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Introduction: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce. Methods: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing. Results: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group. Conclusion: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship. Resumen: Introducción: El papel de la microbiota en los modelos animales de esclerosis múltiple está bien establecido; por el contrario, los estudios en humanos son escasos. Métodos: Estudio transversal descriptivo que compara la composición relativa de la microbiota intestinal en 30 pacientes con esclerosis múltiple (15 tratados con interferón β-1b, 15 sin tratamiento) y 14 controles sanos utilizando la secuenciación de última generación. Resultados: Los sujetos control y los pacientes con esclerosis múltiple presentaron diferente abundancia de los filos Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, y Lentisphaerae y 17 especies bacterianas. Concretamente, la abundancia en Firmicutes, Actinobacteria y Lentisphaerae y 6 especies mostró diferencias al comparar los grupos control y sin tratamiento, desapareciendo esta diferencia cuando se compararon con los pacientes tratados. Se observó reducción estadísticamente significativa en la abundancia de Prevotella copri en pacientes sin tratamiento en comparación con controles, mientras que los tratados con interferón β-1b presentaron un aumento significativo frente a pacientes sin tratamiento, asemejándose al grupo de pacientes sanos control. Conclusión: La composición de la microbiota intestinal fue diferente entre los pacientes con esclerosis múltiple y los controles, y entre los pacientes sin tratamiento y los tratados con interferón β-1b. En la mayoría de los casos, no se encontraron diferencias entre los pacientes tratados y los controles sanos, siendo especialmente evidente con P. copri. Esto podría indicar que la influencia del interferón β-1b sobre la microbiota intestinal podría subyacer en los beneficios clínicos observados en pacientes con esclerosis múltiple que siguen este tratamiento. Serán necesarios estudios longitudinales y funcionales para poder mostrar causalidad.

Background Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results. In this study, we investigated the use of a next-generation sequencing (NGS) metagenomic approach for monitoring the microbiota composition and uncovering the possible presence of pathogens in mice housed in specific pathogen-free (SPF) or conventional (non-SPF) facilities. Results Analysis of metagenomic NGS assay through public and free algorithms and databases allowed to precisely assess the composition of mouse gut microbiome and quantify the contribution of the different microorganisms at the species level. Sequence analysis allowed the uncovering of pathogens or the presence of imbalances in the microbiota composition. In several cases, fecal pellets taken from conventional facilities were found to carry gene sequences from bacterial pathogens (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Streptococcus pyogenes, Rodentibacter pneumotropicus, Citrobacter rodentium, Staphylococcus aureus), intestinal protozoa (Entamoeba muris, Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera, Syphacia obvelata), eukaryotic parasites (Myocoptes musculinus) and RNA virus (Norwalk virus). Thus, the use of NGS metagenomics can reduce the number of tests required for the detection of pathogens and avoid the use of sentinel mice. Conclusions In summary, in comparison with standard approaches, which require multiple types of test, NGS assay can detect bacteria, fungi, DNA and RNA viruses, and eukaryotic parasites from fecal pellets in a single test. Considering the need to protect animal well-being and to improve the success and reproducibility of preclinical studies, this work provides the proof-of-concept that the use of NGS metagenomics for health monitoring of laboratory mice is a feasible and dependable approach, that is able to broaden the current concept of health monitoring of laboratory mice from “pathogen surveillance” to a more inclusive “microbiota surveillance”.

RESUMEN Desde un punto de vista microbiológico, tanto en el tratamiento antimicrobiano empírico como el dirigido en la infección respiratoria se fundamenta en el perfil de sensibilidad de los microrganismos aislados y los posibles mecanismos de resistencia que puedan presentar. Estos últimos puedan variar en diferentes áreas geográficas según los perfiles de prescripción y los programas de vacunación. Los antibióticos betalactámicos, las fluoroquinolonas y los macrólidos son los antimicrobianos más empleados en la exacerbación de la enfermedad pulmonar obstructiva crónica y la neumonía adquirida en la comunidad. En su prescripción se deben tener en cuenta aspectos como la actividad intrínseca, el efecto bactericida y su capacidad para evitar el desarrollo de resistencias. Este último está relacionado con los parámetros PK/PD, la concentración preventiva de mutantes y la denominada ventana de selección. Mas reciente ha crecido en importancia el potencial impacto ecológico, no solo sobre la microbiota intestinal, sino también sobre la respiratoria. El mantenimiento del estado de eubiosis requiere el uso de antimicrobianos con bajo perfil de actuación sobre los microorganismos anaerobios. Con ellos se facilita la resiliencia de las poblaciones bacterianas que integran la microbiota, el estado de resistencia de colonización y se limita el daño colateral relacionado con la emergencia de resistencia a los anti-microbianos en los patógenos que producen las infecciones y las poblaciones bacterianas que integran la microbiota.

The objective of this study was to evaluate the use of earthworm meal (EW) and vermi-humus (VH) in broiler diets. A total of 225 day-old male broilers were divided into 5 treatment groups with 3 repetitions of 3 birds each. The treatment groups were: T1 – control (no EW or VH; T2 − 1.0% EW and 0% VH; T3 − 1.0% EW and 1.0% VH; T4 − 1.0% EW and 1.5% VH; and T5: 1.0% EW and 2.0% VH. The birds received (EW) and (VH) for 14 d, and after this period, they received the common diet. The birds were reared for 42 d and, at 42 d, one representative broiler chicken per pen, close to the average body weight, was selected for blood sampling using a sterile needle and heparinised vacuum tube. Performance data, blood results, immunity, ileum morphology and microbiota, the relative weight of carcass components and gastrointestinal organs, malondialdehyde (MDA) content, and breast and thigh meat quality were evaluated. EW and VH had a positive effect on the immune response of broilers, as well as producing a reduction in the aerobic bacteria in the birds’ intestines.Highlights Protein is a limiting factor for broiler performance, carcass yield, and meat quality; Poultry industry is searching for new protein sources which can be used on broiler diets; Insects meal are good protein sources in broiler nutrition and can be used on diets without compromising its performance.

