The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis / El microbioma urogenital en pacientes con enfermedad renal crónica en diálisis peritoneal

Introduction and objectives: Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters. Materials and methods: Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3–V4 region of the bacterial 16S rRNA gene. Correlations with the patients’ clinical data and inflammatory profile were performed. Results: CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups... (AU)

Introducción y objetivos: Diabetes, dislipemia, edad avanzada, género, infecciones del tracto urinario y toma reciente de antibióticos, entre otras, se han asociado a una disminución en la riqueza del urobioma y a otras fluctuaciones de dicho microbioma.Recientemente, se han descrito alteraciones en losmicrobiomas intestinal y en sangreen pacientes con enfermedad renal crónica (ERC) y, específicamente, en pacientes en diálisis peritoneal (DP).A pesar de ello, aún no existen estudios que describan el microbioma urogenital en pacientes en DP. En el presente trabajo, caracterizamos el urobioma en 46 pacientes en DP. Pacientes y métodos: Se recogieron muestras de orina (micción espontánea), heces y sangre de 46 pacientes en DP del Centro HospitalarUniversitário de São João en Oporto, Portugal. Los criterios de exclusión fueron edad menor a 18 años, incapacidad para entenderel consentimiento informado, e historia de infección y toma de antibióticos en los últimos 3 meses. Las comunidades microbiológicas fueron analizadas por amplificación y secuenciación de las regiones V3-V4 del 16S rRNA bacteriano. Se realizaron correlaciones con los datos clínicos y el perfil inflamatorio de los pacientes. Resultados: Los pacientes en DP presentaron un urobioma único dominado por Bacillota, Actinomycetota yPseudomonadota, y caracterizado por una menor diversidad de Shannon que los microbiomas en sangre e intestinal. Los perfiles taxonómicos de las muestras urogenitales se organizaron en múltiples subtipos dominados por poblaciones de Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, siendo similar al descrito para otros pacientes con ERC no en DP.Género, factor sCD14, diuresis residual yantecedentes de peritonitis se asociaron de forma significativa a cambios en el urobioma... (AU)

Infant Bronchiolitis Endotypes and the Risk of Developing Childhood Asthma: Lessons From Cohort Studies

Severe bronchiolitis (i.e., bronchiolitis requiring hospitalization) during infancy is a heterogeneous condition associated with a high risk of developing childhood asthma. Yet, the exact mechanisms underlying the bronchiolitis-asthma link remain uncertain. Birth cohort studies have reported this association at the population level, including only small groups of patients with a history of bronchiolitis, and have attempted to identify the underlying biological mechanisms. Although this evidence has provided valuable insights, there are still unanswered questions regarding severe bronchiolitis-asthma pathogenesis. Recently, a few bronchiolitis cohort studies have attempted to answer these questions by applying unbiased analytical approaches to biological data. These cohort studies have identified novel bronchiolitis subtypes (i.e., endotypes) at high risk for asthma development, representing essential and enlightening evidence. For example, one distinct severe respiratory syncytial virus (RSV) bronchiolitis endotype is characterized by the presence of Moraxella catarrhalis and Streptococcus pneumoniae, higher levels of type I/II IFN expression, and changes in carbohydrate metabolism in nasal airway samples, and is associated with a high risk for childhood asthma development. Although these findings hold significance for the design of future studies that focus on childhood asthma prevention, they require validation. However, this scoping review puts the above findings into clinical context and emphasizes the significance of future research in this area aiming to offer new bronchiolitis treatments and contribute to asthma prevention. (AU)

Estudio de la microbiota vaginal en los resultados de la terapia de reproducción asistida / Study of the vaginal microbiota in results of assisted reproduction therapies

