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Human microbiome

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https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#1
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27904735/urinary-metabolomics-of-young-italian-autistic-children-supports-abnormal-tryptophan-and-purine-metabolism
#2
Federica Gevi, Lello Zolla, Stefano Gabriele, Antonio M Persico
BACKGROUND: Autism spectrum disorder (ASD) is still diagnosed through behavioral observation, due to a lack of laboratory biomarkers, which could greatly aid clinicians in providing earlier and more reliable diagnoses. Metabolomics on human biofluids provides a sensitive tool to identify metabolite profiles potentially usable as biomarkers for ASD. Initial metabolomic studies, analyzing urines and plasma of ASD and control individuals, suggested that autistic patients may share some metabolic abnormalities, despite several inconsistencies stemming from differences in technology, ethnicity, age range, and definition of "control" status...
2016: Molecular Autism
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#3
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27900395/microbiome-and-metabolic-disease-revisiting-the-bacterial-phylum-bacteroidetes
#4
REVIEW
Elizabeth L Johnson, Stacey L Heaver, William A Walters, Ruth E Ley
Bacterial species composition in the gut has emerged as an important factor in obesity and its related metabolic diseases such as type 2 diabetes. Out of thousands of bacterial species-level phylotypes inhabiting the human gut, the majority belong to two dominant phyla, the Bacteroidetes and Firmicutes. Members of the Bacteroidetes in particular have been associated with human metabolic diseases. However, their associations with disease are not always consistent between studies. Delving deeper into the diversity within the Bacteroidetes reveals a vast diversity in genomes and capacities, which partly explain how not all members respond equally to similar environmental conditions in their hosts...
November 29, 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/27899504/gene-function-analysis-in-the-ubiquitous-human-commensal-and-pathogen-malassezia-genus
#5
Giuseppe Ianiri, Anna F Averette, Joanne M Kingsbury, Joseph Heitman, Alexander Idnurm
: The genus Malassezia includes 14 species that are found on the skin of humans and animals and are associated with a number of diseases. Recent genome sequencing projects have defined the gene content of all 14 species; however, to date, genetic manipulation has not been possible for any species within this genus. Here, we develop and then optimize molecular tools for the transformation of Malassezia furfur and Malassezia sympodialis using Agrobacterium tumefaciens delivery of transfer DNA (T-DNA) molecules...
November 29, 2016: MBio
https://www.readbyqxmd.com/read/27898455/clinical-implications-of-the-microbiome-in-urinary-tract-diseases
#6
Andreas Hiergeist, André Gessner
PURPOSE OF REVIEW: The purpose of this review is to outline and evaluate the most recent literature on the role of the microbiome in urinary tract diseases. RECENT FINDINGS: High throughput molecular DNA sequencing of bacterial 16S rRNA genes enabled the analysis of complex microbial communities inhabiting the human urinary tract. Several recent studies have identified bacterial taxa of the urinary microbiome to impact urinary tract diseases including interstitial cystitis, urgency urinary incontinence or calcium oxalate stone formation...
November 24, 2016: Current Opinion in Urology
https://www.readbyqxmd.com/read/27898428/beneficial-effects-of-a-dietary-weight-loss-intervention-on-human-gut-microbiome-diversity-and-metabolism-are-not-sustained-during-weight-maintenance
#7
Femke-Anouska Heinsen, Daniela Fangmann, Nike Müller, Dominik M Schulte, Malte C Rühlemann, Kathrin Türk, Ute Settgast, Wolfgang Lieb, John F Baines, Stefan Schreiber, Andre Franke, Matthias Laudes
OBJECTIVE: In the present study, we examined the effect of a very low-calorie diet(VLCD)-based obesity program on human gut microbiome diversity and metabolism during weight loss and weight maintenance. METHODS: Obese subjects underwent 3 months of VLCD followed by 3 months of weight maintenance. A lean and an obese control group were included. The microbiome was characterized by performing high-throughput dual-indexed 16S rDNA amplicon sequencing. RESULTS: At baseline, a significant difference in the Firmicutes/Bacteroidetes ratio between the lean and obese individuals was observed (p = 0...