[ES] Las bacterias resistentes a múltiples antibióticos, como el Enterococo resistente a vancomicina (ERV), son un problema creciente en los pacientes hospitalizados, por lo que se necesita estrategias alternativas para combatir estos patógenos. Las infecciones causadas por ERV suelen comenzar con la colonización del tracto intestinal, un paso crucial que se afectado por la presencia de la microbiota. Sin embargo, los antibióticos alteran la microbiota y esto promueve la colonización de ERV. Una vez que el patógeno ha colonizado el intestino, alcanza niveles muy altos pudiendo diseminar a otros órganos y pacientes. A pesar de su importancia, se sabe muy poco sobre los genes que codifica para colonizar el intestino y sobre el mecanismo por el cual la microbiota suprime su colonización intestinal, siendo los dos objetivos principales. En primer lugar hemos utilizado una metodología previamente descrita (Zhang et al., 2017, BMC Genomics), basada en la generación de una librería de mutantes por transposición junto a secuenciación masiva, con el fin de identificar los genes codificados por ERV necesarios para la colonización del intestino en ratones. Además, hemos realizado análisis metatranscriptómicos para identificar aquellos genes más expresados. El análisis ha identificado genes cuya interrupción reduce significativamente la colonización intestinal en el intestino grueso. Los genes que más afectaron a la colonización codifican proteínas relacionadas con la absorción o el transporte de diversos nutrientes como los carbohidratos (subunidad EIIAB del transportador PTS de manosa, el regulador transcripcional de la familia LacI, ácido N-acetilmurámico 6-fosfato eterasa) o iones (proteína transportadora dependiente de ATP (ABC) y proteínas del grupo [Fe-S]). El papel de estos genes en la colonización se ha confirmado mediante experimentos de mutagénesis directa y de competición con la cepa salvaje. Además, estos genes afectan a la colonización intestinal con diferentes antibióticos (clindamicina y vancomicina). Para identificar el mecanismo molecular por el cual cada gen afecta a la colonización, hemos realizado experimentos in vitro y ex vivo además del análisis transcriptómico. Los experimentos in vitro confirman que las proteínas del grupo [Fe-S] están involucradas en el transporte iones de hierro, principalmente Fe3+. Por otra parte, los genes de la subunidad EIIAB del transportador de manosa y del ácido N-acetilmurámico 6-fosfato eterasa son necesarios para la utilización de la manosa y el ácido N-acetilmurámico, respectivamente, azúcares que suelen estar presentes en el intestino. También confirmamos que el regulador transcripcional de la familia LacI es un represor que afecta a proteínas transportadoras ABC, probablemente implicadas en la absorción de carbohidratos. Además, algunos de estos genes están codificados principalmente por cepas clínicas de E. faecium y en menor medida por cepas comensales. En segundo lugar, estudiamos los mecanismos de protección de un consorcio de cinco bacterias comensales, que anteriormente se había demostrado que disminuían la colonización intestinal por ERV en ratones. Mediante transcriptómica, metabolómica y los ensayos in vivo observamos que el consorcio bacteriano inhibe el crecimiento de ERV mediante la reducción de nutrientes, concretamente fructosa. Por último, el análisis ARN-Seq in vivo de cada aislado en combinación con los ensayos ex vivo e in vivo demostraron que una sola bacteria (Olsenella sp.) proporciona protección. En conjunto, los resultados obtenidos han identificado la función de genes específicos requeridos por ERV para colonizar el intestino. Además, hemos identificado un mecanismo mediante el cual la microbiota confiere protección. Estos resultados podrían conducir a nuevos enfoques terapéuticos para prevenir las infecciones causadas por este patógeno multiresistente a los antibióticos., [CA] Els bacteris resistents a múltiples antibiòtics, com el Enterococo resistent a vancomicina (ERV), són un problema creixent en els pacients hospitalitzats, que són resistents a la majoria d'antibiòtics disponibles per la qual cosa es necessita estratègies alternatives per a combatre aquests patògens. Les infeccions causades per ERV solen començar amb la colonització del tracte intestinal, un pas crucial que es veu afectat per la presència de la microbiota. No obstant això, els antibiòtics alteren la microbiota i això promou la colonització de ERV. Una vegada que el patogen ha colonitzat l'intestí, aconsegueix nivells molt alts podent disseminar a altres òrgans i pacients. Malgrat la seua importància, se sap molt poc sobre els gens que codifica ERV per a colonitzar l'intestí i sobre el mecanisme pel qual la microbiota suprimeix la seua colonització intestinal. En primer lloc hem utilitzat una metodologia prèviament descrita (Zhang et al., 2017, BMC Genomics), basada en la generació d'una llibreria de mutants per transposició junt amb seqüenciació massiva, amb la finalitat d'identificar els gens codificats per ERV necessaris per a la colonització de l'intestí en ratolins. A més a més, hem realitzat anàlisi metatranscriptòmics per a identificar aquells gens més expressats. L'anàlisi ha identificat gens quina interrupció redueix significativament la colonització intestinal en l'intestí gros. Els gens que més van afectar la colonització codifiquen proteïnes relacionades amb l'absorció o el transport de diversos nutrients com els carbohidrats (subunitat EIIAB del transportador PTS de manosa, el regulador transcripcional de la família LacI, àcid N-acetilmuràmic 6-fosfat eterasa) o ions (proteïna transportadora dependent d'ATP (ABC) i proteïnes del grup [Fe-S]). El paper d'aquests gens en la colonització s'ha confirmat mitjançant experiments de mutagènesis directa i de competició amb el cep salvatge. A més, aquests gens afecten la colonització intestinal amb diferents antibiòtics (clindamicina i vancomicina). Per a identificar el mecanisme molecular pel qual cada gen afecta a la colonització, hem realitzat experiments in vitro i ex viu a més de l'anàlisi transcriptòmic. Els experiments in vitro confirmen que les proteïnes del grup [Fe-S] estan involucrades en el transport d'ions de ferro, principalment Fe3+. D'altra banda, els gens de la subunitat EIIAB del transportador PTS de manosa i de l'àcid N-acetilmuràmic 6-fosfat eterasa són necessaris per a la utilització de la manosa i l'àcid N-acetilmuràmic, respectivament, sucres que solen estar presents en l'intestí. També confirmem que el regulador transcripcional de la família LacI és un repressor que afecta proteïnes transportadores ABC, probablement implicades en l'absorció de carbohidrats. A més a més, alguns d'aquests gens estan codificats principalment per ceps clínics de E. faecium i en menor mesura per ceps comensals. En segon lloc, estudiem els mecanismes de protecció d'un consorci de cinc bacteris comensals, que adès s'havia demostrat que disminuïen la colonització intestinal per ERV en ratolins. Amb l'ús de transcriptòmica, metabolòmica i els assajos in vivo observem que el consorci bacterià inhibeix el creixement de ERV mitjançant la reducció de nutrients, concretament fructosa. Finalment, l'anàlisi ARN-Seq in vivo de cada aïllat en combinació amb els assajos ex viu i in vivo van demostrar que un sol bacteri (Olsenella sp.) proporciona protecció. En conjunt, els resultats obtinguts han identificat la funció de gens específics requerits per ERV per a colonitzar l'intestí. A més, hem identificat un mecanisme mitjançant el qual la microbiota confereix protecció. Aquests resultats podrien conduir a nous enfocaments terapèutics per a previndre les infeccions causades per aquest patogen multiresistent als antibiòtics., [EN] Multidrug-resistant bacteria, such as vancomycin-resistant-Enterococcus (VRE), are an increasing problem in hospitalized patients. Some VRE strains can be resistant to most available antibiotics, thus, alternative strategies to antibiotics are urgently needed to combat these challenging pathogens. Infections caused by VRE frequently start by colonization of the intestinal tract, a crucial step that is impaired by the presence of the intestinal microbiota. Administration of antibiotics disrupts the microbiota, which promotes VRE intestinal colonization. Once VRE has colonized the gut, it reaches very high levels, which promotes its dissemination to other organs and its transfer to other patients. Despite the relevance of VRE gut colonization, very little is known about the genes encoded by this pathogen to colonize the gut and about the mechanisms by which the microbiota suppresses VRE gut colonization. In this thesis, we have utilized a previously described methodology (Zhang et al., 2017, BMC Genomics), based on the generation of a transposon mutant library coupled with high-throughput sequencing, in order to identify VRE encoded genes required for colonization of the mouse intestinal tract. In addition, we have performed metatranscriptomic analysis in mice to identify VRE genes specifically expressed in the gut. Our analysis has identified genes whose disruption significantly reduces VRE gut colonization in the large intestine. The genes that most affected VRE gut colonization encoded for proteins related to the uptake or transport of diverse nutrients such as carbohydrates (PTS mannose transporter subunit EIIAB, LacI family DNA-binding transcriptional regulator, N-acetylmuramic acid 6-phosphate etherase) or ions (phosphate ABC transporter ATP-binding protein and proteins from [Fe-S] cluster). The role of these genes in gut colonization has been confirmed through targeted mutagenesis and competition experiments against a wild type strain. Moreover, these genes affect gut colonization under different antibiotic treatments (clindamycin and vancomycin). To elucidate the mechanism by which each gene influences gut colonization, we have performed in vitro and ex vivo experiments besides transcriptomic analysis. In vitro experiments confirm that proteins from [Fe-S] cluster are involved in the transport of different forms of iron ions, mostly Fe3+. On the other hand, the PTS mannose transporter subunit EIIAB and N-acetylmuramic acid 6-phosphate etherase genes are required for the utilization of mannose and N-acetyl-muramic acid, respectively, sugars that are usually present in the intestinal environment. We have also confirmed that LacI family DNA-binding transcriptional regulator is a repressor that affects the expression of genes encoding for an ABC transporter probably involved in the uptake of carbohydrates. Furthermore, we have confirmed that some of these genes are encoded mainly by E. faecium clinical strains but not or to a lower extent by commensal strains. Secondly, we studied the mechanisms of protection of a consortium of five commensals bacteria, previously shown to restrict VRE gut colonization in mice. Functional transcriptomics in combination with targeted metabolomics and in vivo assays performed in this thesis indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose. Finally, in vivo RNA-Seq analysis of each bacterial isolate of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the protective effect. Altogether, the results obtained have identified the function of specific genes required by VRE to colonize the gut. In addition, we have identified a specific mechanism by which the microbiota confers protection against VRE colonization. These results could lead to novel therapeutic approaches to prevent infections caused by this pathogen.