El microbioma del tracto genital femenino es determinante para mantener un entorno saludable. La microbiota vaginal normal se caracteriza por la abundancia de Lactobacillus, que confieren protección a la vagina huésped contra microorganismos potencialmente patógenos que pueden provocar infecciones del aparato urinario y enfermedades de transmisión sexual. Las alteraciones en la microbiota vaginal por factores intrínsecos, como la edad o el ciclo menstrual, o externos, como la actividad sexual o el embarazo, pueden conducir a un estado de disbiosis microbiana y al desarrollo de enfermedades con efecto perjudicial en la fertilidad. También se ha señalado que la microbiota vaginal puede desempeñar un papel clave en el éxito de las terapias de reproducción asistida. El objetivo de esta revisión es identificar y evaluar los estudios sobre el papel de la microbiota vaginal en la salud de la mujer y la reproducción humana.(AU)

The microbiome of the female genital tract is essential to maintenance a healthy environment. The normal vaginal microbiota is defined by the abundance of Lactobacillus. These microbes confer the host vagina protection from potentially pathogenic microorganisms that may cause urinary tract infections and sexually transmitted diseases. Changes in the vaginal microbiota due to inherent factors, such as age or menstrual period, or external factors like sexual activity or pregnancy, can lead to microbial dysbiosis and the development of pathologies in relation of reduced rates of conception. It has also been suggested that vaginal microbiota may play a key role in the success of assisted reproductive therapies. The objective of this review is to identify and evaluate trials of the vaginal microbiota role in women's health and human reproduction.(AU)

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities. (AU)

De la microbiota como “cisne negro”: El extraño caso de los amiloides bacterianos y la neurodegeneración / Microbiota as a ‘black swan’: The extrange case of bacterial amyloids and neurodegeneration

La microbiota humana es la compleja comunidad de microorganismos que colonizan nuestros epitelios, con especial presencia en el intestino grueso. Investigaciones recientes vinculan a la microbiota con diversas patologías, entre las cuales aquí me ocuparé de las enfermedades neurodegenerativas. Metabolitos generados por las bacterias de nuestra microbiota tienen propiedades moduladoras de la inflamación, interaccionado con receptores específicos en el epitelio intestinal, permeando el tejido subyacente y abriéndose paso hacia los vasos sanguíneos, alcanzando así el sistema nervioso central (SNC). Por otra parte, proteínas con el potencial de agregar ordenadamente en forma de amiloides, secretadas por las bacterias para construir la matriz que entreteje las biopelículas que les permiten persistir en el intestino, pueden utilizar para llegar al SNC una vía alternativa: las terminaciones parasimpáticas del nervio vago, propagándose como priones (amiloides infectivos), lo que constituye el denominado “eje intestino-cerebro”. Una vez en el SNC, los amiloides bacterianos pueden promover la agregación de proteínas amiloidogénicas implicadas en neurodegeneración (α-sinucleína, Tau, Ab, Sod1). En este artículo se revisan y ponderan algunas de las recientes evidencias experimentales que, principalmente en sistemas modelo animales, asignan un papel central para la microbiota en la etiología de las enfermedades neurodegenerativas, así como los estudios realizados en el laboratorio del autor que han conducido al desarrollo de un sistema modelo mínimo, exclusivamente bacteriano, que recapitula aspectos moleculares esenciales de una enfermedad neurodegenerativa.(AU)

The human microbiota is the complex community of microorganisms that colonize our epithelia, with a special presence in the large intestine. Recent research links the microbiota to various pathologies, among which I will focus here on neurodegenerative diseases. Metabolites generated by the bacteria of our microbiota have inflammation-modulating properties, interacting with specific receptors in the intestinal epithelium, permeating the underlying tissue and making their way into the blood vessels, thus reaching the central nervous system (CNS). On the other hand, proteins with the potential to aggregate in the form of amyloids, secreted by bacteria to build the matrix that interweaves the biofilms that allow them to persist in the intestine, can use an alternative route to reach the CNS: the parasympathetic endings of the vagus nerve, spreading as prions (infective amyloids), in what is known as the “gut-brain axis”. Once in the CNS, bacterial amyloids can promote aggregation of amyloidogenic proteins involved in neurodegeneration (α-synuclein, Tau, Ab, Sod1). This article reviews and discusses some of the recent experimental evidence that, mainly in animal model systems, assigns a central role for the microbiota in the aetiology of neurodegenerative diseases, as well as the studies performed in the laboratory of the author that have led to the development of a minimal, exclusively bacterial model system that recapitulates essential molecular aspects of a neurodegenerative disease.(AU)

