Endometrial whole metabolome profile at the receptive phase: influence of Mediterranean Diet and infertility

Introduction: Several metabolite classes have been identified in human endometrium, including lipids, nucleotides, amino acids, organic acids, and sugars. The first studies suggest the importance of metabolites in endometrial functions, as imbalance in uterine metabolites has been associated with low implantation rate and endometriosis. Nevertheless, most of studies have put emphasis on specific metabolite classes, and we lack the knowledge of the whole metabolome composition in human uterus. Further, a healthy dietary pattern has been shown to potentially protect against different endometrial dysfunctions and is a potential modulator of metabolomic composition and, consequently, the intrauterine microenvironment. The Mediterranean Diet (MD), characterized by a high intake of fruits, vegetables, cereals, nuts, legumes, fish, and olive oil, and a low consumption of meat, dairy products, and processed foods, has been associated with a wide range of benefits for health. Indeed, the MD pattern has displayed a beneficial role in endometriosis management and fertility; however, the relationship between the MD and the endometrial metabolome is still unknown. In our study, we set out to analyze receptivephase endometrial metabolome profiles among women with infertility and their associations with MD. Methods: The study included women with male factor infertility (n=8), unexplained infertility (n=10), recurrent implantation failure (n=14), and endometriosis (n=13). The endometrial metabolome was analyzed with ultrahigh-performance liquid chromatography-tandem mass spectroscopy (UPLC–MS/MS). The MD adherence of the participants was assessed using the 14-point MEDAS questionnaire of adherence to the MD. Results: We provide the whole metabolome profile of the endometrium, where 925 different metabolites were identified. Among these metabolites, lipids comprised the largest part, where polyunsaturated fatty acids (PUFAs) prevailed. Women with endometriosis and recurrent implantation failure were found to have lower levels of PUFAs compared to women with male factor and unexplained infertility (i.e., no clear endometrial alterations), identifying a metabolome profile associated with infertility diagnoses where altered endometrial functions are suspected. Moreover, MD adherence seemed to be associated with the endometrial metabolomic profile in a manner dependent on the health status of the uterus. Conclusion: The study findings provide insight into the molecular background of female infertility and lead to identification of potential molecular biomarkers and possibilities for modulating the endometrial microenvironment and, thereby, endometrial functions involved in embryo implantation and infertility.MCIN/AEI Endo-Map PID2021-12728OB-100 ENDORE SAF2017-87526-R PRE2018-085440 RYC-2016-21199 FPU19/03745 FPU19/01638 FPU19/01609ERFD A way of making EuropeESF Investing in your futureFEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento ROBIN A-CTS-614-UGR20 IRENE P20_00158University of Granada Plan Propio de Investigacion PPJIB2021-02Plan de Recuperacion, Transformacion y resiliencia, Ayudas para la recualificacion del sistema universitario espanol, Ayudas Margarita Sala

Focal Mechanisms for Subcrustal Earthquakes Beneath the Gibraltar Arc

Earthquakes below 50‐km depth are usually associated with active subduction, and the direction of faulting is aligned with the orientation of the subduction zone. Faulting in 42 earthquakes beneath the Gibraltar Arc and Alboran Sea shows different characteristics. The most abundant solutions show horizontal slip, in agreement with relative plate motion between Africa and Europe. Further solutions are associated with shortening and suggest compression from the basal drag of the Earth's mantle on the moving plates. In turn, no signature of active subduction was found. Images of the Earth's interior from teleseismic waves suggest a relation between the earthquakes and a stalled remnant of ~150‐Ma‐old oceanic material that once formed the connection between two oceans and later has been buried beneath the Gibraltar Arc.We received financial support through Mineco/Feder Project CGL2015‐67130‐C2‐2‐R and Junta de Andalucía research group RNM 10

Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination

We thank all men who generously donated testicular material for the purpose of this study. We also acknowledge the research support by Copan Italia S.p.A Inc., and Clearblue, SPD Swiss Precision Diagnostics GmbH. This study is part of a PhD Thesis conducted at the Official Doctoral Program in Biomedicine of the University of Granada, Spain. This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grant numbers RYC-2016-21199 and ENDORE (SAF2017-87526-R); by FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento: MENDO (B-CTS-500-UGR18); by Junta de Andalucia: (PAIDI P20_00158) by the University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES), and the Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European Regional Development Fund: (SOMM17/6107/UGR); by Spanish Ministry of Science, Innovation, and Universities: (PRE2018085440 and FPU19/01638); and by Spanish Ministry of Education, Culture, and Sport: (FPU15/01193). Funding for open access charge: Universidad de Granada/CBUA Sequence data of all testicular spermatozoa and negative control samples have been deposited in the National Centre for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra) under the BioProject ID PRJNA643898. The preliminary results of this study were presented as a poster communication at the 35th Annual ESHRE Meeting (Vienna, 2019).Research question: The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition? Design: The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed. Results: Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa. Conclusions: Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.Copan Italia S.p.A Inc.ClearblueSPD Swiss Precision Diagnostics GmbHSpanish GovernmentEuropean Commission RYC-2016-21199 SAF2017-87526-RFEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento: MENDO B-CTS-500-UGR18 Junta de Andalucia PAIDI P20_00158University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of ExcellenceUnit of Excellence on Exercise and Health (UCEES)Junta de Andalucia Consejeria de Conocimiento, Investigacion y UniversidadesEuropean Commission SOMM17/6107/UGRSpanish Government PRE2018085440 FPU19/01638 FPU15/01193Universidad de Granada/CBUA Sequence BioProject PRJNA64389