IntroductionThe intestinal microbiota comprises bacteria, fungi, archaea, protists, helminths and viruses that symbiotically inhabit the digestive system. To date, research has provided limited data on the possible association between an active lifestyle and a healthy composition of human microbiota. This review was aimed to summarize the results of human studies comparing the microbiome of healthy individuals with different physical activity amounts.MethodsWe searched Medline/Ovid, NIH/PubMed, and Academic Search Complete between August–October 2020. Inclusion criteria comprised: (a) cross-sectional studies focused on comparing gut microbiome among subjects with different physical activity levels; (b) studies describing human gut microbiome responses to any type of exercise stimulus; (c) studies containing healthy adult women and men. We excluded studies containing diet modifications, probiotic or prebiotic consumption, as well as studies focused on diabetes, hypertension, cancer, hormonal dysfunction. Methodological quality and risk of bias for each study were assessed using the Risk Of Bias In Non-randomized Studies—of Interventions tool. The results from cross-sectional and longitudinal studies are shown independently.ResultsA total of 17 articles were eligible for inclusion: ten cross-sectional and seven longitudinal studies. Main outcomes vary significantly according to physical activity amounts in longitudinal studies. We identified discrete changes in diversity indexes and relative abundance of certain bacteria in active people.ConclusionAs literature in this field is rapidly growing, it is important that studies incorporate diverse methods to evaluate other aspects related to active lifestyles such as sleep and dietary patterns. Exploration of other groups such as viruses, archaea and parasites may lead to a better understanding of gut microbiota adaptation to physical activity and sports and its potentially beneficial effects on host metabolism and endurance.

Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere. Made available in DSpace on 2021-04-22T12:33:54Z (GMT). No. of bitstreams: 1 Crop-type.pdf: 3986814 bytes, checksum: 821c0c429ef4059018e435040228ca78 (MD5) Previous issue date: 2021

Aim of this frontier review has been to highlight the role of microbiota in healthy subjects and in patients affected by renal diseases with particular reference to renal transplantation. The microbiota has a relevant role in conditioning the healthy status and the diseases. In particular gut microbiota is essential in the metabolism of food and has a relevant role for its relationship with the immune system. The indigenous microbiota in patients with chronic renal failure is completely different than that of the healthy subjects and pathobionts appear. This abnormality in microbiota composition is called dysbiosis and may cause a rapid deterioration of the renal function both for activating the immune system and producing large quantity of uremic toxins. Similarly, after renal trans-plantation the microbiota changes with the appearance of pathobionts, principally in the first period because of the assumption of immunosuppressive drugs and antibiotics. These changes may deeply interfere with the graft outcome causing acute rejection, renal infections, diarrhea, and renal interstitial fibrosis. In addition, change in the microbiota may modify the metabolism of immuno-suppressive drugs causing in some patients the need of modifying the immunosuppressant dosing. The restoration of the indigenous microbiota after transplantation is important, either to avoiding the complications that impair the normal renal graft, and because recent studies have documented the role of an indigenous microbiota in inducing tolerance towards the graft. The use of prebiotics, probiotics, smart bacteria and diet modification may restore the indigenous microbiota, but these studies are just at their beginning and more data are needed to draw definitive conclusions.

Na atualidade, as disbioses, a ruptura da barreira intestinal e a inflamação tornaram-se preocupações da avicultura industrial, uma vez que culminam no comprometimento fisiológico e produtivo das aves. Objetivou-se discutir o papel da microbiota intestinal das aves no desenvolvimento animal, bem como evidenciar os benefícios e/ou prejuízos causados por esses microrganismos. A metodologia adotada foi estudo descritivo, sendo realizada a revisão bibliográfica de trabalhos científicos publicados em diferentes bases indexadas, com recorte temporal das últimas décadas. Verificou-se que o uso do sequenciamento do gene ribossômico do RNA (rRNA) 16S constitui importante ferramenta para identificar e enumerar as bactérias intestinais presentes em aves de produção. No que concerne à composição da microbiota, no intestino delgado encontram-se principalmente os gêneros Lactobacillus, Estreptococcus, Enterococcus, Bifidobacterium, Bacterioides, Clostridium, Fusobacterium e coliformes. No intestino grosso, Lactobacillus, Bacterioides, Proteobacteria, Bacillus, Clostridium e Bifidobacterium. No intestino delgado, as bactérias participam do metabolismo melhorando a absorção de nutrientes, hidrolisam polissacarídeos produzindo ácidos graxos de cadeia curta, que serão absorvidos e participarão de rotas metabólicas importantes no fornecimento de fontes de carbono e energia para as aves. Apesar dos benefícios da microbiota em promover um ambiente intestinal estável, em situações desfavoráveis, tais como no manejo criatório inadequado, pode atuar como agentes patogênicos, produzir metabólitos tóxicos e prejudicar o desempenho produtivo das aves.

Humans live in a close association with a complex microbial ecosystem that is collectively termed microbiota. Microbiota is concentrated in the last part of the gastrointestinal tract, where it ferments undigested food residues and produces various metabolites that have a systemic influence on human physiology. The composition of microbiota is influenced by genetic and environmental factors that shape a unique ecosystem in each human. Despite considerable compositional variations, the functional output of the ecosystem is highly similar in all healthy individuals. Although it is still not possible to define normal microbiota, comparisons between patients suffering from a number of chronic diseases with unknown etiology and controls have shown that patients have specific, dysbiotic microbiota composition. While it still remains to be determined if the microbiota dysbiosis is an etiological factor or a consequence of a disease, these findings have initiated intensive microbiota research. Numerous proven functions of microbiota include contribution to the digestion, synthesis of essential metabolites (vitamins and amino acids) and the intensive crosstalk with the immune, the endocrine and the nervous system. Even though this field of research is still in an early stage, it is clear that microbial metabolites can have various effects on humans including direct beneficial effect, toxicity, but also more subtle interactions since microbial products can act as immune regulating or neuro-signaling molecules. The complex network of bidirectional interactions between microbiota and humans is unexplored but highly potent for development of novel strategies to preserve and improve health., Los humanos viven en la relación cercana con el ecosistema microbiano complejo que se denomina microbioma. La microbioma está concentrada en la última parte del tracto gastrointestinal, donde fermenta los residuos de la comida no digerida y produce varios metabolitos que tienen influencia sistemática en la fisiología humana. La composición de la microbioma está influenciada por los factores genéticos y ambientales que forman un ecosistema único en cada humano. A pesar de las variaciones composicionales considerables, el output funcional del ecosistema es muy similar en todos los individuales sanos. Aunque todavía no es posible definir la microbioma normal, las comparaciones entre los pacientes que sufren algunas enfermedades crónicas con etiología desconocida y los controles han demostrado que los pacientes tienen una composición específica, disbiótica de microbioma. Mientras todavía queda por determinar si la disbiosis de la microbioma es un factor etiológico o consecuencia de la enfermedad, estos hallazgos han estimulado investigaciones intensivas de la microbioma. Numerosas funciones atestadas de microbioma incluyen la contribución a la digestión, síntesis de metabolitos esenciales (vitaminas y aminoácidos) y diafonía intensiva con los sistemas inmune, endocrino y nervioso. Aunque este campo de investigación todavía está en una fase temprana, está claro que los metabolitos microbianos tienen varios efectos en los humanos, incluyendo efecto beneficial directo, toxicidad, pero también interacciones más finas, dado que los productos microbianos pueden funcionar como moléculas de regulación inmune y de neuro-señalización. La red compleja de interacciones bidireccionales entre la microbioma y los humanos está por explorar con potencial muy alto para desarrollar estrategias novedosas para preservar y mejorar la salud.