Hidradenitis supurativa / Hidradenitis suppurativa

La hidradenitis supurativa (HS) es una enfermedad inflamatoria crónica y recurrente derivada de la unidad pilosebácea, que afecta aproximadamente al 1% de la población general. Se caracteriza clínicamente por nódulos inflamatorios, abscesos y túneles en las áreas intertriginosas del cuerpo, especialmente en las regiones axilar, inguinal y anogenital. La etiopatogenia de la HS no está totalmente aclarada, aunque se considera que es multifactorial, y resultado de una compleja interacción entre factores genéticos, hormonales, ambientales e inmunológicos. En este sentido, determinadas citocinas proinflamatorias como el factor de necrosis tumoral-alfa (TNF-α), la interleucina (IL)-1β y la IL-17, entre otras, parecen desempeñar un papel fundamental en la patogénesis de la enfermedad. Actualmente, la HS es considerada una enfermedad inflamatoria sistémica asociada con numerosas comorbilidades, incluyendo enfermedades cardiovasculares, inmunomediadas y trastornos endocrino-metabolicos. El tratamiento de la HS debe realizarse con un enfoque individualizado y orientado al paciente, considerando modalidades de tratamiento médico y quirúrgico.(AU)

Hidradenitis suppurativa (HS) is a chronic and debilitating inflammatory disease derived from the pilosebaceous unit, that affects approximately 1% of the general population. Clinically, it is characterized by inflammatory nodules, abscesses, and tunnels in the intertriginous areas of the body, especially in the axillary, inguinal, and anogenital regions. The etiopathogenesis of HS is not completely understood, although it is considered to be multifactorial, and the result of a complex interaction between genetic, hormonal, environmental, and immunological factors. In this sense, several proinflammatory cytokines, such as tumor necrosis factor-alpha (TNF-α), interleukin (IL)-L-1β, and IL-17, among others, appear to play a crucial role in the pathogenesis of the disease. Currently, HS is recognized as a systemic disease associated with numerous comorbidities, including cardiovascular, immune-mediated, and endocrine-metabolic diseases. The treatment of HS must be carried out with an individualized and patient-oriented approach, considering medical and surgical treatment modalities.(AU)

Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time / Comunidades bacterianas a lo largo del tracto digestivo y respiratorio de los loros: los efectos del tipo de muestra, especie y tiempo

Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.(AU)

The initial composition and structure of microbial community determined the yield and quality of Baijiu during the spontaneous fermentation / La composición inicial y la estructura de la comunidad microbiana determinaron el rendimiento y la calidad del Baijiu durante la fermentación espontánea

The microbiota during pit mud fermentation is a crucial factor in Baijiu brewing since it determines the yield and flavor. However, the impact of the microbial community during the initial fermentation stage on Baijiu quality remains uncertain. Herein, high-throughput sequencing was employed to investigate the microbial diversities and distribution during Baijiu fermentation in individual pit mud workshops at both initial and late stages. During the initial fermentation stage, the bacterial community exerted a more pronounced effect on Baijiu quality than the fungal community. And the high-yield pit mud workshop exhibited lower richness and evenness, as well as greater Bray-Curtis dissimilarity during Baijiu fermentation. Lactobacillus was the dominant genus and biomarker in high-yield pit mud, and it constituted the only genus within the bacterial association network during the late fermentation stage. Fungal communities tended to maintain a simple association network with selected core species. Based on the correlation network, Rhizopus and Trichosporon were identified as biomarkers in Baijiu fermentation process. Together, Lactobacillus and Rhizopus could serve as bio-indicators for Baijiu quality during the initial fermentation stage. Therefore, these findings provided novel insights into microbiota interactions during fermentation and the impact of initial microbiota on final Baijiu quality.(AU)