November 30, 2016: Obesity Facts
https://www.readbyqxmd.com/read/27898282/comparative-fingerprinting-of-the-human-microbiota-in-diabetes-and-cardiovascular-disease
#8
Emanuel Vamanu, Diana Pelinescu, Ionela Sarbu
Diabetes and cardiovascular diseases are major causes of morbidity and mortality worldwide, and are associated with changes in the human gut microbiota. To better understand the relationships between diet, disease, and the colonic microbiome, we used the in vitro GIS1 system and repetitive element palindromic polymerase chain reaction (rep-PCR) to determine the microbial fingerprints in individuals with these diseases and compared them with the fingerprints in healthy controls. Clear differences were apparent in the three groups...
November 29, 2016: Journal of Medicinal Food
https://www.readbyqxmd.com/read/27896917/on-the-pathogenesis-of-mtor-associated-stomatitis-mias-studies-using-an-organotypic-model-of-the-oral-mucosa
#9
Stephen Sonis, Paulette Wright Andreotta, Gregory Lyng
OBJECTIVE: mTOR inhibitor treatment of solid cancers is associated with mTOR inhibitor-associated stomatitis (mIAS) a common, significant, dose-limiting toxicity, with aphthous-like lesions. Our objective was to assess the utility of a new organotypic model in defining mIAS' pathogenesis. MATERIALS AND METHODS: The effect of everolimus on organotypic human oral mucosa was studied. Sterile specimens were assessed 24 hr and 48 hr after exposure to varying concentrations of everolimus...
November 29, 2016: Oral Diseases
https://www.readbyqxmd.com/read/27895265/gut-homeostasis-microbial-dysbiosis-and-opioids
#10
Fuyuan Wang, Sabita Roy
Gut homeostasis plays an important role in maintaining animal and human health. The disruption of gut homeostasis has been shown to be associated with multiple diseases. The mutually beneficial relationship between the gut microbiota and the host has been demonstrated to maintain homeostasis of the mucosal immunity and preserve the integrity of the gut epithelial barrier. Currently, rapid progress in the understanding of the host-microbial interaction has redefined toxicological pathology of opioids and their pharmacokinetics...
November 28, 2016: Toxicologic Pathology
https://www.readbyqxmd.com/read/27893703/generation-of-genome-scale-metabolic-reconstructions-for-773-members-of-the-human-gut-microbiota
#11
Stefanía Magnúsdóttir, Almut Heinken, Laura Kutt, Dmitry A Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jäger, Joanna Baginska, Paul Wilmes, Ronan M T Fleming, Ines Thiele
Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available...
November 28, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27893069/new-medical-and-surgical-insights-into-neonatal-necrotizing-enterocolitis-a-review
#12
Brandy L Frost, Biren P Modi, Tom Jaksic, Michael S Caplan
Importance: Necrotizing enterocolitis (NEC) has long remained a significant cause of morbidity and mortality in neonatal intensive care units. While the mainstay of treatment for this devastating condition remains largely supportive, research efforts continue to be directed toward understanding pathophysiology as well as how best to approach surgical management when indicated. Observations: In this review, we first examine recent medical observations, including overviews on the microbiome and a brief review of the use of probiotics...
November 21, 2016: JAMA Pediatrics
https://www.readbyqxmd.com/read/27892936/influence-of-early-life-exposure-host-genetics-and-diet-on-the-mouse-gut-microbiome-and-metabolome
#13
Antoine M Snijders, Sasha A Langley, Young-Mo Kim, Colin J Brislawn, Cecilia Noecker, Erika M Zink, Sarah J Fansler, Cameron P Casey, Darla R Miller, Yurong Huang, Gary H Karpen, Susan E Celniker, James B Brown, Elhanan Borenstein, Janet K Jansson, Thomas O Metz, Jian-Hua Mao
Although the gut microbiome plays important roles in host physiology, health and disease(1), we lack understanding of the complex interplay between host genetics and early life environment on the microbial and metabolic composition of the gut. We used the genetically diverse Collaborative Cross mouse system(2) to discover that early life history impacts the microbiome composition, whereas dietary changes have only a moderate effect. By contrast, the gut metabolome was shaped mostly by diet, with specific non-dietary metabolites explained by microbial metabolism...