[EN] The importance of the microbiota for host health and disease is now widely appreciated. Microbial communities that inhabit the human body have been proposed as an essential aspect of the hypothesis focused on the developmental origin of health and disease (DOHaD), suggesting that altered microbial exposure during infancy could play a role in the risk of some immune-based diseases, such as obesity, allergy development or T2 diabetes mellitus. Indeed, associational studies have related perinatal factors that could disrupt neonatal microbial colonization, such as antibiotic intake, Csection and formula feeding, to these diseases later in life. Some authors have suggested that the interaction between the initial microbiome and the developing immune system could be crucial for a correct maturation of the latter. However, the exact molecular mechanisms that regulate the host−microbiome interconnection during this period are still unknown. Furthermore, despite the importance of maternal microbiota on initial neonatal microbial seeding, data concerning the effect of these perinatal factors on maternal microbiota are still scarce. Objectives: The general aim of the thesis was to to ascertain the impact of perinatal factors, such as mode and place of delivery, antibiotic use, maternal diet and gestational age on maternal-neonatal microbiota composition and their implications on health outcomes. Subjects: Participants in this study were part of a larger longitudinal cohort study conducted in the Mediterranean area, between 2015 and 2019. Mothers were enrolled in the Hospital Universitario y Politécnico La Fe, Hospital Clinico Universitario de Valencia, primary health-care units from Valencia and CEIC-Parc de Salut MAR. In this thesis, faecal samples at birth, 7 and 31 days were used as well as the saliva, amniotic fluid and placenta samples from a subset of participants. Methods: Next-generation sequencing targeting the V3−V4 region of the 16S rRNA gene was performed to assess the microbiota composition at each time point. Enzymelinked immunosorbent assay and Luminex assay were used for the determination of the molecular hormonal, metabolic and immune status of the participants and/or cellular models. Quantitative polymerase chain reaction (PCR) and reverse transcription PCR were also performed in a quantitative measurement of microbiota composition and for the assessment of gene expression in placental tissue and cellular models, respectively. The culture of different cell lines, including intestinal epithelial cells (Caco-2), mucusproducer cells (LSTH-17) and monocyte-like cells (THP-1), were used for the in vitro assays. Results and conclusion: Maternal microbiota at delivery was influenced by several perinatal factors, including immune status of amniotic cavity, diet during gestation and delivery mode. Maternal consumption of fat was positively related to Firmicutes spp. while carbohydrates, fibre and polyunsaturated fatty acids (PUFA) intakes were associated with higher relative abundance of Bacteroidetes and Proteobacteria levels. Some of these relations were also reflected in the neonatal microbiota at delivery. Indeed, children born by C-section and from mothers with higher fat intakes showed higher body mass index (BMI) index z-scores than those born from mothers with higher fibre consumption. Two bacterial profiles were found during the study. The first one was composed of health-related bacteria with short-chain fatty acids (SCFA) production activity, such as Roseburia, Faecalibacterium, Blautia, Lachnospira or Bacteroides genera. This group was associated with a distinct amniotic cytokine profile characterized by higher concentrations of IL-2, IL-5, IL-17 and TNF-α. Indeed, salivary cortisol concentration also showed positive relations with some of these genera independently of the delivery mode. The other group was characterized by Finegoldia, Peptoniphilus, Anaeroaoccus, Porphyromonas and Campylobacter genera. Those were associated with another amniotic cytokine profile dominated by IL-4, IL-13, IL-18, and IL-10 cytokines and more highly represented in mothers who had undergone a Csection. Some of these genera were negatively associated with salivary cortisol concentration. Thus, our results suggested that amniotic fluid immune status and cortisol concentration were related to maternal microbiota at delivery with implications also in neonatal microbiota. Furthermore, we described the effect of mode and place of birth in the microbial colonization evolution during the first month of life, showing that neonates born by Csection had a distinct microbial pattern and higher BMI index z-scores than vaginalborn infants, both at home and hospital. We proposed an in vitro molecular mechanism by which the differences observed in C-section-born neonates in terms of microbiota composition would promote a shift in immune system maturation through the lack of immune stimulation observed in these samples compared with those from vaginal-born infants, especially those from the home birth group. Thus, disruptions in the colonization process during the first month of life could have long-lasting consequences through an alteration of immune system development during this period., [ES] El gran impacto del microbioma humano sobre la salud del huésped es ampliamente conocido. Se cree que las comunidades microbianas que habitan el cuerpo humano serían un aspecto fundamental en la hipótesis promulgada sobre el posible origen de la enfermedad durante el desarrollo (DOHad) sugiriendo que alteraciones en la exposición microbiana durante la infancia podrían estar implicadas en el mayor riesgo de algunas enfermedades de base inmunológica como la obesidad, la alergia o la diabetes mellitus de tipo II. Además, se han encontrado relaciones significativas entre este tipo de enfermedades con algunos factores perinatales que se han descrito como disruptores del proceso de colonización, como la cesárea, el uso de antibióticos o la alimentación mediante leche de formula. Algunos autores sugieren que la interacción entre la microbiota inicial y el sistema inmunológico que está desarrollándose sería crucial para una correcta maduración de este. Sin embargo, los mecanismos exactos que mediarían en esta relación huésped-microbiota durante este periodo todavía se desconocen. Además, a pesar de la importancia de la microbiota materna para el inicio del proceso de colonización, todavía es escasa la información sobre como los diferentes factores perinatales afectan a la microbiota materna. Objetivos: El objetivo general de esta tesis fue definir el impacto de los diferentes factores perinatales como el tipo de parto, el uso de antibióticos, la dieta materna o la edad gestacional en la composición de la microbiota materno-neonatal y sus posibles implicaciones para la salud. Participantes: Los participantes del presente análisis son parte de un estudio longitudinal de cohorte desarrollado en el área mediterránea entre 2015 y 2019. Las madres fueron reclutadas en el Hospital Universitario y Politécnico de la Fe, el Hospital Clínico Universitario de Valencia, centros de atención primaria de la ciudad de Valencia y el CEIC-Parc de Salut MAR. En el presente trabajo se utilizaron las muestras fecales recogidas al parto, a los 7 y 31 días, así como las muestras de saliva, líquido amniótico y placenta de un grupo reducido de participantes. Métodos: Se utilizaron técnicas de secuenciación de nueva generación dirigidas a la región V3-V4 del gen 16S rRNA para la determinación de la composición de la microbiota de cada muestra a los tiempo estudiados. Además, el ensayo por inmunoadsorción ligado a enzimas y la técnica Luminex fueron usadas para la determinación de moléculas relacionadas con el estado hormonal, metabólico e inmune de las muestras y/o de los ensayos celulares. La PCR cuantitativa y la de transcripción reversa fueron usadas para realizar una medida cuantitativa de la composición microbiana y de la expresión de algunos genes seleccionados en las muestras de placenta y modelos celulares, respectivamente. EL cultivo de diferentes líneas celulares, como líneas epiteliales (Caco-2), productoras de moco (LSTH-17) y líneas similares a macrófagos (THP-1) fueron utilizadas en los ensayos in vitro. Resultados y conclusión: La microbiota materna al parto estuvo influenciada por diversos factores perinatales, incluyendo el estado inmunológico de la cavidad amniótica, la dieta durante el embarazo y el tipo de parto. El consumo materno de grasa estuvo positivamente relacionado con Fimicutes spp. Mientras que el consumo de carbohidratos, fibra y ácidos grasos poliinsaturados fueron asociados con mayores abundancias relativas de los filos Bacteroidetes y Proteobacteria. Algunas de estas relaciones fueron observadas también en la microbiota neonatal. Además, los niños nacidos por cesárea y de madres con altos consumos de grasa mostraron mayores IMC (índice de masa corporal) z-scores que aquellos que nacieron de madres consumidoras de fibra. Dos patrones microbianos fueron encontrados a lo largo de todos los análisis. El primero de ellos estaba compuesto por especies asociadas a la salud y productoras de SCFA como los géneros Roseburia, Faecalibacterium, Blautia, Lachnospira o Bacteroides. Este grupo estuvo asociado a un perfil de citoquinas caracterizado por IL2, IL-5, IL-17 y TNF-α. Los niveles de cortisol en saliva estuvieron positivamente correlacionados con algunos de estos géneros independientemente del tipo de parto. El otro patrón microbiano estuvo caracterizado por los géneros Finegoldia, Peptoniphilus, Anaeroaoccus, Porphyromonas y Campylobacter. Estos estuvieron relacionados con un perfil de citoquinas en la cavidad amniótica dominados por la presencia de IL-4, IL-13, IL-18 y IL-10 y con el parto por cesárea. Además, algunos de estos géneros estuvieron negativamente correlacionados con los niveles de cortisol en saliva. Así, nuestros resultados sugieren que el ambiente inmunológico de la cavidad uterina y la concentración de cortisol estuvieron relacionados con la composición de la microbiota materna al parto con implicaciones para la microbiota neonatal. Además, describimos el efecto del tipo de parto y el lugar en el proceso de colonización durante el primer mes de vida mostrando que los niños nacidos por cesárea tienen un perfil diferencial de microbiota y mayores IMC z-scores que los niños nacidos de forma vaginal, tanto en el hospital como en casa. En nuestra investigación, hemos propuesto un mecanismo molecular por el cual las diferencias en la composición microbiana de los niños nacidos por cesárea podrían provocar una alteración en la maduración del sistema inmunológico mediante la falta de imnunoestimulación observada estas muestras comparadas con aquellas obtenidas de los niños nacidos por parto vaginal, especialmente de aquellos nacidos en casa. Así, las alteraciones en el proceso de colonización durante el primer mes de vida podrían tener consecuencias a largo plazo en la salud infantil debido a una alteración del desarrollo del sistema inmunológico durante este periodo., [CA] El gran impacte del microbioma humà sobre la salut humana del hoste és amplament reconegut. Es creu que les comunitats microbianes que habiten el cos humà serien un aspecte fonamental en la hipòtesi promulgada sobre el possible origen de la malaltia durant el desenvolupament (coneguda com DOHad) suggerint que alteracions en l’exposició microbiana al llarg de la infància podrien estar implicades en el augment del risc a patir algunes malalties amb base immunològica com són l’obesitat, l’al·lèrgia o la diabetis mellitus tipus II. Així mateix, s’han trobat relacions significatives entre aquest tipus de malalties amb alguns factors perinatals que s’han descrit com disruptors del procés de colonització, com la cesària, l’ús d’antibiòtics o l’alimentació mitjançant llet de fórmula. Alguns autors suggereixen que la interacció entre la microbiota inicial i el sistema immunològic que estaria desenvolupant-se seria crucial per a una correcta maduració d’aquest últim. No obstant això, els mecanismes exactes que mediten en aquesta relació hoste-microbiota durant aquest període encara es desconeixen. A pesar de la importància de la microbiota materna en l’inici del procés de colonització, encara és escassa la informació sobre els diferents factors perinatals que afecten a la microbiota materna. Objectius: L’objectiu general d’aquesta tesi fou definir l’impacte dels diferents factors perinatals com el tipus de part, l’ús d’antibiòtics, la dieta materna o l’edat gestacional en la composició de la microbiota materno-neoantal i les possibles implicacions sobre la salut. Participants: Els participants del present anàlisi són part d’un estudi longitudinal de cohort de l’àrea mediterrània entre el 2015 i 2019. Les mares van ser reclutades en l’Hospital Universitari i Politècnic La Fe, l’Hospital Clínic Universitari de València, centres d’atenció primària de la ciutat de València i el CEIC-Pac de Salut Mar de Catalunya. En el present treball s’utilitzaren les mostres fecals recollides al part, als 7 i als 31 dies, així com les mostres de saliva, líquid amniòtic i placenta. Mètodes: S’utilitzaren tècniques de seqüenciació de nova generació dirigides a la regió V3-V4 del gen 16S rRNA per a la determinació de la composició de la microbiota de cada mostra als temps estudiats. Així mateix, l’assaig per immune adsorció lligat a enzims i la tècnica Luminex foren utilitzades per a la determinació de molècules relacionades amb l’estat hormonal, metabòlic e immunològic de les mostres i/o els assajos cel·lulars. La PCR quantitativa i la de transcripció en mode revers foren utilitzades per a realitzar una mesura quantitativa de la composició de la microbiota i de l’expressió d’alguns gens seleccionats en les mostres de placenta i models cel·lulars, respectivament. El cultiu de diferents tipus cel·lulars, com tipus epitelials (Caco-2), productors de moc (LSTH-17) i línies similars a macròfags (THP-1) foren utilitzades en els assajos in vitro. Resultats i conclusió: La microbiota materna en el moment del part va estar influenciada per diversos factors perinatals, incloent l’estat immunològic de la cavitat amniòtica, la dieta durant l’embaràs i el tipus de part. El consum matern de greix es va vore associat amb Fimicutes spp. Pel contrari, el consum de carbohidrats, fibra i àcids grassos poliinsaturades es van veure relacionats amb majors abundàncies relatives dels phylum Bacteroidetes i Proteobacteria. Algunes d’aquestes relacions foren també observades en la microbiota neonatal. Tan mateix, els nounats nascuts per cesària i de mares consumidores de greixos van mostrar majors índexs de massa corporal (IMC) zscores que els nonats nascuts de mares consumidores de fibra. Dos patrons microbians es trobaren al llarg de totes les anàlisis. La primera d’elles va estar composta per espècies associades amb la salut i productes d’àcids grassos de cadena curta (SCFA), com són els gèneres Rosburia, Faecalibacterium, Blautia, Lachnospira o Bacteroides. Aquest grup va estar associat a un perfil de citocines caracteritzat per interleucines (IL)-2, IL-5, IL-17 i TNF-alpha. Els nivells de cortisol en saliva al part estigueren positivament correlacionats amb alguns d’aquests grups , independentment del tipus de part. L’altre patró microbià estava caracteritzat per els gèneres Finegoldia, Peptoniphilus, Anaeroccocus, Porphyromonas i Campylobacter. Aquests grups foren relacionats amb el part per cesària i un perfil de citoquines en la cavitat amniòtica dominat per la presència de IL-4, IL-13, IL.18 i IL-10. A més, alguns d’aquests gèneres estigueren negativament relacionats amb els nivells de cortisol en saliva en el moment del part. Així, els nostres resultats suggereixen que l’ambient immunològic de la cavitat uterina i la concentració de cortisol tenien una relació amb la composició de la microbiota materna al part amb implicacions per a la microbiota neonatal. Tan mateix, descrivim l’efecte del tipus de part i el lloc de naixement (hospital vs. casa) en el procés de colonització durant el primer mes de vida, mostrant que els nonats nascuts per cesària tenien un perfil diferencial de microbiota i majors índexs de massa corporal (IMC) z-scores que aquells nonats nascuts de forma vaginal, tant a l’hospital com a casa. En la nostra investigació, hem proposat un mecanisme molecular pel qual les diferències en la composició microbiana podrien provocar una alteració en la maduració del sistema immunològic mitjançant una manca de inmuno-estimulació, observada en les mostres obtingudes dels nounats nascuts per cesària, especialment si es compara amb aquells nascuts a casa. Així, les alteracions en el procés de colonització, durant el primer mes de vida podrien tenir conseqüències a llarg termini en la salut infant debut a alteracions en el desenvolupament del sistema immunològic durant el període.