In vitro assessment of biofunctional properties of Lactiplantibacillus plantarum strain Jb21-11 and the characterization of its exopolysaccharide / Evaluación in vitro de las propiedades biofuncionales de Lactiplantibacillus plantarum cepa Jb21-11 y caracterización de su exopolisacárido

The microbiota of traditional food provides a rich reservoir of biodiversity to find new strains with interesting features for novel functional food formulation. Therefore, this study aimed to investigate the biofunctional potential of the lactic acid bacteria (LAB) strain Jb21-11 isolated from Jben, a traditional Algerian fresh cheese. This isolate was selected out of a collection of 154 LAB based on its exopolysaccharide (EPS) phenotype and was preliminarily identified by polyphasic characterization as Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) and its biofunctional properties were then assessed in vitro. The tested strain demonstrated good resistance to gastric juice, acidity around pH 2, and 2% (v/v) bile salts, which are important characteristics for potential biofunctional LAB candidates. It also showed a good production of ropy EPS with 674 mg/L on MRS medium. However, this ability appears to compromise the adhesion of the strain to Caco-2 cells (less than 1%), which according to our results, seems not to be related to autoaggregation and hydrophobicity (44.88 ± 0.028% and 16.59 ± 0.012%). Furthermore, promising antimicrobial activity against three pathogenic bacteria (Escherichia coli, Staphylococcus aureus, and Salmonella) was detected probably due to antimicrobial metabolites excreted during fermentation process into the medium. Moreover, the strain L. plantarum Jb21-11 displayed a therapeutic functionality with both anti-inflammatory and immunomodulatory action using RAW 264.7 cells. The chemical features of the novel ropy Jb21-11-EPS were also investigated revealing the presence of three monosaccharides, namely, mannose, galactose, and glucose, with a molar ratio of 5.42:1.00:4.52 linked together by α- and β-glycosidic bonds, presenting a relatively high molecular weight of 1.08 × 105 Da of interest for a texturing potential. Therefore, the new producing EPS strain Jb21-11 is a promising candidate for use as an adjunct culture for improving the texture of functional food.(AU)

Combined Effects of Early Life Stress and Prolonged Exposure to Western Diet on Emotional Responses and Gut Microbiota / Efectos Combinados del Estrés Vital Temprano y la Exposición Prolongada a la Dieta Occidental Sobre las Respuestas Emocionales y la Microbiota Intestinal

Background: Exposure to early life stress (ELS) and maternal consumption of a high-fat and high-sugar diet can have detrimental effects on adult emotional responses. The microbiota and gut-brain axis have been proposed as playing a mediating role in the regulation of stress and emotion. Method: Young male rats were exposed to maternal separation (MS) together with maternal and postnatal consumption of a HFS diet (45%kcal saturated fat, 17%kcal sucrose). Anxiety-like behaviour was evaluated using an elevated zero-maze, and depression-like behaviour using the forced-swim and sucrose preference tests. Microbiota composition and derived metabolites were also analysed in faecal samples using a gas chromatograph and mass spectrometry. Results: Combined exposure to MS and lifelong consumption of a HFS diet partially reversed the abnormal anxiety-like and depression-like behaviours in early adulthood caused by each adverse factor alone. Diet composition had a greater negative impact than ELS exposure on the gut microbiota, and both environmental factors interacted with microbiota composition partially counteracting their negative effects. Conclusions: The effects of exposure to early life stress and a HFS diet independently are partially reversed after the combination of both factors. These results suggest that ELS and diet interact to modulate adult stress response and gut microbiota.(AU)

