia no invasiva que permite cuantificar la proliferación celular. Además, se ha realizado un análisis del ciclo celular mediante citometría de flujo, ya que una posible hipótesis era que este extracto afectase a la división celular. Finalmente, se observó un efecto sobre la línea celular dependiente de la concentración. Aunque dicho efecto se atribuyó inicialmente a un descenso en la proliferación, los resultados de citometría no parecen reflejar esta idea y dan pie a nuevas hipótesis, incluidas una alteración en la morfología/adhesión celular o un efecto anti-proliferativo que no se detectaría debido a la aparición de mecanismos de resistencia. Además, un segundo análisis con citometría de flujo descarta su efecto sobre la viabilidad celular. Por otro lado, la elevada complejidad del extracto requiere de un fraccionamiento previo, por ejemplo mediante cromatografía líquida, para poder identificar qué moléculas son responsables del efecto observado. Antes de llevar a cabo esta operación, es necesaria una optimización de las condiciones de separación, lo cual se presenta en este trabajo utilizando la técnica de cromatografía en capa fina. De esta forma, se consiguió establecer condiciones óptimas tanto para cromatografía en fase reversa con mezclas de acetonitrilo y agua, como para fase normal con mezclas de hexano y acetato de etilo, acetato de etilo y metanol, y cloroformo y metanol., [EN] The global interest in probiotics has gained a great relevance over the last few years due to its importance in both the maintenance of a balanced gut microbiota, and the treatment of several diseases, including certain type of cancers. In the present study, the anti-proliferative effect from a bacterial extract which has been obtained from probiotic strain, Lactobacillus acidophilus, has been tested on the HT29 cell line, derived from a colon adenocarcinome. This effect could be observed thanks to a non-invasive impedance assay, which allows for cell proliferation quantification. Furthermore, a cell cycle analysis through flow cytometry has been also carried out in order to get a better idea about the action mechanism of the extract, as one of the main hypothesis would be its possible impact on the cell division. Finally it could be observed an effect over the cell line dependent on concentration. Although this effect had been previously associated with a decrease in cell proliferation, it seems that flow cytometry results do not reflect this idea and thus, several hypothesis have been purposed, including changes in cell morphology/adhesion or an anti-proliferative effect which was not detected because of resistance mechanisms. Additionally, a second flow cytometry analysis showed no effect on cell viability. On the other hand, the huge complexity of the extract requires a previous separation through liquid chromatography, in order to be able to identify which molecule or molecules are responsible for the observed effect. Before performing this technique, it is necessary to carry out an optimization through thin layer chromatography, which is included in this study. At the end, several optimal conditions have been reached for both reverse phase with mixtures of acetonitrile and water, and normal phase with mixtures of hexane and ethyl acetate, ethyl acetate

Probiotics are used to improve human health due to their capability to induce beneficial effects in gastrointestinal diseases and modulate the immune response. However, scarce information is known about the bacterial active compounds and the metabolic pathways of interaction with immune cells. In the present study, we analyzed the immune response elicited by surface-associated proteins, the whole surface extract (WSE) and the genomic DNA of three strains from the main representative probiotic species for human consumption, L. acidophilus DSM20079T, L. rhamnosus GG, B. longum NCIMB 8809, using an in vitro model of human PBMCs from healthy donors. Eighteen cytokines were quantified using Luminex Technology to understand the immune pathways modulate by bacterial extracts. Overall, the bacterial fractions elicited a different immune response in PBMCs, whereas the isolated DNA was able to induce a higher Th17-like response that could lead to a protective effect in the epithelial barrier function.

[Background] The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications. [Results] This work introduces BlasterJS viewer, a new JavaScript library for the lightweight development of Web-based applications supporting the visualisation of BLAST outputs. BlasterJS detaches from similar data viewers by focusing on the visual and interactive display of sequence similarity results and being completely independent of BLAST services. BlasterJS is compatible with the text outputs generated by the BLAST family of programs, namely BLASTp, BLASTn, BLASTx, tBLASTn, and tBLASTx, and works in all major Web browsers. Furthermore, BlasterJS is available through the EBI’s BioJS registry 5, which extends its potential use to a wider scope of bioinformatics applications. [Conclusions] BlasterJS is new Javascript library that enables easy and seamless integration of visual and interactive representations of BLAST outputs in Web-based applications supporting sequence similarity search. BlasterJS is free accessible at http://sing-group.org/blasterjs/.

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.

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.

Se sabe que las bacterias de la microbiota intestinal humana poseen efectos beneficiosos en el hospedador, entre ellos estimular el sistema inmunológico y proteger contra la actividad carcinogénica de elementos de la dieta. Por ello, se ha propuesto que los probióticos podrían tener un papel en la prevención del desarrollo del cáncer colorrectal. El objetivo de este trabajo fue estudiar el efecto de diferentes péptidos procedentes de bacterias de la microbiota humana sobre la proliferación de células de adenocarcinoma colónico humano. Para ello, se seleccionaron 41 péptidos del metaproteoma del tracto digestivo humano por presentar alta similitud (mayor del 60%) con péptidos de actividad antiproliferativa o inmunomoduladora ya conocida. Se incubaron células de adenocarcinoma colónico humano HT-29 en presencia de dichos péptidos cuantificando la proliferación mediante el dispositivo xCELLigence RTCA. Se compararon los resultados con controles negativos sin péptido y controles positivos con el quimioterápico 5-fluorouracilo. Los péptidos que mostraron mayor actividad antiproliferativa se ensayaron a distintas concentraciones para determinar su concentración inhibitoria del 50%. Como conclusión, 21 de los 41 péptidos estudiados presentaron actividad antiproliferativa, siendo más relevante el efecto observado con cuatro de ellos (DW15, GR16, TS13 y VV15). Este efecto fue de menor magnitud que utilizando un agente quimioterápico clásico y requirió un tiempo de incubación más largo.

[Purpose] Short-chain fatty acids (SCFAs) formation by intestinal bacteria is regulated by many different factors, among which dietary fibre is currently receiving most attention. However, since fibre-rich foods are usually good dietary sources of phenolic compounds, which are also known to affect the microbiota, authors hypothesize that the regular intake of these bioactive compounds could be associated with a modulation of faecal SCFA production by the intestinal microbiota. [Methods] In this work, food intake was recorded by means of a validated Food Frequency Questionnaire. Fibres were determined using Marlett food composition tables, and phenolic compounds were obtained from Phenol-Explorer Database. Analysis of SCFA was performed by gas chromatography–flame ionization/mass spectrometry and quantification of microbial populations in faeces by quantitative PCR. [Results] Klason lignin and its food contributors, as predictors of faecal butyrate production, were directly associated with Bacteroides and Bifidobacterium levels, as well as lignans with Bacteroides. Also, anthocyanidins, provided by strawberries, were associated with faecal propionate and inversely related to Lactobacillus group. [Conclusions] These results support the hypothesis we put forward regarding the association between some vegetable foods (strawberries, pasta, lentils, lettuce and olive oil) and faecal SCFA. More studies are needed in order to elucidate whether these associations have been mediated by the bacterial modulatory effect of the bioactive compounds, anthocyanins, lignans or Klason lignin, present in foodstuffs.

In this paper we bring together two perspectives onto one single issue: the relevance of fundamental research. We depart from the personal experience of a scientist to arrive at a philosophical reasoning, which allows us to detach ourselves from the question what is this for? We conclude that, even if there are plenty of examples of the utility of fundamental research, that question is of no use in identifying good scientific work.

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