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

El microbioma del tracto reproductor masculino: desvelando su composición y orígenes

Almost every part of our body has coevolved microbial community and as more knowledge of the human microbiota (i.e., community of microorganisms) is acquired, it is becoming evident that microorganisms have a significant impact on our health and well-being. However, an imbalance in this host-microbe relationship can lead to a disease. In the context of human reproductive health, the microbiome (i.e., microorganisms and their genomes) of semen is a field of increasing scientific interest, although this microbial niche has received relatively limited attention compared to other body sites. Despite the evidence of seminal microbiome, a few studies have investigated the sources and acquisition pathways of microorganisms present in the semen. Likewise, the complete influence of the microbes of adjacent sites and its association with male fertility remains unclear. Recent studies have shown that semen harbours its own set of microbes which is polymicrobial and for a low biomass. Further, it has been shown that microorganisms in the semen substantially vary between individuals, suggesting that each has its unique and potentially individual bacterial community profile. Also, certain correlations have been established between the presence of specific bacteria in semen and its quality parameters. Further, bacteria are shared among partners and this bidirectional exchange can influence the microbial make-up of either partner with an implication on their health. This Doctoral Thesis studies the origin of the seminal microbial communities. The objectives of this Doctoral Thesis were: 1) to investigate the existence of microbes in human testicular samples; 2) to uncover potential sources and routes of microbial colonisation in the semen, and the effect of sterilisation method of vasectomy on seminal microenvironment; 3) to compile available data of microbial niches within couples, to assess the shared microbes within couple, and to determine the potential impact of female and male reproductive tract microbiomes on couple’s health; and 4) to highlight the methodological considerations and provide recommendations for low biomass microbial studies using endometrium as the study model. Four studies were carried out to address these objectives, with the main findings being: 1) human maturing spermatozoa from testicle biopsies harbour its unique low biomass microbial signature, with a possible role in the functional sperm development, which could be one source of the seminal microbial composition (Study I). 2) We found considerable differences in microbial diversity when comparing pre- and post-vasectomy semen samples which suggest that vasectomy influences the seminal microbial composition. Further, semen shares 50% of bacterial communities with urine, underscoring the intricate relationships between anatomically close but functionally distinct niches (Study II). 3) During unprotected sexual intercourse, the vaginal and seminal microbes mix and influence each other, forming the “seminovaginal microbiota” which influences the species composition of the couple’s reproductive tract, having both beneficial and detrimental effects on the health of couples (Study III). 4) The reproductive microbiome field requires clear, reproducible, and well-controlled study design to elucidate the healthy seminal microbiome. When analysing low microbial biomass tissue (as the testicle and semen), systematic control and elimination of possible contamination is crucial to obtain reliable microbiome data over the host information and to minimise misinterpretation of the results. We have proposed a set of guidelines for conducting microbiome studies on low biomass reproductive sites (Study IV).Casi todas las partes de nuestro cuerpo han coevolucionado con una comunidad microbiana, y a medida que adquirimos más conocimiento sobre la microbiota humana (comunidad de microorganismos), se vuelve evidente que los microorganismos tienen un impacto significativo en nuestra salud y bienestar. Sin embargo, un desequilibrio en esta relación huésped-microorganismo puede llevar enfermedades. En el contexto de la salud reproductiva humana, el microbioma (microorganismos y sus genomas) del semen es un campo de creciente interés científico, aunque este nicho microbiano ha recibido relativamente poca atención en comparación con otras áreas del cuerpo. A pesar de la evidencia del microbioma seminal, pocos estudios han investigado el origen y las vías de adquisición de los microorganismos presentes en el semen. Del mismo modo, la influencia de los microorganismos de sitios adyacentes y su asociación con la fertilidad masculina aún no está clara. Estudios recientes han demostrado que el semen alberga su propio conjunto de microorganismos, que es polimicrobiano y de baja biomasa. Además, se ha observado que los microorganismos en el semen varían considerablemente entre los individuos, lo que sugiere que cada uno tiene su perfil único y potencialmente individual de comunidad bacteriana. También se han establecido ciertas correlaciones entre la presencia de determinadas bacterias en el semen y sus parámetros de calidad. Además, se ha demostrado que las bacterias se comparten entre las parejas y este intercambio bidireccional puede influir en la composición microbiana de cada miembro de la pareja, con implicaciones para su salud. Esta Tesis Doctoral estudia el origen de las comunidades microbianas del semen. Los objetivos de esta Tesis Doctoral fueron: 1) investigar la existencia de microorganismos en muestras testiculares humanas; 2) descubrir posibles fuentes y rutas de colonización microbiana en el semen, y el efecto del método de esterilización masculina (vasectomía) en el microambiente seminal; 3) recopilar datos disponibles sobre los nichos microbianos dentro de las parejas, evaluar los microorganismos compartidos y determinar el impacto potencial de los microbiomas del tracto reproductivo femenino y masculino en la salud de la pareja; y 4) resaltar las consideraciones metodológicas y brindar recomendaciones para estudios microbianos de baja biomasa, utilizando el endometrio como modelo de estudio. Se llevaron a cabo cuatro estudios para abordar estos objetivos, siendo los principales hallazgos los siguientes: 1) los espermatozoides humanos obtenidos de biopsias testiculares albergan su propio microbioma de baja biomasa, con un posible papel en el desarrollo funcional de los espermatozoides, pudiendo ser un origen de la composición microbiana seminal (Estudio I). 2) Encontramos diferencias significativas en la diversidad microbiana al comparar muestras de semen antes y después de la vasectomía, lo que sugiere que la vasectomía influye en la composición microbiana seminal. Además, el semen comparte el 50% de las comunidades bacterianas con la orina, lo que subraya las relaciones complejas entre nichos anatómicamente cercanos, pero funcionalmente distintos (Estudio II). 3) Durante las relaciones sexuales sin protección, los microorganismos vaginales y seminales se mezclan e influyen mutuamente, formando el “microbioma seminovaginal” que influye en la composición de especies del tracto reproductivo de la pareja, con efectos beneficiosos y perjudiciales para su salud (Estudio III). 4) El campo del microbioma reproductivo requiere un diseño de estudio claro, reproducible y bien controlado para determinar el microbioma seminal en individuos sanos. Al analizar tejidos con baja biomasa microbiana (como el testículo y el semen), el control sistemático y la eliminación de posible contaminación son cruciales para obtener datos precisos del microbioma y minimizar la interpretación errónea de los resultados. Hemos propuesto un conjunto de pautas para llevar a cabo estudios del microbioma en sitios reproductivos de baja biomasa (Estudio IV).Tesis Univ. Granada.Contrato predoctoral del programa de Formación de Profesorado Universitario (referencia: FPU19/01638) del Ministerio de UniversidadesROBIN project (“The seminal microbiome: alive with function?”) (A-CTS-614-UGR20)European Regional Development Fund (FEDER) and Regional Ministry of Economic Transformation, Industry, Knowledge, and Universities of Andalusia and ENDORE project (“Search for biomarkers of uterine receptivity and developing a molecular test”) (SAF2017-87526-R)Spanish Ministry of Economy, Industry, and Competitiveness (MINECO) and FEDE

