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Background: Cancer is the second leading cause of death in the world. Unfortunately, survival rates for cancer patients have stayed poor for many decades. Thus, there is an unmet need to identify novel strategies for early cancer detection and prevention. Recent studies suggest that the gut microbiome including bacteria may have a role in cancer initiation and progression. These bacteria play a vital role in maintaining homeostasis in the body. An imbalance in the bacterial composition may cause diseases including cancer. This evidence led us to hypothesize that the changes in the composition of the gut microbiome can be used as a biomarker for early cancer detection. To test this hypothesis, we focused on analyzing the microbial community of colorectal and blood cancers, which have poor survival rates. Methods and Results: To analyze the association of cancer with the microbiome, we used a published microbiome dataset of leukemic and healthy individuals that were collected by sequencing stool samples (Oliver et al., 2022). We identified that specific bacteria are either abundant, such as Faecalibacterium (1.17 fold), or reduced, such as Clostridium (0.32 fold, p value=0.0029), in leukemia patients compared to healthy controls. We observed similar correlations by analyzing the published colorectal cancer data (Flemer et al., 2017) in which Prevotella increased by 3.75 fold and Escherichia/Shigella increased by 4.0 fold in colorectal cancer while Blautia is reduced compared to healthy controls. Faecalibacterium, which is abundant in leukemia, is reduced in colorectal cancer. Further, we found that treatment of leukemia patients normalized the abundance of these bacteria to the level of healthy patients. To improve analysis efficiency, we applied machine learning algorithms to predict the presence of cancer in patients based on the composition of bacteria, age, gender, and symptoms. Among the tested algorithms, the decision tree and Random Forest both had very high false-negative rates, with 45.5% and 40% respectively, as well as having low sensitivities, with 50% and 60% respectively. The support Vector Machine had a suboptimal false-negative rate of 28.6% and good sensitivity of 80%. Finally, the Neural network had a good false-negative rate of 16.7% and great sensitivity of 90%. Overall, our results suggest that different cancers have an abundance of specific bacteria that can be used as biomarkers for cancer detection. Conclusion: We demonstrate that the increased abundance of certain bacteria in the microbiome can be used as a biomarker for cancer detection. Our data set was small for this project, but the machine learning approaches can be used to further predict cancer These are clinically relevant findings as a microbiome test would be non-invasive and easily accessible that can be performed at a routine checkup. Citation Format: Ekansh Mittal, Andrew Oliver, Kenza El Alaoui, Carolyn Haunschild, Julio Avelar-Barragan, Laura F. Mendez Luque, Katrine Whiteson, Angela G. Fleischman. Specific gut microbial community is associated with specific cancer types: A strategy for cancer detection and prevention [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5908.

Deux vases en bronze attribues a la periode romaine font partie des collections d’œuvres d’art qu’Auguste Dutuit legua au Petit Palais a son deces, en 1902. En 1980, ils furent consideres comme des creations a l’antique du xixe siecle. Neanmoins, les reproductions de plusieurs dessins du debut du xixe s. appartenant a la Lewis Walpole Library de l’universite de Yale ont recemment circule dans la communaute scientifique. Ils attestent qu’au xviiie s., les deux vases faisaient partie de la collection d’Horace Walpole en Angleterre. De fait, l’un d’entre eux fut publie des 1707, alors qu’il se trouvait encore a Rome. Cet article retrace d’abord leur provenance et leur passage dans plusieurs collections privees notables. Il demontre ensuite que plusieurs aspects stylistiques – notamment les decors figures et floraux en relief sur leur panse – initialement consideres comme indicateurs de leur origine moderne, confirment au contraire leur origine antique.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome. ispartof: NATURE MICROBIOLOGY vol:4 issue:10 pages:1727-1736 ispartof: location:England status: published

