The role of different microbiota in metastatic brain tumors

View full abstracthttps://openworks.mdanderson.org/leading-edge/1005/thumbnail.jp

Elucidating the Role of Microbiome in Low- and High-Grade Glioma

https://openworks.mdanderson.org/sumexp22/1117/thumbnail.jp

High Fiber Dietary Intervention Induces Change in Role of Faecalibacterium Prausnitzii in Gut Microbiome Ecosystem

https://openworks.mdanderson.org/sumexp23/1036/thumbnail.jp

Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study

Background: The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking are associated with differences in the oral and gut microbiota, in comparison to non-smoking controls. Methods: We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Results: Tobacco smokers had significantly different bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with a higher relative abundance of Prevotella (P = 0.006) and lowered Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. Discussion: The current pilot data demonstrate that tobacco smoking is associated with signicant differences in the oral and gut microbiome in humans. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted

Network Analysis of Gut Microbiome Throughout a Whole Foods Based High Fiber Dietary Intervention Reveals Complex Community Dynamics in Melanoma Survivors

https://openworks.mdanderson.org/sumexp22/1139/thumbnail.jp

Impact of a Whole Foods Based High Fiber Diet on Gut Microbiome in Melanoma Survivors

https://openworks.mdanderson.org/sumexp21/1237/thumbnail.jp

SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives

VirMAP for Cancer: Characterization of the Intratumoral Virome in Virally-Associated Cancers and a Resource for Investigators

View full abstracthttps://openworks.mdanderson.org/leading-edge/1040/thumbnail.jp

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi

A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral cavity. Therefore, to recognize which gut fungi are likely to have a sustained influence on human health, there is a need to separate transient members of the GI tract from true colonizers. To identify colonizing fungi, the eukaryotic rRNA operon’s second internal transcribed spacer (ITS2) was sequenced from the stool, saliva, and food of healthy adults following consumption of different controlled diets. Unlike most bacterial 16S rRNA genes, the only fungal ITS2 operational taxonomic units (OTUs) detected in stool DNA across multiple diets were also present in saliva and/or food. Additional analyses, including culture-based approaches and sequencing of the 18S rRNA gene, ITS2 cDNA, and DNA extracted using alternative methods, failed to detect additional fungi. Two abundant fungi, Saccharomyces cerevisiae and Candida albicans, were examined further in healthy volunteers. Saccharomyces became undetectable in stool when a S. cerevisiae-free diet was consumed, and the levels of C. albicans in stool were dramatically reduced by more frequent cleaning of teeth. Extremely low fungal abundance, the inability of fungi to grow under conditions mimicking the distal gut, and evidence from analysis of other public datasets further support the hypothesis that fungi do not routinely colonize the GI tracts of healthy adults

Behavior of diarrhea caused by viruses and bacteria in regions located near the Equator

Introducción: La enfermedad diarreica aguda (EDA) es un problema de salud a nivel mundial que afecta a la población infantil de distintas regiones. Casi todos los estudios epidemiológicos se han hecho en países con estaciones y poco se informa su comportamiento en países sin estaciones, donde la EDA es endémica con picos epidémicos. Objetivos: Contribuir a conocer la conducta de EDA en Colombia y determinar si su comportamiento es diferente en niños menores de cinco años en dos regiones distintas entre sí en geografía y clima. Materiales y métodos: Se hizo un estudio descriptivo en dos localidades colombianas. Una en la costa atlántica y otra en el centro del país. La muestra se obtuvo en menores de cinco años que consultaron por diarrea a centros asistenciales de cada región. Los microorganismos bacterianos se identificaron mediante pruebas bioquímicas y los virus con técnicas inmunoenzimáticas. En el análisis estadístico se siguieron un ensayo bivariado y pruebas Z de normalidad para verificar si el clima modifica el comportamiento de EDA y si se presenta de manera distinta en las dos regiones. Resultados: En ambas zonas (Cartagena, Bolívar y Facatativa, Cundinamarca) predominó la diarrea viral, frente a la EDA bacteriana. También en ambas el rotavirus fue prevalente. Fue mucho más baja la presencia de astrovirus y adenovirus. No hubo datos con significación estadística para demostrar que las condiciones ambientales y las propias de los niños, alteran el comportamiento de la EDA, pero sí se observó que la EDA por rotavirus se comporta de manera diferente al analizar en forma comparativa las dos regiones del estudio. Introduction: The infectious acute diarrhea (IAD) constitutes an important health problem affecting a large number of children worldwide. The morbility index associated with the IAD in children under five years of age, involves between 2.6% and 3.3% episodes/child/year, with mortality index of 3.2 millions per year. Most of the epidemiological studies have been performed in countries belonging to temperate zones but little is known concerning the tropics, where this infection is endemic. Objectives: The aim of this study was to contribute to the knowledge of the IAD in Colombia comparing two geographic and climatically different regions, one located at the Caribbean coast (Cartagena) and another of the central highland (Facatativá). We analyzed the etiology of the two regions identifying the source of the infection. Material and methods: Diarrheic samples from children under five years of age who had medical assistance in local hospitals were collected during 14 months. Bacteria were isolated in selective media and typified with biochemical methods. The presence of viruses was detected with immunoassay commercial kits. Analyses of independent variables (age, gender, temperature, rainfall and humidity) were evaluated with bivariated and Z tests and correlated with the presence of the infection in both regions. Results: The predominance of viral diarrhea was higher in both regions (29.2% and 21.4%) compared with the bacterial source of infections (16% and 15%) for Cartagena and Facatativá, respectively. Rotavirus was the most frequent pathogen with prevalences around 24.8% and 18%, respectively. Astrovirus and enteric adenovirus had prevalences below 3%. There were no significant statistic differences between the regions studied accounting for the infection or supporting that different climate conditions or child characteristics could be associated with diarrhea. However, the Z test showed that rotavirus and in general, all viral infections follow different patterns when analyzed comparatively in both regions