catalaEn la present tesi doctoral es van analitzar els mecanismes de defensa indirecta de dos patrons de citrics amb diferent nivell de susceptibilitat per a l’herbivor Tetranychus urticae (el mes resistent, Citrus aurantium, i el mes susceptible, C. reshni) mitjancant assajos de comportament amb els tres depredadors fitoseids de l’aranya amb diferents nivells d’especialitzacio en la seua dieta. Tambe, s’han caracteritzat els volatils associats a l’aranya roja i al mandariner Cleopatra induit pels volatils del bord infestat. En segon lloc, s’ha aprofundit en l’estudi de l’aranya roja, estudiant el seu microbioma, ja que s’ha demostrat que els bacteris simbionts poden influir en els parametres biologics dels artropodes, sent una de les especies bacterianes mes importants Wolbachia spp. Finalment, s’ha caracteritzat la resposta dels dos genotips de citrics a la infestacio de Polyphagotarsonemus latus per dilucidar les defenses, el perfil volatil i els mecanismes moleculars implicats en aquesta interaccio. EnglishIn the present doctoral thesis, the defensive response of citrus to two phytophagousmite species, the two-spotted spider mite Tetranychus urticae and the broad mite, Polyphagotarsonemus latus, has been studied, as well as the interaction of the main natural enemies of the two-spotted spider mite. In addition, the study of the microbiome of this phytophagous has been carried out to determine its composition as well as the role of symbiont bacteria. First of all, the mechanisms of indirect defense of two citrus rootstocks with different levels of susceptibility to the herbivore T. urticae (the most resistant, sour orange Citrus aurantium, and the most susceptible, Cleopatra mandarin C. reshni) were analyzed. To do this, a series of behavioral tests were conducted with three phytoseiid predator species of the spider mite with different diet levels of specialization to determine the role of herbivory-induced volatiles plant (HIPVs) in the citrus indirect defense. Moreover, volatiles associated with the spider mite and Cleopatra mandarin induced by T. urticae-infested sour orange have been characterized. Although the preference for less defended plants with presumably more prey density was expected, the response of the three phytoseiid mites studied depends on the plant genotype, the presence of the prey and their feeding habits. Secondly, the study of the key pest T. urticae has been deepened, specifically studying its microbiome, since it has been shown that symbiont bacteria can influence the biological parameters of arthropods. One of the key species is Wolbachia, which is part of a group of intracellular proteobacteria capable of manipulating the reproduction of their hosts. The microbiota characterization of T. urticae could provide new biological control strategies. For doing this, the bacterial community has been analyzed by massive sequencing of the 16S rDNA of two related subpopulations of T. urticae (treated and not treated with tetracycline antibiotic) from a clementine orchard in the region of La Plana maintained as lab strain. Mating assays have been performed between these two lines to determine the effect of the microbiota on the reproduction of the herbivore. The results show how the Wolbachia specie is the most abundant, it can be removed by the antibiotic and this bacterium induces cytoplasmic incompatibility affecting the reproduction of the mite. Finally, the response of the two citrus genotypes has been characterized when they are infested by P. latus to elucidate the defenses, the volatile profile and the molecular mechanisms involved in this interaction. The results demonstrate that the response of citrus to P. latus depends on the plant genotype and affects, at least, the expression of the main defensive pathways genes, that are, jasmonic (JA) and salicylic acid (SA) and the profile of released volatiles. Curiously and contrary to what happens with T. urticae, Cleopatra mandarin sustains lower P. latus populations compared with sour orange. The characterization of these effects can help improve current control practices against this pest.