Dietary shifts can have a direct impact on the gut microbiome by preferentially selecting for microbes capable of utilizing the various dietary nutrients. The intake of dietary fiber has decreased precipitously in the last century, while consumption of processed foods has increased. Fiber, or microbiota-accessible carbohydrates (MACs), persist in the digestive tract and can be metabolized by specific bacteria encoding fiber-degrading enzymes. The digestion of MACs results in the accumulation of short-chain fatty acids (SCFAs) and other metabolic by-products that are critical to human health. Here, we implemented a 2-week dietary fiber intervention aiming for 40 to 50 g of fiber per day within the context of a course-based undergraduate research experience (CURE) (n = 20). By coupling shotgun metagenomic sequencing and targeted gas chromatography-mass spectrometry (GC-MS), we found that the dietary intervention significantly altered the composition of individual gut microbiomes, accounting for 8.3% of the longitudinal variability within subjects. Notably, microbial taxa that increased in relative abundance as a result of the diet change included known MAC degraders (i.e., Bifidobacterium and Lactobacillus). We further assessed the genetic diversity within Bifidobacterium, assayed by amplification of the groEL gene. Concomitant with microbial composition changes, we show an increase in the abundance of genes involved in inositol degradation. Despite these changes in gut microbiome composition, we did not detect a consistent shift in SCFA abundance. Collectively, our results demonstrate that on a short-term timescale of 2 weeks, increased fiber intake can induce compositional changes of the gut microbiome, including an increase in MAC-degrading bacteria. IMPORTANCE A profound decrease in the consumption of dietary fiber in many parts of the world in the last century may be associated with the increasing prevalence of type II diabetes, colon cancer, and other health problems. A typical U.S. diet includes about ∼15 g of fiber per day, far less fiber than the daily recommended allowance. Changes in dietary fiber intake affect human health not only through the uptake of nutrients directly but also indirectly through changes in the microbial community and their associated metabolism. Here, we conducted a 2-week diet intervention in healthy young adults to investigate the impact of fiber consumption on the gut microbiome. Participants increased their average fiber consumption by 25 g/day on average for 2 weeks. The high-fiber diet intervention altered the gut microbiome of the study participants, including increases in known fiber-degrading microbes, such as Bifidobacterium and Lactobacillus.

Salmonella enterica subsp. enterica serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three S. Typhimurium DT104 strains associated with a 2009 outbreak caused by ground beef, including the outbreak source strain and two clinical strains. The goal of the study was to gain a stronger understanding of the genomics and genomic epidemiology of highly clonal S. typhimurium DT104 strains associated with bovine sources. Our study found no single nucleotide polymorphisms (SNPs) between the ground beef source strain and the clinical isolates from the 2009 outbreak. SNP analysis including twelve other S. typhimurium strains from bovine and clinical sources, including both DT104 and non-DT104, determined DT104 strains averaged 55.0 SNPs between strains compared to 474.5 SNPs among non-DT104 strains. Phylogenetic analysis separated the DT104 strains from the non-DT104 strains, but strains did not cluster together based on source of isolation even within the DT104 phage type. Pangenome analysis of the strains confirmed previous studies showing that DT104 strains are missing the genes for the allantoin utilization pathway, but this study confirmed that the genes were part of a deletion event and not substituted or disrupted by the insertion of another genomic element. Additionally, cgMLST analysis revealed that DT104 strains with cattle as the source of isolation were quite diverse as a group and did not cluster together, even among strains from the same country. Expansion of the analysis to 775 S. typhimurium ST19 strains associated with cattle from North America revealed diversity between strains, not limited to just among DT104 strains, which suggests that the cattle environment is favorable for a diverse group of S. typhimurium strains and not just DT104 strains.

