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https://www.readbyqxmd.com/read/28088924/microbiology-of-otitis-media-in-indigenous-australian-children-review
#1
J Jervis-Bardy, A S Carney, R Duguid, A J Leach
OBJECTIVES: To review research addressing the polymicrobial aetiology of otitis media in Indigenous Australian children in order to identify research gaps and inform best practice in effective prevention strategies and therapeutic interventions. METHODS: Literature review. RESULTS: Studies of aspirated middle-ear fluid represented a minor component of the literature reviewed. Most studies relied upon specimens from middle-ear discharge or the nasopharynx...
January 16, 2017: Journal of Laryngology and Otology
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#2
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073918/identical-bacterial-populations-colonize-premature-infant-gut-skin-and-oral-microbiomes-and-exhibit-different-in-situ-growth-rates
#3
Matthew R Olm, Christopher T Brown, Brandon Brooks, Brian Firek, Robyn Baker, David Burstein, Karina Soenjoyo, Brian C Thomas, Michael Morowitz, Jillian Banfield
The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28070760/the-generation-r-study-design-and-cohort-update-2017
#4
Marjolein N Kooijman, Claudia J Kruithof, Cornelia M van Duijn, Liesbeth Duijts, Oscar H Franco, Marinus H van IJzendoorn, Johan C de Jongste, Caroline C W Klaver, Aad van der Lugt, Johan P Mackenbach, Henriëtte A Moll, Robin P Peeters, Hein Raat, Edmond H H M Rings, Fernando Rivadeneira, Marc P van der Schroeff, Eric A P Steegers, Henning Tiemeier, André G Uitterlinden, Frank C Verhulst, Eppo Wolvius, Janine F Felix, Vincent W V Jaddoe
The Generation R Study is a population-based prospective cohort study from fetal life until adulthood. The study is designed to identify early environmental and genetic causes and causal pathways leading to normal and abnormal growth, development and health from fetal life, childhood and young adulthood. This multidisciplinary study focuses on several health outcomes including behaviour and cognition, body composition, eye development, growth, hearing, heart and vascular development, infectious disease and immunity, oral health and facial growth, respiratory health, allergy and skin disorders of children and their parents...
December 2016: European Journal of Epidemiology
https://www.readbyqxmd.com/read/28069753/the-influence-of-the-microbiome-on-allergic-sensitization-to-food
#5
REVIEW
Catherine H Plunkett, Cathryn R Nagler
The alarming increase in the incidence and severity of food allergies has coincided with lifestyle changes in Western societies, such as dietary modifications and increased antibiotic use. These demographic shifts have profoundly altered the coevolved relationship between host and microbiota, depleting bacterial populations critical for the maintenance of mucosal homeostasis. There is increasing evidence that the dysbiosis associated with sensitization to food fails to stimulate protective tolerogenic pathways, leading to the development of the type 2 immune responses that characterize allergic disease...
January 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28049818/impact-of-short-chain-galactooligosaccharides-on-the-gut-microbiome-of-lactose-intolerant-individuals
#6
M Andrea Azcarate-Peril, Andrew J Ritter, Dennis Savaiano, Andrea Monteagudo-Mera, Carlton Anderson, Scott T Magness, Todd R Klaenhammer
Directed modulation of the colonic bacteria to metabolize lactose effectively is a potentially useful approach to improve lactose digestion and tolerance. A randomized, double-blind, multisite placebo-controlled trial conducted in human subjects demonstrated that administration of a highly purified (>95%) short-chain galactooligosaccharide (GOS), designated "RP-G28," significantly improved clinical outcomes for lactose digestion and tolerance. In these individuals, stool samples were collected pretreatment (day 0), after GOS treatment (day 36), and 30 d after GOS feeding stopped and consumption of dairy products was encouraged (day 66)...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28049409/negative-binomial-mixed-models-for-analyzing-microbiome-count-data
#7
Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K Benson, Nengjun Yi
BACKGROUND: Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions between the microbiome and host environmental/clinical factors. In addition to the well-known properties of microbiome count measurements, for example, varied total sequence reads across samples, over-dispersion and zero-inflation, microbiome studies usually collect samples with hierarchical structures, which introduce correlation among the samples and thus further complicate the analysis and interpretation of microbiome count data...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045919/alterations-in-gut-microbiome-composition-and-barrier-function-are-associated-with-reproductive-and-metabolic-defects-in-women-with-polycystic-ovary-syndrome-pcos-a-pilot-study
#8
Lisa Lindheim, Mina Bashir, Julia Münzker, Christian Trummer, Verena Zachhuber, Bettina Leber, Angela Horvath, Thomas R Pieber, Gregor Gorkiewicz, Vanessa Stadlbauer, Barbara Obermayer-Pietsch
BACKGROUND: Polycystic ovary syndrome (PCOS) is a common female endocrinopathy of unclear origin characterized by hyperandrogenism, oligo-/anovulation, and ovarian cysts. Women with PCOS frequently display overweight, insulin resistance, and systemic low-grade inflammation. We hypothesized that endotoxemia resulting from a leaky gut is associated with inflammation, insulin resistance, fat accumulation, and hyperandrogenemia in PCOS. In this pilot study, we compared the stool microbiome, gut permeability, and inflammatory status of women with PCOS and healthy controls...