Viruses are obligate intracellular pathogens that require the protein synthesis machinery of the host cells to replicate. These microorganisms have evolved mechanisms to avoid detection from the host immune innate and adaptive response, which are known as viral evasion mechanisms. Viruses enter the host through skin and mucosal surfaces that happen to be colonized by communities of thousands of microorganisms collectively known as the commensal microbiota, where bacteria have a role in the modulation of the immune system and maintaining homeostasis. These bacteria are necessary for the development of the immune system and to prevent the adhesion and colonization of bacterial pathogens and parasites. However, the interactions between the commensal microbiota and viruses are not clear. The microbiota could confer protection against viral infection by priming the immune response to avoid infection, with some bacterial species being required to increase the antiviral response. On the other hand, it could also help to promote viral evasion of certain viruses by direct and indirect mechanisms, with the presence of the microbiota increasing infection and viruses using LPS and surface polysaccharides from bacteria to trigger immunosuppressive pathways. In this work, we reviewed the interaction between the microbiota and viruses to prevent their entry into host cells or to help them to evade the host antiviral immunity. This review is focused on the influence of the commensal microbiota in the viruses' success or failure of the host cells infection.

The poultry red mite (PRM), Dermanyssus gallinae (De Geer, 1778), is a worldwide distributed ectoparasite and considered a major pest affecting the laying hen industry in Europe. Based on available information in other ectoparasites, the mite microbiome might participate in several biological processes and the acquisition, maintenance and transmission of pathogens. However, little is known about the role of PRM as a mechanical carrier or a biological vector in the transmission of pathogenic bacteria. Herein, we used a metaproteomics approach to characterize the alphaproteobacteria in the microbiota of PRM, and variations in its profile with ectoparasite development (nymphs vs. adults) and feeding (unfed vs. fed). The results showed that the bacterial community associated with D. gallinae was mainly composed of environmental and commensal bacteria. Putative symbiotic bacteria of the genera Wolbachia, C. Tokpelaia and Sphingomonas were identified, together with potential pathogenic bacteria of the genera Inquilinus, Neorickettsia and Roseomonas. Significant differences in the composition of alphaproteobacterial microbiota were associated with mite development and feeding, suggesting that bacteria have functional implications in metabolic pathways associated with blood feeding. These results support the use of metaproteomics for the characterization of alphaproteobacteria associated with the D. gallinae microbiota that could provide relevant information for the understanding of mite-host interactions and the development of potential control interventions., This work was partially supported by the European Cooperation in Science and Technology (COST), Improving Current Understanding and Research for Sustainable Control of the Poultry Red Mite Dermanyssus Gallinae–COREMI Project (Action FA 1404) (https://www.coremi.eu/home.html). JFLB was supported by Doctorado Industrial contract (DI-14-06917) from Ministerio de Ciencia, Innovación y Universidades (Spain) and Sabiotec S. A. MV was supported by the University of Castilla-La Mancha (Spain).

Alzheimer’s disease is a neurodegenerative disorder characterized by the loss of cognitive functions. The prevalence of this disease worldwide is high, and therefore it is important to have a better understanding of the oral health needs and conditions of individuals with this disorder. The present study was carried out in a population with E280A mutation for Alzheimer’s disease. The goal was to describe the salivary characteristics of persons with early familial Alzheimer’s disease, in order to detect changes in the oral microbiome that can guide the dental management of these patients. Methods: transversal study in 37 participants living in the Metropolitan Area of the city of Medellín, aged 53 ± 6 years in average, in different stages of the disease: mild: 8, moderate: 7, and severe: 22, and evaluated by neuropsychological tests. Salivary samples were collected, evaluating saliva secretion rate and saliva buffer capacity, and conducting microbial analysis of the species most commonly found in the mouth. Results: 45.9% of participants showed a decreased rate of stimulated salivary secretion; salivary buffer capacity was decreased in 83.87% of participants, with average pH values of 3.449 ± 0.89 after the Ericsson test. Buffer capacity was altered in participants with decreased secretion rate and in those with no alteration in salivary secretion rate. High levels of microbial growth were observed, mainly for Streptococcus mutans and Candida albicans. Conclusions: this study suggests that other factors besides the pharmacological ones, like age and disease severity, may affect the salivary rate flow in patients with early familial Alzheimer’s disease. Keywords: familial Alzheimer’s disease, xerostomia, Buffer capacity, stimulated saliva. RESUMEN: La enfermedad de Alzheimer es una alteración neurodegenerativa caracterizada por la pérdida de funciones cognitivas. Existe una alta prevalencia de esta enfermedad a nivel mundial, por lo que resulta oportuno tener una mayor comprensión de las necesidades y condiciones de salud bucal de los sujetos con este desorden. El presente estudio se llevó a cabo en una población con mutación E280A para la enfermedad de Alzheimer. El objetivo consistió en describir las características salivares de las personas con enfermedad de Alzheimer familiar precoz, con el fin de detectar cambios en el microbioma bucal que puedan orientar el manejo odontológico de estos pacientes. Métodos: estudio transversal en 37 participantes que habitan el Área Metropolitana de la ciudad de Medellín, con una edad promedio de 53 ± 6 años, en diferentes estadios de la enfermedad: leve: 8, moderada: 7 y grave: 22, evaluados mediante pruebas neuropsicológicas. Se tomaron muestras salivares, se evaluó la tasa de secreción salivar y la capacidad buffer de la saliva y se efectuó un análisis microbiano de las principales especies presentes en boca. Resultados: el 45,9% de los participantes presentaron una tasa disminuida de secreción salivar estimulada; la capacidad buffer salivar estuvo disminuida en el 83,87% de los participantes, con valores promedios de pH luego de la prueba de Ericsson de 3,449 ± 0,89. La capacidad buffer se encontró alterada tanto en los participantes con tasa de secreción disminuida como en aquellos con tasa de secreción salivar no alterada. Se observó alto crecimiento microbiano, principalmente de Streptococcus mutans y Candida albicans. Conclusiones: este estudio sugiere que pueden existir otros factores, además de los farmacológicos, que afectan la tasa de flujo salivar en los pacientes con enfermedad de Alzheimer familiar precoz, como la edad y la severidad de la enfermedad. Palabras clave: enfermedad de Alzheimer familiar, xerostomía, capacidad Buffer, saliva estimulada.

Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host–parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern., Article impact statement: Applying genetic, epigenetic, and microbial analyses to wildlife disease can inform active management and improve conservation outcomes.

Mycoplasma hyopneumoniae is the etiologic agent of swine enzootic pneumonia. However other mycoplasma species and secondary bacteria are found as inhabitants of the swine respiratory tract, which can be also related to disease. In the present study we have performed a total DNA metagenomic analysis from the lungs of pigs kept in a field condition, with suggestive signals of enzootic pneumonia and without any infection signals to evaluate the bacteria variability of the lungs microbiota. Libraries from metagenomic DNA were prepared and sequenced using total DNA shotgun metagenomic pyrosequencing. The metagenomic distribution showed a great abundance of bacteria. The most common microbial families identified from pneumonic swine's lungs were Mycoplasmataceae, Flavobacteriaceae and Pasteurellaceae, whereas in the carrier swine's lungs the most common families were Mycoplasmataceae, Bradyrhizobiaceae and Flavobacteriaceae. Analysis of community composition in both samples confirmed the high prevalence of M. hyopneumoniae. Moreover, the carrier lungs had more diverse family population, which should be related to the lungs normal flora. In summary, we provide a wide view of the bacterial population from lungs with signals of enzootic pneumonia and lungs without signals of enzootic pneumonia in a field situation. These bacteria patterns provide information that may be important for the establishment of disease control measures and to give insights for further studies.

Celiac disease (CD) is an autoimmune and multisystem gluten-related disorder that causes symptoms involving the gastrointestinal tract and other organs. Pathogenesis of CD is only partially known. It had been established that ingestion of gluten proteins present in wheat and other cereals are necessary for the disease and develops in individuals genetically predisposed carrying the DQ2 or DQ8 human leukocyte antigen haplotypes. In this review, we had pay specific attention on the last discoveries regarding the three cellular components mainly involved in the development and maintenance of CD: T-cells, B-cells, and microbioma. All of them had been showed critical for the interaction between inflammatory immune response and gluten peptides. Although the mechanisms of interaction among overall these components are not yet fully understood, recent proteomics and molecular studies had shed some lights in the pathogenic role of tissue transglutaminase 2 in CD and in the alteration of the intestinal barrier function induced by host microbiota.

The phyllosphere is colonized by complex microbial communities, which are adapted to the harsh habitat. Although the role and ecology of nonpathogenic microorganisms of the phyllosphere are only partially understood, leaf microbiota could have a beneficial role in plant growth and health. Pesticides and biocontrol agents are frequently applied to grapevines, but the impact on nontarget microorganisms of the phyllosphere has been marginally considered. In this study, we investigated the effect of a chemical fungicide (penconazole) and a biological control agent ( Lysobacter capsici AZ78) on the leaf microbiota of the grapevine at three locations. Amplicons of the 16S rRNA gene and of the internal transcribed spacer were sequenced for bacterial and fungal identification, respectively. Pyrosequencing analysis revealed that the richness and diversity of bacterial and fungal populations were only minimally affected by the chemical and biological treatments tested, and they mainly differed according to grapevine locations. Indigenous microbial communities of the phyllosphere are adapted to environmental and biotic factors in the areas where the grapevines are grown, and they are resilient to the treatments tested. The biocontrol properties of phyllosphere communities against downy mildew differed among grapevine locations and were not affected by treatments, suggesting that biocontrol communities could be improved with agronomic practices to enrich beneficial populations in vineyards.

Gut microbiota is the community of live microorganisms residing in the digestive tract. There are many groups of researchers worldwide that are working at deciphering the collective genome of the human microbiota. Modern techniques for studying the microbiota have made us aware of an important number of nonculturable bacteria and of the relation between the microorganisms that live inside us and our homeostasis. The microbiota is essential for correct body growth, the development of immunity, and nutrition. Certain epidemics affecting humanity such as asthma and obesity may possibly be explained, at least partially, by alterations in the microbiota. Dysbiosis has been associated with a series of gastrointestinal disorders that include non-alcoholic fatty liver disease, celiac disease, and irritable bowel syndrome. The present article deals with the nomenclature, modern study techniques, and functions of gut microbiota, and its relation to health and disease.

The most invalidating and life-threatening complication in Hirschsprung’s disease patients (HSCR) is Hirschsprung’s disease-associated enterocolitis (HAEC). The mechanisms underlying enterocolitis have not been identified. The limited knowledge of the role of intestinal microflora is in part due to the complexity of the intestinal microbiome and to the limitation of cultivation-based technologies, given that less than 25% of the intestinal bacterial species can be cultured. We used amplified ribosomal DNA restriction analysis (ARDRA) with four different restriction enzymes to study variations of microflora composition of the stools of a selected HSCR patient in different clinical conditions (acute phase vs. remission). We assessed a total of 15 stool specimens belonging to the same 3-year-old male patient suffering from HSCR, which were harvested during 4 HAEC episodes and remission phases. Restriction analysis showed that HAEC episodes seem to cluster together at ARDRA analysis, thus suggesting a sort of predisposing bacterial community for HAEC development and the need for a microflora equilibrium to maintain wellness. This approach proved to be effective, useful and powerful in assessing microflora dynamics and indicated that the differences in microflora associated with acute HAEC or remission are likely to result from a combination of disease activity and different antibiotic therapies. ARDRA proved to be useful in discriminating disease versus remission. Our findings indicated that HAEC results from a change in the equilibrium between bacterial species or from altered discrimination of harmless from harmful microorganisms, challenging the definition of pathogenic and non-pathogenic species. Based on these results, we propose ARDRA as a rapid inexpensive tool to assess microflora dynamics during HAEC episodes.

During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. The microbiota varies with age, with features that depend on the body site, host lifestyle and health status. The challenge is therefore to identify and characterize these microbial communities and use this information to learn how they function and how they can influence the host in terms of health and well-being. Here we provide an overview of some of the recent studies involving the human microbiota and about how these communities might affect host health and disease. A special emphasis is given to studies related to tuberculosis, a disease that claims over one million lives each year worldwide and still represents a challenge for control in many countries, including Colombia. En las últimas décadas ha incrementado nuestro conocimiento sobre la gran cantidad de microorganismos que conviven con nosotros, comunidades que colectivamente se conocen como la microbiota humana. El número de microorganismos que conforman la microbiota supera el número de células del cuerpo humano por un factor de diez aproximadamente y aporta un gran repertorio de genes y procesos metabólicos. La diversidad de la microbiota humana y su potencial metabólico brindan al hospedero una serie de funciones que complementan sus procesos y a su vez pueden influir sobre la salud del ser humano en formas que apenas se empiezan a conocer. La microbiota varía desde el nacimiento hasta la vejez del individuo, con características que dependen del sitio corporal, del estilo de vida y del estado de salud del hospedero. El reto actual es aprovechar el conocimiento derivado de la identificación y caracterización de estas comunidades microbianas para entender cómo funcionan estos microorganismos y cómo pueden influir de forma positiva o negativa sobre la salud del humano. En este documento ofrecemos una revisión general de algunos estudios recientes sobre la microbiota humana y su posible efecto en el hospedero en términos de salud y bienestar. Igualmente, se mencionan estudios sobre microbiota y su posible asociación con la tuberculosis, una enfermedad que todavía cobra más de un millón de vidas anualmente a nivel mundial y cuyo control todavía representa un gran reto en varios países del mundo, incluido Colombia.