Recent research has elucidated many factors which play a role in the development and composition of human microbiomes. In this study we briefly examine the microbiomes of saliva and fecal samples from 71 indigenous individuals, and chicha samples from 28 single family households in a remote community in the Ecuadorian Amazon. Fecal and saliva samples were collected at two separate time points whereas chicha samples were collected at four time points, once each day of the fermentation process. In total 324 samples were collected: 113 saliva, 108 chicha, and 103 fecal. Microbial composition and diversity were assessed using shotgun metagenome sequence data. Chicha samples were found to be nearly entirely composed of the order Lactobacillales, accounting for 90.1% of the relative abundance. Saliva samples also contained a high relative abundance of Lactobacillales (31.9%) as well as being composed of Neisseriales (12.8%), Actinomycineae (8.7%), Bacteroidales (7.0%), Clostridiales (6.8%), Micrococcineae (6.5%), and Pasteurellales (6.0%). Fecal samples were largely composed of the three orders Clostridiales (33.7%), Bacteroidales (21.9%), and Bifidobacteriales (16.5%). Comparison of α-diversity, as calculated by Shannon’s Diversity Index, in mothers and their offspring showed no significant difference between the two groups in either fecal or saliva samples. Comparison of β-diversity in fecal and saliva samples, as calculated by the Bray-Curtis Dissimilarity measure, within household units and between differing households showed that members of the same household were significantly less dissimilar to each other than to members of other households in the community. Average microbiome composition for individuals within fecal and saliva samples was assessed to determine the impact of an individual’s household on the composition of their microbiome. Household was determined to have a significant impact on both fecal and oral microbiome compositions.

Fecal microbiota transplantation may reduce urinary tract infection by altering gut microbiome.

Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions., Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition.

This protocol presents a low volume methodology for the Nextera DNA Flex Library Prep Kit (96 Samples). This method increases the number of sequencing libraries which can be generated using each kit from 384 samples (4 x 96-wells) to 864 samples (9 x 96-wells). While other low-cost methods have been deveolped for this purpose, this protocol is a very straightforward method utilizing reduced reagent and sample volumes. Update: The "Nextera DNA Flex Library Prep" kit has been renamed to "Illumina DNA Prep" with the appropriate indexes having been similarly renamed. While all reagents and steps remain identical, an updated version of this protocol may be published to account for any differences between the protocols.

Background Britain is becoming an increasingly sedentary society; public health statistics tell us our health is being affected by our everyday lifestyle choices with reduced levels of physical activity and increasing levels of obesity contributing to increased demands on health and social care systems. On average, the UK workforce spends 9 hours sitting down per day. This is particularly prominent amongst GPs and certain senior physician roles in hospital, where clinics contribute to a large amount of the workload. Standing has been shown to put less stress on the lower back and other joints, burn more energy than sitting down and increase productivity and energy levels. Thus, evidence shows it is healthier to stand more during the day, but is it feasible in a healthcare setting? The aim of this study was to investigate whether patients would prefer to sit or stand for their consultations and the reasoning behind their choices. Methods A consultation room within the rheumatology outpatient department in Sunderland Royal Hospital was fitted with an adjustable standing desk. During clinics, patients were offered a standing consultation on entry to the room. A focused questionnaire was created and given to patients, consisting of 6 questions on the demographics of the patients, whether they wanted a standing consultation or not and what their reasoning was for their decision. This was an opportunistic study that included 39 patients over a 3-week period. Results In total, 39 questionnaires were given out, with each patient being offered a standing consultation. The results found that 13 patients opted for a standing consultation and 23 patients preferred to sit down. Not wanting to stand due to an MSK problem was the most prevalent answer with 16 patients using that as their reasoning. Conclusion In an increasingly sedentary population, the introduction of standing desks could help to reduce this behaviour in healthcare professionals and contribute positively to health. This study also highlights the question of positive modelling of patient behaviours, by healthcare professionals demonstrating the benefits of standing, it could encourage patients to begin to integrate it into their own lives. If we remove the 16 patients that did not want to stand due to an MSK problem, then the results show that 13/23 (56%) of patients wanted a standing consultation, so why not offer the choice? Increasing the sample size and trialling the desk in another department, where MSK problems are less prevalent, is the logical next step to develop this research. Following further investigation, the implementation of standing desks throughout more healthcare departments could help to reduce sedentary behaviour, increase productivity, lessen sick days amongst staff and demonstrate healthy living to patients. Disclosures A. Oliver None. G. Raftery None. D. Coady None.

Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. We aimed to improve scientific training by engaging students enrolled in an upper division elective course in a human microbiome CURE. The “Fiber Force” course is aimed at studying the effect of a wholesome high-fiber diet (40 to 50 g/day for two weeks) on the students’ gut microbiomes. Enrolled students participated in a noninvasive diet intervention, designed health surveys, tested hypotheses on the effect of a diet intervention on the gut microbiome, and analyzed their own samples (as anonymized aggregates). The course involved learning laboratory techniques (e.g., DNA extraction, PCR, and 16S sequencing) and the incorporation of computational techniques to analyze microbiome data with QIIME2 and within the R software environment. In addition, the learning objectives focused on effective student performance in writing, data analysis, and oral communication. Enrolled students showed high performance grades on writing, data analysis and oral communication assignments. Pre- and post-course surveys indicate that the students found the experience favorable, increased their interest in science, and heightened awareness of their diet habits. Fiber Force constitutes a validated case of a research experience on microbiology with the capacity to improve research training and promote healthy dietary habits.

Background Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. Results For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4635-8) contains supplementary material, which is available to authorized users.

Introduction EUS guided tissue acquisition is an extensively used investigation to confirm the histopathological diagnosis in PB lesions. The Joint Advisory Group (JAG) suggests an adequacy rate of more than 75% for EUS-Fine Needle Aspiration cytology (FNAC) [1]. The aim of this study was to determine the diagnostic performance, adequacy of tissue acquisition and safety of EUS-FNA in PB lesions in a non-HPB centre in the UK. Methods We carried out a retrospective audit of all patients (identified from endoscopy and pathology database) who underwent EUS-FNA between 1st January 2015 and 31st December 2018. Data collected include patient demographics, cross-sectional imaging, cytopathological diagnoses (Panc 1 to 5 based on European cytopathology classification of PB terminology[2]; neuroendocrine tumours were included in Panc 5), treatment modality, complications and 30 day procedure related mortality. Final diagnoses were confirmed from EUS FNAC, surgical resection specimen or cross-sectional imaging discussed in a MDT setting (if histology negative). Results A total of 152 patients [mean age 66.9 years, 53.9% females] underwent 161 PB EUS-FNAC procedures. 135 patients had a final diagnosis of cancer. 144 (89.4%) samples were deemed adequate for analysis. Sensitivity, specificity, overall accuracy, positive predictive value (PPV) and negative predictive value (NPV) were 87.7%, 100%, 88.9%, 100%, and 46.7% respectively [with Panc3 included as false negative in patients with cancer as final diagnosis]. These figures would improve to 94.2%, 100%, 94.8%, 100%, and 66.7% respectively if Panc3 is excluded from false negative category in cancer group. There was no procedure related complications or mortality. Conclusion This study confirms that EUS-FNA of PB lesions can be highly effective and safely carried out in a non-HPB centre. Overall adequacy of tissue acquisition is in compliance with JAG guidelines. Our diagnostic yield is in in keeping with the published literature[2]. Our NPV is relatively low because the purpose of EUS-FNA was to confirm suspected cancer on cross-sectional imaging. Reference 1. JAG (Joint Advisory Group) on Gastrointestinal Endoscopy the. Guidance - JAG Summary guide to quality and safety indicators Dumonceau JM, et al. Indications, results, and clinical impact of endoscopic ultrasound (EUS)-guided sampling in gastroenterology: European Society of Gastrointestinal Endoscopy (ESGE) Clinical Guideline. Endoscopy 2017;49:695–714

Combination of non-nicotine pharmacotherapies has been underexamined for cigarette smoking cessation. A randomized, double-blind, parallel-group double-dummy study evaluated two medications, bupropion (BUP) and naltrexone (NTX), in treatment-seeking cigarette smokers (N = 121) over a 7-week treatment intervention with 6-month follow-up. Smokers were randomized to either BUP (300 mg/day) + placebo (PBO) or BUP (300 mg/day) + NTX (50 mg/day). The primary outcome was biochemically verified (saliva cotinine, carbon monoxide) 7-day, point-prevalence abstinence. BUP + NTX was associated with significantly higher point-prevalence abstinence rates after 7-weeks of treatment (BUP + NTX, 54.1%; BUP + PBO, 33.3%), P = 0.0210, but not at 6-month follow-up (BUP + NTX, 27.9%; BUP + PBO, 15.0%), P = 0.09. Continuous abstinence rates did not differ, P = 0.0740 (BUP + NTX, 26.2%; BUP + PBO, 13.3%). Those receiving BUP + NTX reported reduced nicotine withdrawal, P = 0.0364. The BUP + NTX combination was associated with elevated rates of some side effects, but with no significant difference in retention between the groups.