November 28, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27891184/effect-of-antibiotic-pre-treatment-and-pathogen-challenge-on-the-intestinal-microbiota-in-mice
#14
Tadasu Iizumi, Takako Taniguchi, Wataru Yamazaki, Geraldine Vilmen, Alexander V Alekseyenko, Zhan Gao, Guillermo I Perez Perez, Martin J Blaser
BACKGROUND: More than 50 years after the discovery of antibiotics, bacterial infections have decreased substantially; however, antibiotics also may have negative effects such as increasing susceptibility to pathogens. An intact microbiome is an important line of defense against pathogens. We sought to determine the effect of orally administered antibiotics both on susceptibility to pathogens and on impact to the microbiome. We studied Campylobacter jejuni, one of the most common causes of human diarrhea, and Acinetobacter baumannii, which causes wound infections...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27888152/an-improved-methodology-to-overcome-key-issues-in-human-fecal-metagenomic-dna-extraction
#15
Jitendra Kumar, Manoj Kumar, Shashank Gupta, Vasim Ahmed, Manu Bhambi, Rajesh Pandey, Nar Singh Chauhan
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (> 23 kb) metagenomic DNA (260/280 ratio > 1...
November 22, 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27887808/norovirus-regulation-by-host-and-microbe
#16
REVIEW
Megan T Baldridge, Holly Turula, Christiane E Wobus
Norovirus (NoV) infection is the leading cause of epidemic gastroenteritis globally, and can lead to detrimental chronic infection in immunocompromised hosts. Despite its prevalence as a cause of diarrheal illness, the study of human NoVs (HNoVs) has historically been limited by a paucity of models. The use of murine NoV (MNoV) to interrogate mechanisms of host control of viral infection has facilitated the exploration of different genetic mouse models, revealing roles for both innate and adaptive immunity in viral regulation...
October 28, 2016: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/27887570/metamis-a-metagenomic-microbial-interaction-simulator-based-on-microbial-community-profiles
#17
Grace Tzun-Wen Shaw, Yueh-Yang Pao, Daryi Wang
BACKGROUND: The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data. RESULTS: In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27886085/dirty-money-a-matter-of-bacterial-survival-adherence-and-toxicity
#18
Frank Vriesekoop, Jing Chen, Jenna Oldaker, Flavien Besnard, Reece Smith, William Leversha, Cheralee Smith-Arnold, Julie Worrall, Emily Rufray, Qipeng Yuan, Hao Liang, Amalia Scannell, Cryn Russell
In this study we report the underlying reasons to why bacteria are present on banknotes and coins. Despite the use of credit cards, mobile phone apps, near-field-communication systems, and cryptocurrencies such as bitcoins which are replacing the use of hard currencies, cash exchanges still make up a significant means of exchange for a wide range of purchases. The literature is awash with data that highlights that both coins and banknotes are frequently identified as fomites for a wide range of microorganisms...
November 23, 2016: Microorganisms
https://www.readbyqxmd.com/read/27884206/large-scale-benchmarking-reveals-false-discoveries-and-count-transformation-sensitivity-in-16s-rrna-gene-amplicon-data-analysis-methods-used-in-microbiome-studies
#19
Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard, Johannes Waage
BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons into operational taxonomic units (OTUs). Strategies for detecting differential relative abundance of OTUs between sample conditions include classical statistical approaches as well as a plethora of newer methods, many borrowing from the related field of RNA-seq analysis...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27883906/infant-food-applications-of-complex-carbohydrates-structure-synthesis-and-function
#20
Dorothy L Ackerman, Kelly M Craft, Steven D Townsend
Professional health bodies such as the World Health Organization (WHO), the American Academy of Pediatrics (AAP), and the U.S. Department of Health and Human Services (HHS) recommend breast milk as the sole source of food during the first year of life. This position recognizes human milk as being uniquely suited for infant nutrition. Nonetheless, most neonates in the West are fed alternatives by 6 months of age. Although inferior to human milk in most aspects, infant formulas are able to promote effective growth and development...
November 11, 2016: Carbohydrate Research
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