2017: PloS One
https://www.readbyqxmd.com/read/28034306/influence-of-maternal-breast-milk-ingestion-on-acquisition-of-the-intestinal-microbiome-in-preterm-infants
#9
Katherine E Gregory, Buck S Samuel, Pearl Houghteling, Guru Shan, Frederick M Ausubel, Ruslan I Sadreyev, W Allan Walker
BACKGROUND: The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and nutrition have all been shown to play a role in the assembly of the intestinal microbiome during early life. For preterm infants, who are disproportionately at risk of inflammatory intestinal disease (i.e., necrotizing enterocolitis), a unique set of clinical factors influence the establishment of the microbiome...
December 30, 2016: Microbiome
https://www.readbyqxmd.com/read/28030364/statistical-models-and-computational-algorithms-for-discovering-relationships-in-microbiome-data
#10
Mateen R Shaikh, Joseph Beyene
Microbiomes, populations of microscopic organisms, have been found to be related to human health and it is expected further investigations will lead to novel perspectives of disease. The data used to analyze microbiomes is one of the newest types (the result of high-throughput technology) and the means to analyze these data is still rapidly evolving. One of the distributions that have been introduced into the microbiome literature, the Dirichlet-Multinomial, has received considerable attention. We extend this distribution's use uncover compositional relationships between organisms at a taxonomic level...
December 28, 2016: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28027580/effects-of-predation-and-nutrient-enrichment-on-the-success-and-microbiome-of-a-foundational-coral
#11
Elizabeth C Shaver, Andrew A Shantz, Ryan McMinds, Deron E Burkepile, Rebecca L Vega Thurber, Brian R Silliman
By inflicting damage to prey tissues, consumer species may increase stress in prey hosts and reduce overall fitness (i.e., primary effects, such as growth or reproduction) or cause secondary effects by affecting prey interactions with other species such as microbes. However, little is known about how abiotic conditions affect the outcomes of these biotic interactions. In coral reef communities, both nutrient enrichment and predation have been linked to reduced fitness and disease facilitation in corals, yet no study to date has tested their combined effects on corals or their associated microbial communities (i...
December 27, 2016: Ecology
https://www.readbyqxmd.com/read/28025202/calypso-a-user-friendly-web-server-for-mining-and-visualizing-microbiome-environment-interactions
#12
Martha Zakrzewski, Carla Proietti, Jonathan J Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause
: Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates...
December 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28019040/a-small-sample-multivariate-kernel-machine-test-for-microbiome-association-studies
#13
Xiang Zhan, Xingwei Tong, Ni Zhao, Arnab Maity, Michael C Wu, Jun Chen
High-throughput sequencing technologies have enabled large-scale studies of the role of the human microbiome in health conditions and diseases. Microbial community level association test, as a critical step to establish the connection between overall microbiome composition and an outcome of interest, has now been routinely performed in many studies. However, current microbiome association tests all focus on a single outcome. It has become increasingly common for a microbiome study to collect multiple, possibly related, outcomes to maximize the power of discovery...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28013141/closed-nutrient-recycling-via-microbial-catabolism-in-an-eco-engineered-self-regenerating-mixed-anaerobic-microbiome-for-hydrogenotrophic-methanogenesis
#14
Savvas Savvas, Joanne Donnelly, Tim P Patterson, Richard Dinsdale, Sandra R Esteves
A novel eco-engineered mixed anaerobic culture was successfully demonstrated for the first time to be capable of continuous regeneration in nutrient limiting conditions. Microbial catabolism has been found to support a closed system of nutrients able to enrich a culture of lithotrophic methanogens and provide microbial cell recycling. After enrichment, the hydrogenotrophic species was the dominating methanogens while a bacterial substratum was responsible for the redistribution of nutrients. q-PCR results indicated that 7% of the total population was responsible for the direct conversion of the gases...