To review the significance of a new type of neutrophil cell death (NETosis) in diabetes and cardiometabolic diseases.Diabetes and the metabolic syndrome are characterized by activation of the innate immune system. In this framework, neutrophils are front line defences against infections, but can also turn deleterious if abnormally stimulated. NETosis refers to a type of cell death whereby neutrophils release nuclear material and granule enzymes that together form the NETs (neutrophil extracellular traps). As NETs entrap bacteria, NETosis is instrumental to the clearance of microorganisms, but an exaggerated NETosis response can also lead to tissue damage in several pathological conditions. In diabetes, the finely tuned balance of NETosis required to protect the human body from microorganisms yet avoiding self-damage seems to be lost. In fact, in vitro induction of NETosis and circulating concentrations of NET-associated proteins appear to be enhanced in diabetic patients. Furthermore, NETs contribute to endothelial damage, thrombosis, and ischemia/reperfusion injury, making it a novel player in the pathobiology of cardiovascular disease. Though the cellular events taking place during NETosis have been described and directly visualized, its molecular machinery is still incompletely understood. Protein kinase C (PKC) and NADPH oxidase (NOX) are two important targets to counter NETosis in the setting of diabetes.NETosis appears to be part of an abnormal response to damage in diabetes that, in turn, can promote or aggravate end-organ complications. We suggest that this will be a hot topic of investigation in diabetology in the near future.

Objective: Triggered by the growing knowledge on the link between the intestinal microbiome and human health, the interest in probiotics is ever increasing. The authors aimed to review the recent literature on probiotics, from definitions to clinical benefits, with emphasis on children. Sources: Relevant literature from searches of PubMed, CINAHL, and recent consensus statements were reviewed. Summary of the findings: While a balanced microbiome is related to health, an imbalanced microbiome or dysbiosis is related to many health problems both within the gastro-intestinal tract, such as diarrhea and inflammatory bowel disease, and outside the gastro-intestinal tract such as obesity and allergy. In this context, a strict regulation of probiotics with health claims is urgent, because the vast majority of these products are commercialized as food (supplements), claiming health benefits that are often not substantiated with clinically relevant evidence. The major indications of probiotics are in the area of the prevention and treatment of gastro-intestinal related disorders, but more data has become available on extra-intestinal indications. At least two published randomized controlled trials with the commercialized probiotic product in the claimed indication are a minimal condition before a claim can be sustained. Today, Lactobacillus rhamnosus GG and Saccharomyces boulardii are the best-studied strains. Although adverse effects have sporadically been reported, these probiotics can be considered as safe. Conclusions: Although regulation is improving, more stringent definitions are still required. Evidence of clinical benefit is accumulating, although still missing in many areas. Misuse and use of products that have not been validated constitute potential drawbacks. Resumo: Objetivo: Motivado pelo conhecimento cada vez maior da associação entre o microbioma intestinal e a saúde humana, o interesse nos probióticos vem crescendo cada vez mais. Os autores visaram analisar a última literatura a respeito dos probióticos, de definições a benefícios clínicos com ênfase nas crianças. Fontes dos dados: Foi analisada a literatura relevante de pesquisas do PubMed, do CINAHL e dos últimos consensos. Síntese dos dados: Apesar de um equilíbrio no microbioma estar relacionado à saúde, um desequilíbrio no microbioma ou disbiose está relacionado a vários problemas de saúde no trato gastrointestinal, como diarreia e doença inflamatória intestinal, e fora do trato gastrointestinal, como obesidade e alergia. Nesse contexto, a regulamentação rigorosa dos probióticos a alegações de saúde é urgente, pois a grande maioria desses produtos é comercializada como alimentação (suplementos), alegando benefícios à saúde que frequentemente não são comprovados com evidências clinicamente relevantes. As principais indicações de probióticos são feitas na área da prevenção e tratamento de doenças gastrointestinais, porém mais dados têm sido disponibilizados a respeito de indicações extraintestinais. Pelo menos dois ensaios clínicos controlados e randomizados publicados com o probiótico comercializado na indicação declarada são a condição mínima antes de uma afirmação poder ser mantida. Atualmente, o Lactobacillus rhamnosus GG e Saccharomyces boulardii são as melhores cepas estudadas. Apesar de efeitos adversos terem sido esporadicamente relatados, os probióticos podem ser considerados seguros. Conclusões: Apesar de a regulamentação estar aumentando, ainda são necessárias definições mais rigorosas. As evidências de benefícios clínicos estão aumentando, apesar de ainda ausentes em várias áreas. O uso inadequado e a utilização de produtos não validados constituem possíveis desvantagens. Keywords: Bifidobacteria, Gastro-intestinal microbiota, Lactobacillus, Microbiome, Probiotic, Palavras-chave: Bifidobactérias, Microbiota gastrointestinal, Lactobacillus, Microbioma, Probiótico

Gut microbiota can undoubtedly be considered as an organ capable, internally to our body, of affecting its wellness and health, stimulating the immune system, playing a role in certain cases of cancer and generally combating several inflammatory and infectious diseases (Rajilic-Stojanovic et al. 2007). An adequate life style and dietary supplementation of functional ingredients can support it, with indubitable advantages not only for consumer but also for the economy, taking into consideration the increasing cost of healthcare in all ...

The study of the human microbiome or community of microbes and collection of genomes found in the human body is one of the fastest growing research areas because many diseases are reported to be associated with microbiome imbalance or dysbiosis. With the improvement in novel sequencing techniques, researchers are now generating millions of sequences of different sites from the human body and evaluating specific differences in microbial communities. The importance of microbiome constituency is so relevant that several consortialike MetaHIT and HMP are focusing mainly on the human microbiome. The aim of this review is to highlight points of research in this field, mainly focusing on particular factors that modulate the microbiome and important insights into its potential impact on our health and well-being. Fil: Bakhtiar, Syeda M.. Universidade Federal Do Minas Gerais. Instituto de Ciências Biológicas; Brasil; Fil: Leblanc, Jean Guy Joseph. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Centro de Referencia para Lactobacilos (i); Argentina; Universidad Nacional de Tucuman. Facultad de Medicina; Argentina; Fil: Salvucci, Emiliano Jesus. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto de Ciencia y Tecnología de Alimentos Córdoba; Argentina; Fil: Ali, Amjad. Universidade Federal Do Minas Gerais. Instituto de Ciências Biológicas; Brasil; Fil: Martin, Rebeca. Institut National de la Recherche Agronomique. Commensal and Probiotics-Host Interactions Laboratory; Francia; AgroParisTech; Francia; Fil: Langella, Philippe. Institut National de la Recherche Agronomique. Commensal and Probiotics-Host Interactions Laboratory; Francia; AgroParisTech; Francia; Fil: Chatel, Jean-Marc. Institut National de la Recherche Agronomique. Commensal and Probiotics-Host Interactions Laboratory; Francia; AgroParisTech; Francia; Fil: Miyoshi, Anderson. Universidade Federal Do Minas Gerais. Instituto de Ciências Biológicas; Brasil; Fil: Bermudez Humaran, Luis G.. Institut National de la Recherche Agronomique. Commensal and Probiotics-Host Interactions Laboratory; Francia; AgroParisTech; Francia; Fil: Azevedo, Vasco. Universidade Federal Do Minas Gerais. Instituto de Ciências Biológicas; Brasil

El metagenoma humano es una composición de los genes de las células eucarióticas del Homo sapiens y los genes presentes en los miles de millones de ge-nomas de los microorganismos que colonizan nuestro cuerpo (microbioma). La gran colección de microbios que colonizan en nuestro intestino se ha estimado que oscila entre 10 - 100 trillones de organismos. El micro-bioma intestinal codifica para capacidades metabólicas que se mantienen sin dilucidar pero que incluyen la degradación de componentes indigeribles de nuestra dieta. La obesidad se produce por alteraciones en la regulación de la ingesta, el gasto y el almacenamiento calórico en el organismo (cuerpo). Comparaciones de la microbiota intestinal distal de ratones genéticamente obesos y sus compañeros normales de camada, así como las de voluntarios humanos obesos y delgados han revelado que la obesidad se asocia con cambios en la abundancia relativa de las dos divisiones dominantes de bacterias (phylum), los Bacteroidetes y los Firmicutes. Esos resultados sugieren que la microbiota intestinal afecta a la adquisición de nutrientes y la regulación de la energía. En este artículo se revisa la evidencia publicada que apoya el papel potencial de la flora intestinal en el desarrollo de la obesidad y explora el rol que la modificación de la microbiota intestinal puede jugar en su tratamiento futuro.

The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.