Antecedentes: El estrés temprano (ET) y el consumo materno de una dieta alta en grasas y azúcares (HFS) pueden tener efectos perjudiciales sobre las respuestas emocionales en la adultez. La microbiota y el eje intestino-cerebro podrían mediar la regulación del estrés y las emociones. Método: Ratas macho jóvenes se expusieron a separación materna (SM) y a consumo materno y postnatal de una dieta HFS (45%kcal grasa saturada, 17%kcal sacarosa). Se evaluó el comportamiento ansioso mediante el laberinto cero elevado y el comportamiento depresivo mediante natación forzada y preferencia por sacarosa. Se analizó la microbiota en heces empleando cromatografía de gas y espectrometría de masas. Resultados: La exposición combinada a la SM y el consumo de una dieta HFS revirtió parcialmente la ansiedad y depresión en adultos causadas independientemente por cada factor adverso. La dieta influyó negativamente más que la exposición a ET en la microbiota y ambos factores modificaron su composición contrarrestando parcialmente sus efectos negativos. Conclusiones: Los efectos del ET y una dieta HFS por independiente varían con respecto a los efectos de la combinación de ambos factores, sugiriendo que el ET y la dieta interactúan modulando en el adulto la respuesta al estrés y la microbiota intestinal.(AU)

Evaluation of antimicrobial activity of kefir drink against escherichia coli, salmonella typhimurium and shigella flexneri / Evaluación de la actividad antimicrobiana de la bebida de kéfir contra escherichia coli, salmonella typhimurium y shigella flexneri

Objetivo: Evaluar la actividad antimicrobiana de la bebida de Kéfir contra Escherichia coli, Salmonella typhimurium y Shigella flexneri. Método: El kéfir utilizado en la investigación fue adquirido en Toluca, Estado de México. Se realizó una reactivación del kéfir con leche pasteurizada y se analizaron 3 carbohidratos (miel, azúcar y piloncillo) en diferentes concentraciones y tiempos, 80, 100, 120% y 24, 48 y 72 horas respectivamente. Los microorganismos cultivables aislados se caracterizaron por técnicas fenotípicas, bioquímicas y de espectroscopia de masas. El pH inicial y final se determinaron durante el tiempo de estudio. La actividad antimicrobiana se realizó extrayendo los metabolitos presentes en el fermento con el método de Kirby-Bauer, además se evaluó el fermento directo, para determinar si hubo inhibición con las cepas de Escherichia coli ATCC 11229, Salmonella typhimurium ATCC 14028 y Shigella flexneri ATCC 12022. Resultados: Se observó que en los tres carbohidratos utilizados a una concentración de 120% y en un tiempo de 72 h, fue donde se obtuvo un pH menor (3,51 a 3,64) comparado con su concentración inicial (6,50 a 6,64). A partir de los metabolitos extraídos en los diferentes fermentos, no se obtuvo halo de inhibición con las cepas analizadas. Sin embargo, al usar fermentos directos, se observó que en los carbohidratos utilizados (azúcar, miel, piloncillo) existía la presencia de un halo de inhibición o el crecimiento de colonias distintas de las evaluadas. Los microorganismos cultivables aislados fueron: Pichia kudriavzevii (levadura); Enterococcus sp (coco grampositivo) y Lactobacillus sp (bacilo grampositivo). Conclusiones: Los fermentos de kéfir hechos con diferentes carbohidratos, llegaron a presentar un grado de inhibición solo como un consorcio contra microorganismos Gram-negativos analizados.Palabras Clave: Kéfir; fermentación microbiota; infección; actividad antimicrobiana.(AU)