Understanding bacterial responses to physiological conditions is an important priority for combating opportunistic infections. The majority of CF patients succumb to inflammation and necrosis in the airways, arising from chronic infection due to ineffective mucociliary clearance. Steep pH gradients characterize the CF airways but are not often incorporated in standard microbiology culture conditions. Stenotrophomonas maltophilia is a prevalent CF opportunistic pathogen also found in many disparate environments, yet this bacterium’s contribution to CF lung damage and its response to changing environmental factors remain largely understudied. Here, we show that pH impacts the physiology and antibiotic susceptibility of S. maltophilia, with implications for the development of relevant in vitro models and assessment of antibiotic sensitivity., The airway fluids of cystic fibrosis (CF) patients contain local pH gradients and are more acidic than those of healthy individuals. pH is a critical factor that is often overlooked in studies seeking to recapitulate the infection microenvironment. We sought to determine the impact of pH on the physiology of a ubiqituous yet understudied microbe, Stenotrophomonas maltophilia. Phylogenomics was first used to reconstruct evolutionary relationships between 74 strains of S. maltophilia (59 from CF patients). Neither the core genome (2,158 genes) nor the accessory genome (11,978 genes) distinguish the CF and non-CF isolates; however, strains from similar isolation sources grouped into the same subclades. We grew two human and six CF S. maltophilia isolates from different subclades at a range of pH values and observed impaired growth and altered antibiotic tolerances at pH 5. Transcriptomes revealed increased expression of both antibiotic resistance and DNA repair genes in acidic conditions. Although the gene expression profiles of S. maltophilia in lab cultures and CF sputum were distinct, we found that the same genes associated with low pH were also expressed during infection, and the higher pH cultures were more similar to sputum metatranscriptomes. Our findings suggest that S. maltophilia is not well adapted to acidity and may cope with low pH by expressing stress response genes and colonizing less acidic microenvironments. As a whole, our study underlines the impact of microenvironments on bacterial colonization and adaptation in CF infections. IMPORTANCE Understanding bacterial responses to physiological conditions is an important priority for combating opportunistic infections. The majority of CF patients succumb to inflammation and necrosis in the airways, arising from chronic infection due to ineffective mucociliary clearance. Steep pH gradients characterize the CF airways but are not often incorporated in standard microbiology culture conditions. Stenotrophomonas maltophilia is a prevalent CF opportunistic pathogen also found in many disparate environments, yet this bacterium’s contribution to CF lung damage and its response to changing environmental factors remain largely understudied. Here, we show that pH impacts the physiology and antibiotic susceptibility of S. maltophilia, with implications for the development of relevant in vitro models and assessment of antibiotic sensitivity.

Pseudomonas aeruginosa is a well-known dominant opportunistic pathogen in cystic fibrosis (CF) with a wide range of metabolic capacities. However, P. aeruginosa does not colonize the airways alone, and benefits from the metabolic products of neighboring cells—especially volatile molecules that can travel between different parts of the airways easily. Here, we present a study that investigates the metabolic, gene expression profiles and phenotypic responses of a P. aeruginosa clinical isolate to fermentation products lactic acid and 2,3-butanediol, metabolites that are produced by facultative anaerobic members of the CF polymicrobial community and potential biomarkers of disease progression. Although previous studies have successfully investigated the metabolic and transcriptional profiles of P. aeruginosa, most have used common lab reference strains that may differ in important ways from clinical isolates. Using transcriptomics and metabolomics with gas chromatography time of flight mass spectrometry, we observe that fermentation products induce pyocyanin production along with the expression of genes involved in P. aeruginosa amino acid utilization, dormancy and aggregative or biofilm modes of growth. These findings have important implications for how interactions within the diverse CF microbial community influence microbial physiology, with potential clinical consequences., In response to fermentation products 2,3-butanediol and lactic acid, expression patterns associated with aggregation and dormancy are induced in Pseudomonas aeruginosa.