Omission of non-poly(A) viral transcripts from the tissue level atlas of the healthy human virome

A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al. describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. Using a workflow that maps the GTEx sequences to the human genome, then screens unmapped sequences to detect viral transcripts, the authors present a quantitative analysis of the presence of different viruses in the nondiseased tissues of over 500 individuals and assess the impact of these viruses on host gene expression. Here we draw attention to an issue not acknowledged in this study. Namely, by relying solely on GTEx datasets, which are enriched for transcripts with poly(A) tails, the analysis will have missed non-poly(A) viral transcripts, rendering this tissue level atlas of the virome incompleteSpanish Ministry of Economy, Industry and Competitiveness (MINECO)European Union (EU) RYC-2016-21199 ENDORE SAF2017-87526-RFEDER/Junta de Andalucía -Consejería de Economía y Conocimiento: MENDO B-CTS-500-UGR18University of Granada Plan Propio de Investigacion 2016 -Excellence actions: Unit of Excellence on Exercise and Health (UCEES) SOMM17/6107/UGRSpanish Ministry of Science, Innovation and Universities PRE2018-0854409 FPU19/0163

Supplementary material Ph.D Thesis (Study III)

Study III: supplementary materia

Supplementary material Ph.D Thesis (Study II)

Study II: supplementary materia