Objective: Evaluate the antimicrobial activity of the Kefir drink against Escherichia coli, Salmonella typhimurium and Shigella flexneri. Method: The Kefir used in the investigation was acquired in Toluca, State of Mexico. We performed a reactivation of Kefir with pasteurized milk and analyzed 3 carbohydrates (honey, sugar and piloncillo) at different concentrations and times, 80, 100, 120% and 24, 48 and 72 hours respectively. Isolated cultivable microorganisms were characterized by phenotypic, biochemical and mass spectroscopy techniques. The initial and final pH were determined during the study time. The antimicrobial activity was carried out by extracting the metabolites present in the ferment with the Kirby-Bauer method, in addition the direct ferment was evaluated, to determine if there was inhibition with the Escherichia coli (ATCC 11229) strains, Salmonella typhimurium (ATCC 14028) and Shigella flexneri (ATCC 12022). Results: It was observed that in the three carbohydrates used at a concentration of 120% and at a time of 72 h, a lower pH was obtained (3.51 to 3.64) compared to their initial concentration (6.50 to 6.64). From the metabolites extracted in the different ferments, no inhibition halo was obtained with the strains analyzed. However, when using direct ferments, it was observed that in the carbohydrates used (sugar, honey, piloncillo) there was the presence of an inhibiting halo or the growth of colonies other than those evaluated. The isolated cultivable microorganisms were: Pichia kudriavzevii (yeast); Enterococcus sp (gram-positive coconut) and Lactobacillus sp (gram-positive bacillus). Conclusions : Kefir ferments made with different carbohydrates, came to present a degree of inhibition only as a consortium against Gram-negative microorganisms analyzed.(AU)

Compositional and functional diversities of core microbial communities in wild and artificial Ophiocordyceps sinensis / Diversidades compositivas y funcionales de comunidades microbianas centrales en Ophiocordyceps sinensis silvestre y artificial

Ophiocordyceps sinensis is an entomogenous fungus, and its wildlife resource is very insufficient, as it is widely traded as a natural health product. The artificial culture of O. sinensis is a remarkably effective progress in addressing the problem. Adding microorganisms may improve the process of artificial culture. To analyse the composition and function of the microbial community, high-throughput sequencing was used to explore the microbial community inhabiting wild and artificial O. sinensis and surrounding soil. Significant differences in the microbial communities across groups were revealed by the PCoA analysis. There were 51 fungal and 598 bacterial operational taxonomic units only being assigned to the fruiting bodies of wild O. sinensis (Wf) by the Venn diagram. From the LEfSe analysis, 39 fungal taxa and 75 bacterial taxa were enriched in Wf. Enzymes that were highly abundant in the core fungi were involved in physiological metabolic processes. Metabolic pathways were dominated in the core bacteria, followed by environmental information processing. The core microorganisms, with the marked differences between Wf and the other three groups, were essential for wild O. sinensis. Functional analysis verified their involvement in the growth, development, and infection of O. sinensis. These core microorganisms may be a valuable resource for the artificial culture of O. sinensis.(AU)

Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions—a pilot study / La secuenciación metagenómica revela comunidades microbianas de pulmón porcino y genomas ensamblados en metagenoma asociados con lesiones pulmonares: un estudio piloto

Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.(AU)

Gut microbiota disruption during sepsis and the influence of innate metabolites on sepsis prognosis / Alteración de la microbiota intestinal durante la sepsis y influencia de los metabolitos innatos en el pronóstico de la sepsis

Sepsis causes high mortality in intensive care units. Although there have been many studies on the gut microbiota in patients with sepsis, the impact of sepsis on the gut microbiota has not been directly determined because the treatment of sepsis also affects the gut microbiota. Therefore, we designed this animal experiment to explore gut microbiota alterations during sepsis. Mice were divided into two groups, mice that survived less than 3 days and mice that survived more than 3 days. Fecal samples collected on the day of cecal ligation and puncture (CLP), as well as on the 3rd and 7th days after CLP, were subjected to microbial community analysis and nontargeted metabolomics analysis. The results showed significantly lower bacterial diversity in fecal samples after CLP. At the genus level, the fecal samples obtained on the 3rd and 7th days after CLP exhibited significantly increased relative abundances of Bacteroides, Helicobacter, etc., and significantly decreased relative abundances of Alloprevotella, Prevotella, etc. Innate metabolite levels were significantly different in mice that survived less than 3 days and mice that survived more than 3 days. In conclusion, CLP-induced sepsis in mice changes the structure of the gut microbiome, and innate metabolites affect the prognosis of septic mice.(AU)

Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean / Comunidades microbianas en los sedimentos de aguas profundas de la meseta sur de São Paulo, océano Atlántico sudoccidental

Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.(AU)

Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya / La composición de especies del micobioma asociado a las raíces de la invasora ruderal Anthemis cotula L. varía con la elevación en Cachemira Himalaya

Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.(AU)

The Thing (1982): un primer modelo de prediagnóstico para las infecciones y alteraciones de la fisiología / The Thing (1982): A First Prediagnostic Model for Infections and Alterations of Physiology

The Thing / La cosa (El enigma de otro mundo) (1982) de John Carpenter, supone un reto audiovisual para pensar en el descubrimiento de claves para la detección temprana de infecciones hostiles. La búsqueda de técnicas rápidas y sencillas para la resolución de casos supone la diferencia entre la supervivencia y mantenerse en la desconfianza para un grupo que trata de descubrir quienes de ellos están infectados, y no terminar transformados en «otra cosa». Este trabajo permitirá al estudiantado conocer los cambios en el equilibrio homeostático que supondría la relación con los microorganismos de distinta naturaleza presentes en la sangre. (AU)

The Thing (1982) by John Carpenter represents an audiovisual challenge to think about the discovery of keys for the early detection of hostile infections. The search for quick and easy techniques for solving cases means the difference between survival and remaining suspicious for a group that tries to discover which of them are infected, and not end up transformed into «something else». This work will allow the student body to know the changes in the homeostatic balance that the relationship with microorganisms of different nature present in the blood would imply. (AU)

Lentes de contacto y disbiosis ocular, de lo transitorio a lo patológico / Contact lenses and ocular dysbiosis, from the transitory to the pathological

La microbiota ocular normal está compuesta por diferentes comunidades bacterianas Gram negativas y positivas que actúan en la superficie ocular como comensales. Un desequilibrio en la homeostasis de las especies nativas o disbiosis desencadena alteraciones funcionales que eventualmente pueden conllevar afecciones oculares, señalándose al uso de lentes de contacto como el factor predisponente más relevante. Mediante una revisión bibliográfica que incluyó artículos científicos publicados entre el año 2018 y 2022, se analizó la relación entre la microbiota ocular sana, la disbiosis asociada al uso de lentes de contacto que desencadena afecciones oculares. La microbiota ocular en individuos sanos, se compone principalmente por bacterias de los filos: proteobacterias, actinobacteria y firmicutes. Estas comunidades bacterianas al verse asociadas al uso de lentes de contacto desarrollaron disbiosis, observándose un aumento de ciertos géneros como Staphylococcus spp. y Pseudomonas spp., que en condiciones normales son comensales de la superficie ocular, pero al estar aumentada su abundancia condicionan la aparición de diversas afecciones oculares como eventos infiltrativos corneales, queratitis y úlcera corneal bacterianas. Dichas patologías tienden a evolucionar de manera rápida, lo que, sumado a una detección y tratamiento tardíos, puede determinar un pronóstico visual deficiente. Se sugiere que, frente a diversas afecciones de la superficie ocular, los profesionales en el área de oftalmología conozcan la composición de las comunidades de microorganismos que conforman esta microbiota ocular, de manera de distinguir e identificar correctamente el agente causal y, con ello, brindar un tratamiento adecuado y efectivo al usuario (AU)