March 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28008325/lactobacilli-dominance-and-vaginal-ph-why-is-the-human-vaginal-microbiome-unique
#15
Elizabeth A Miller, DeAnna E Beasley, Robert R Dunn, Elizabeth A Archie
The human vaginal microbiome is dominated by bacteria from the genus Lactobacillus, which create an acidic environment thought to protect women against sexually transmitted pathogens and opportunistic infections. Strikingly, lactobacilli dominance appears to be unique to humans; while the relative abundance of lactobacilli in the human vagina is typically >70%, in other mammals lactobacilli rarely comprise more than 1% of vaginal microbiota. Several hypotheses have been proposed to explain humans' unique vaginal microbiota, including humans' distinct reproductive physiology, high risk of STDs, and high risk of microbial complications linked to pregnancy and birth...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28007924/impact-of-periodic-presumptive-treatment-for-bacterial-vaginosis-on-the-vaginal-microbiome-among-women-participating-in-the-preventing-vaginal-infections-trial
#16
Jennifer E Balkus, Sujatha Srinivasan, Omu Anzala, Joshua Kimani, Chloe Andac, Jane Schwebke, David N Fredricks, R Scott McClelland
BACKGROUND: Evidence suggests specific vaginal bacteria that are associated with bacterial vaginosis (BV) may increase risk of adverse health outcomes in women. Among women participating in a randomized trial, we assessed the effect of periodic presumptive treatment (PPT) on detection and concentrations of select vaginal bacteria. METHODS: HIV-uninfected, nonpregnant women from the US and Kenya received intravaginal metronidazole 750mg plus miconazole 200mg or placebo for 5 consecutive nights each month for 12 months...
December 22, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28005908/a-machine-learning-approach-for-using-the-postmortem-skin-microbiome-to-estimate-the-postmortem-interval
#17
Hunter R Johnson, Donovan D Trinidad, Stephania Guzman, Zenab Khan, James V Parziale, Jennifer M DeBruyn, Nathan H Lents
Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators...
2016: PloS One
https://www.readbyqxmd.com/read/28003264/a-general-framework-for-association-analysis-of-microbial-communities-on-a-taxonomic-tree
#18
Zheng-Zheng Tang, Guanhua Chen, Alexander V Alekseyenko, Hongzhe Li
MOTIVATION: Association analysis of microbiome composition with disease-related outcomes provides invaluable knowledge towards understanding the roles of microbes in the underlying disease mechanisms. Proper analysis of sparse compositional microbiome data is challenging. Existing methods rely on strong assumptions on the data structure and fail to pinpoint the associated microbial communities. RESULTS: We develop a general framework to: (a) perform robust association tests for the microbial community that exhibits arbitrary inter-taxa dependencies; (b) localize lineages on the taxonomic tree that are associated with covariates (e...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27999386/reduced-diversity-in-the-bacteriome-of-the-phytophagous-mite-brevipalpus-yothersi-acari-tenuipalpidae
#19
Oscar E Ospina, Steven E Massey, Jose Carlos Verle Rodrigues
Tenuipalpidae comprises mites that transmit viruses to agriculturally important plants. Several tenuipalpid species present parthenogenesis, and in Brevipalpus yothersi, the endosymbiont Cardinium has been associated with female-only colonies. It is unclear what the bacterial composition of B. yothersi is, and how common Cardinium is in those microbiomes. We performed a comparative analysis of the bacteriomes in three populations of B. yothersi and three additional Tetranychoidea species using sequences from V4-fragment of 16S DNA...
December 20, 2016: Insects
https://www.readbyqxmd.com/read/27988219/dietary-changes-impact-the-gut-microbe-composition-in-overweight-and-obese-men%C3%A2-with-prostate-cancer-undergoing-radical%C3%A2-prostatectomy
#20
Andrew D Frugé, Travis Ptacek, Yuko Tsuruta, Casey D Morrow, Maria Azrad, Renee A Desmond, Gary R Hunter, Soroush Rais-Bahrami, Wendy Demark-Wahnefried
BACKGROUND: Diet and obesity influence prostate cancer risk and progression-effects that may be mediated through the gut microbiome. OBJECTIVE: Our aim was to explore relationships among diet, gut microbes, and Gleason sum in overweight and obese prostate cancer patients enrolled in a presurgical weight-loss trial. DESIGN: Randomized controlled trial (NCT01886677) secondary analysis. PARTICIPANTS/SETTING: In 2013-2014, 40 prostate cancer patients in the southeastern United States were randomized and allocated equally to weight-loss and wait-list control arms while they awaited prostatectomy; stool samples were collected on a subset of 22 patients...
December 14, 2016: Journal of the Academy of Nutrition and Dietetics
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