To describe the clinical features of electric powered indoor/outdoor wheelchair users with a muscular dystrophy, likely to influence optimal prescription; reflecting features of muscular dystrophies, conditions secondary to disability, and comorbidities impacting on equipment provision.Cross-sectional retrospective case note review of recipients of electric powered indoor/outdoor wheelchairs provided by a specialist regional wheelchair service. Data on demography, diagnostic/clinical, and wheelchair prescription were systematically extracted.Fifty-one men and 14 women, mean age 23.7 (range 10-67, s.d. 12.95) years, were studied. Forty had Duchenne muscular dystrophy, 22 had other forms of muscular dystrophy, and three were unclassified. Twenty-seven were aged under 19. Notable clinical features included problematic pain (10), cardiomyopathy (5), and ventilatory failure (4). Features related to disability were (kypho)scoliosis (20) and edema/cellulitis (3) whilst comorbidities included back pain (5). Comparison of younger with older users revealed younger users had more features of muscular dystrophy affecting electric powered chair provision (56%) whilst older users had more comorbidity (37%). Tilt-in-space was prescribed for 81% of users, specialized seating for 55% and complex controls for 16%.Muscular dystrophy users were prescribed electric powered indoor/outdoor chairs with many additional features reflecting the consequences of profound muscle weakness. In addition to facilitating independence and participation, electric powered indoor/outdoor chairs have major therapeutic benefits. Implications for rehabilitation Powered wheelchairs have therapeutic benefits in managing muscular dystrophy pain and weakness. The use of specialized seating needs careful consideration in supporting progressive muscle weakness and the management of scoliosis. Pain, discomfort, pressure risk, and muscle fatigue may be reduced by use of tilt-in-space.

Polycyclic aromatic hydrocarbons (PAHs) are believed to be among the causative agents for lung cancer in smokers. PAHs require metabolic activation for carcinogenicity. One pathway produces diol epoxides that react with DNA, causing mutations. Because diol epoxides are converted to tetraols, quantitation of tetraols can potentially be used to identify smokers who may be at higher risk for lung cancer. Our approach uses [D(10)]phenanthrene, a labeled version of phenanthrene, a noncarcinogenic PAH structurally analogous to carcinogenic PAH. Although smokers are exposed to PAH by inhalation, oral dosing would be more practical for phenotyping studies. Therefore, we investigated [D(10)]phenanthrene metabolism in smokers after administration by inhalation in cigarette smoke or orally. Sixteen smokers received 10 μg of [D(10)]phenanthrene in a cigarette or orally. Plasma and urine samples were analyzed for [D(10)]r-1,t-2,3,c-4-tetrahydroxy-1,2,3,4-tetrahydrophenanthrene ([D(10)]PheT), the major end product of the diol epoxide pathway, by gas chromatography-negative ion chemical ionization-tandem mass spectrometry. The ratios of [D(10)]PheT (oral dosing/inhalation) in 15 smokers were 1.03 ± 0.32 and 1.02 ± 0.35, based on plasma area under the concentration-time curve (0-∞) and total 48-h urinary excretion, respectively. Overall, there was no significant difference in the extent of [D(10)]PheT formation after the two different routes of exposure in smokers. A large interindividual variation in [D(10)]PheT formation was observed. These results demonstrate that the level of [D(10)]PheT in urine after oral dosing of [D(10)]phenanthrene can be used to assess individual capacity of PAH metabolism by the diol epoxide pathway.