Normal ocular microbiota is composed of different Gram-negative and positive bacterial communities that act as commensals on the ocular surface. An imbalance in the homeostasis of the native species or dysbiosis triggers functional alterations that can eventually lead to ocular conditions, indicating the use of contact lenses as the most relevant predisposing factor. Through a bibliographic review that added scientific articles published between 2018 and 2022, the relationship between healthy ocular microbiota and dysbiosis associated with the use of contact lenses that trigger ocular conditions was analyzed. The ocular microbiota in healthy individuals is mainly composed of bacteria from the phyla: proteobacteria, actinobacteria and firmicutes. These bacterial communities associated with the use of contact lenses develop dysbiosis, observing an increase in certain genera such as Staphylococcus spp. and Pseudomonas spp., which under normal conditions are commensals of the ocular surface, but as their abundance is increased, they condition the appearance of various ocular conditions such as corneal infiltrative events, bacterial keratitis and corneal ulcer. These pathologies tend to evolve rapidly, which, added to late detection and treatment, can lead to a poor visual prognosis. It is suggested that professionals in the ophthalmology area learn about the composition of the communities of microorganisms that make up this ocular microbiota, in order to correctly distinguish and identify the causative agent, thereby providing a adequate and effective treatment to the user (AU)

The first study characterizing the respiratory microbiome in cystic fibrosis patients in Jordan

Cystic fibrosis (CF) is most commonly seen in Caucasians and is uncommon in the Middle East. This study, based in Jordan, aimed to describe the association between lung exacerbation in CF patients and the respiratory microbiome composition. Using the 16S rRNA marker-gene sequencing, we investigated the microbiota in sputa during exacerbation (E1) and 14 days after the exacerbation (E2) of two CF patients admitted to the hospital. Detected genera with high abundance in the E1-related sputa of the first patient included Achromobacter and Streptococcus. At E2, Achromobacter and Staphylococcus were the highest abundant genera. Regarding the second patient, Veillonella and Streptococcus, were the highest abundant genera at E1. Whereas, Streptococcus and Veillonella were the highest abundant genera. This is the first study, based in Jordan, to report and describe the respiratory microbiome during and after the exacerbation of CF patients. This study suggests that pulmonary exacerbation in CF patients can result in alterations in their respiratory microbiome. A better knowledge of this link could allow more focused use of antibiotics, especially during exacerbations, improving clinical efficacy and patient outcomes. (AU)

Variation of butyrate production in the gut microbiome in type 2 diabetes patients / Variación de la producción de butirato en el microbioma intestinal en pacientes con diabetes tipo 2

Background: Diabetes mellitus type 2 is a common disease that poses a challenge to the healthcare system. The disease is very often diagnosed late. A better understanding of the relationship between the gut microbiome and type 2 diabetes can support early detection and form an approach for therapies. Microbiome analysis offers a potential opportunity to find markers for this disease. Next-generation sequencing methods can be used to identify the bacteria present in the stool sample and to generate a microbiome profile through an analysis pipeline. Statistical analysis, e.g., using Student’s t-test, allows the identification of significant differences. The investigations are not only focused on single bacteria, but on the determination of a comprehensive profile. Also, the consideration of the functional microbiome is included in the analyses. The dataset is not from a clinical survey, but very extensive. Results: By examining 946 microbiome profiles of diabetes mellitus type 2 sufferers (272) and healthy control persons (674), a large number of significant genera (25) are revealed. It is possible to identify a large profile for type 2 diabetes disease. Furthermore, it is shown that the diversity of bacteria per taxonomic level in the group of persons with diabetes mellitus type 2 is significantly reduced compared to a healthy control group. In addition, six pathways are determined to be significant for type 2 diabetes describing the fermentation to butyrate. These parameters tend to have high potential for disease detection. Conclusions: With this investigation of the gut microbiome of persons with diabetes type 2 disease, we present significant bacteria and pathways characteristic of this disease.(AU)