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Introduction: Systemic lupus erythematosus is an autoimmune disease with multisystemic involvement including intestinal inflammation. Lupus-associated intestinal inflammation may alter the mucosal barrier where millions of commensals have a dynamic and selective interaction with the host immune system. Here, we investigated the consequences of the intestinal inflammation in a TLR7-mediated lupus model. Methods: IgA humoral and cellular response in the gut was measured. The barrier function of the gut epithelial layer was characterised. Also, microbiota composition in the fecal matter was analysed as well as the systemic humoral response to differential commensals. Results: The lupus-associated intestinal inflammation modifies the IgA B cell response in the gut-associated lymphoid tissue in association with dysbiosis. Intestinal inflammation alters the tight junction protein distribution in the epithelial barrier, which correlated with increased permeability of the intestinal barrier and changes in the microbiota composition. This permeability resulted in a differential humoral response against intestinal commensals. Discussion: Lupus development can cause alterations in microbiota composition, allowing specific species to colonize only the lupus gut. Eventually, these alterations and the changes in gut permeability induced by intestinal inflammation could lead to bacterial translocation.

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

Faecalibacterium represents one of the most abundant bacterial groups in the human intestinal microbiota of healthy adults and can represent more than 10% of the total bacterial population, Faecalibacterium prausnitzii being the only recognized species up to the past year. Reduction in the abundance of F. prausnitzii in the human gut has been linked to several human disorders, such as Crohn's disease. In this study, we developed a strategy to modify the relative abundance of F. prausnitzii in fecal microbiotas as a means of evaluating its contribution to the immunomodulatory effect of intestinal microbiotas with different F. prausnitzii contents using a peripheral blood mononuclear cell (PBMC) model. We used a polyclonal antibody against the surface of F. prausnitzii M21 to capture the bacterium from synthetic and human fecal microbiotas using immunoseparation techniques. As a proof-of-principle study, the levels of immunomodulation exerted by microbiotas of healthy donors (HDs) with different relative abundances of F. prausnitzii, achieved with the above-mentioned immunoseparation technique, were evaluated in a PBMC model. For this purpose, PBMCs were cocultivated with the modified microbiotas or a pure culture of F. prausnitzii and, subsequently, the microbiota of Crohn's donors was added to the coculture. The cytokine concentration was determined, showing that our experimental model supports the anti-inflammatory effects of this bacterium. IMPORTANCE 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.

[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.

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.

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

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 mixt

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