Polycyclic aromatic hydrocarbons (PAH) are among the likely major causative agents for lung cancer in smokers. PAH require metabolic activation to exert their carcinogenic effects, and one important pathway proceeds through a three-step sequence resulting in the formation of diol epoxides, which react with DNA to produce adducts that can cause mutations and initiate the carcinogenic process. However, no previous published studies have examined this critical pathway in humans specifically exposed to PAH by inhalation of cigarette smoke. This study used a unique approach employing a stable isotope derivative of phenanthrene, the simplest PAH with a bay region, a feature closely associated with PAH carcinogenicity. Twelve subjects each smoked a cigarette to which [D(10)]phenanthrene had been added. Plasma was analyzed for [D(10)]r-1,t-2,3,c-4-tetrahydroxy-1,2,3,4-tetrahydrophenanthrene ([D(10)]PheT), the major end product of the diol epoxide metabolism pathway of phenanthrene. The analysis was performed by gas chromatography--negative ion chemical ionization--tandem mass spectrometry, using [(13)C(6)]PheT as internal standard. The results demonstrated that the three-step pathway resulting in the formation of diol epoxides, as monitored by [D(10)]PheT, occurred with remarkable rapidity. Levels of [D(10)]PheT in plasma of all subjects were maximal at the earliest time points examined, 15-30 min after smoking the cigarette containing [D(10)]phenanthrene, and decreased thereafter. These results demonstrate that the formation of a PAH diol epoxide occurs rapidly in smokers. Because PAH diol epoxides are mutagenic and carcinogenic, the results clearly demonstrate immediate negative health consequences of smoking, which should serve as a major warning to anyone contemplating initiating tobacco use.

The human microbiome is composed of trillions of micro-organisms living in symbiosis with the human body. The interest in the microbiome and the clinical impact of its disruption (dysbiosis) has grown exponentially in the past years, especially in the oncology field. Microbiota play an instructive role in chronic inflammatory disorders and determine response to checkpoint inhibitors cancers, such as melanoma. Increased inflammation in myeloproliferative neoplasms (MPN) drive many of the symptoms associated with this disease and inflammation also likely plays an important role as a driver of the disease. We hypothesized that the microbiome may be dysregulated in MPN which could contribute to the increased inflammatory cytokines seen in this disease and that the microbiome could also potentially impact symptom burden. We compared the gut microbiota of 25 patients with classical MPN, essential thrombocythemia (ET), polycythemia vera (PV) and primary and secondary myelofibrosis (MF) to that of 25 normal controls. Whenever possible, co-inhabiting adults such as a spouse were used as normal controls. Exclusion criteria were acute illness and antibiotics treatment for three months preceding the study. Each participant collected three stool specimens in the course of one week and a subset of the group (n=20) had peripheral blood drawn. The stool microbiome was analyzed using 16S rRNA sequencing and plasma inflammatory cytokines (TNFα, IL-6, IL-8, IL-17a, IL-10, IFNγ, IFNa2, IL-22, IL1-β, GRO, IP-10) were measured using Luminex multiplex analysis. Participants also completed an intake survey which included symptom burden (MPN-SAF TSS) and dietary intake. Characteristics of our MPN patient cohort and normal controls are shown in Table 1. Plasma levels of TNFα and IP-10 were significantly higher in the MPN group versus normal controls (respectively p=0.013 and p=0.0050). We divided the group into those with high (MPN-SAF > 20) and low (MPN-SAF ≤ 20) symptom burden, 7 (28%) patients had high symptom burden affecting considerably their quality of life. Fatigue and early satiety were the most common complaints. GRO (CXCL1) was significantly lower in MPN patients MPN patients with a lower symptom burden (p=0.0287) as compared to those with a high symptom burden. The 16S rRNA gene sequencing did not reveal a significant difference between MPN patients and their healthy counterparts (PERMANOVA, p = 0.83), a large amount of variance in the microbiome data was explained by the individual (PERMANOVA, p= 0.0001), in concordance with other studies suggesting that the microbiome is highly individualistic. To determine whether certain taxa are differentially represented in MPN patients as compared to normal controls, a SIMPER test was used. Prevotellaceae, a family of bacteria implicated in chronic inflammatory conditions, was 20% higher in MPN patients than in normal controls. To test which cytokines explained the most variance in the microbiome data, a distance-based linear model was used (DistLM). TNFα and IL-17a, taken alone, explain 18.7% and 14.5% respectively. The microbiome of patients with a high symptom burden was not significantly different from MPN patients with low symptom burden. We did find a significant difference between the microbiomes of patients treated with Ruxolitinib versus Hydroxyurea. Taken together, this pilot study suggests that inflammation associated with MPN may be driving changes in the microbiome at a finer level, undetected when comparing broad microbial diversity metrics between health and disease. It is still not clear whether the inflammation first modulates the microbiome or whether the gut microbiota triggers the inflammatory signals driving the disease. A larger number of subjects may help answer these questions. Disclosures No relevant conflicts of interest to declare.

Internal corrosion sometimes occurs under deposits of solid particles on the bottom of transmission pipelines. The solids trap water with soluble products and other nutrients which can support the development of microbial communities and may lead to Microbiologically Influenced Corrosion (MIC). Corrosion processes associated with the metabolic activities of specific bacteria have been discussed elsewhere, but the simple presence of large microbial populations may increase the risk of internal corrosion owing to the ability of biofilms to extract and concentrate water at the pipe floor. As a method to monitor the internal corrosion threat in transmission pipelines and recommend mitigating activities for corrosion management, reliable microbial content and corrosion activity correlations are desired. Sludge samples have been obtained from cleaning pigs at the pipe trap and analyzed using Biological Activity Reaction Test (BART™) (or serial dilution test), Dean-Stark analysis, XRD and EDX. These tests provide information about certain bacterial populations, water / solid / hydrocarbon content, and crystalline/elemental composition of these solids, respectively. Despite best efforts, bacterial population/activity of pipeline sludge samples exhibit high variability and are difficult to correlate to actual internal corrosion in a pipeline. Considering that bacterial populations in pipeline sludge may be a meaningful representation of the internal corrosion threat to a transmission pipeline, a more rigorous approach on the sludge sampling procedure is necessary to improve the accuracy and reliability of the bacterial assays. It is also important to control such variables as storage temperature of the samples, exposure to air, and storage duration prior to enumeration — as these may affect the viability of the sample and enumeration results. This report presents historical pipeline sludge analysis data and suggests a method to evaluate data containing high variability. Practical recommendations to reduce data variability through handling and storage of sludge samples are also discussed.

This dissertation investigates the effect of grain boundaries (GBs) in polycrystalline graphene on the tensile fracture behavior and thermal conductivity of the graphene sheets. Current techniques to fabricate large-scale graphene intrinsically introduce defects, e.g., GBs, resulting in polycrystalline graphene sheets. Though GBs in graphene are expected to affect the mechanical properties of graphene, mechanistic understanding and quantitative determination of such effects are far from mature. For example, existing studies on the effect of GBs on the tensile behavior of graphene only focus on a twin GB perpendicular to the tensile loading direction. However, GBs in a polycrystalline graphene sheet under uniaxial tension could be subject to tension in any arbitrary directions, depending on the GB and grain orientation in the graphene sheet. In this dissertation, we focus on the effect of GBs on the tensile and thermal response of polycrystalline graphene. The fracture process of polycrystalline graphene sheets under uniaxial tension was studied using molecular dynamics (MD) simulations to determine how GBs affects the ultimate strength and critical failure strain of the graphene. We also study the flow of heat through polycrystalline graphene to determine the effect of GBs on the thermal conductivity of graphene. A comprehensive study including 24 GB misorientation angles ranging from 2.1° to 54.3° and the whole range of loading angle (i.e., that between a GB and in-plane tensile loading direction, ranging from 0° to 90°) was carried out to quantitatively determine the effect of GBs. Stress-strain data were generated from the MD simulations and the failure strength and critical strain were analyzed. A theoretical model combining continuum mechanics theory and disclination dipole theory was introduced to predict the failure strength of the polycrystalline graphene sheets, which was shown to be in good agreement with the MD simulation results. Various failure modes of polycrystalline graphene under tension were also analyzed. The thermal conductivity of polycrystalline graphene as a function of GB misorientation angle and thermal loading angle was also quantitatively determined through systematic simulations. The quantitative findings from this dissertation could potentially bridge the knowledge gap toward a better understanding of defects and their effects on two-dimensional materials, and also shed light on possible defect control and engineering to achieve desirable properties of graphene in applications.