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Human microbiome

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https://www.readbyqxmd.com/read/28239609/application-of-taxonomic-modeling-to-microbiota-data-mining-for-detection-of-helminth-infection-in-global-populations
#1
Mahbaneh Eshaghzadeh Torbati, Makedonka Mitreva, Vanathi Gopalakrishnan
Human microbiome data from genomic sequencing technologies is fast accumulating, giving us insights into bacterial taxa that contribute to health and disease. The predictive modeling of such microbiota count data for the classification of human infection from parasitic worms, such as helminths, can help in the detection and management across global populations. Real-world datasets of microbiome experiments are typically sparse, containing hundreds of measurements for bacterial species, of which only a few are detected in the bio-specimens that are analyzed...
December 2016: Data (Basel)
https://www.readbyqxmd.com/read/28239408/the-effects-of-probiotics-on-depressive-symptoms-in-humans-a-systematic-review
#2
REVIEW
Caroline J K Wallace, Roumen Milev
BACKGROUND: Patients suffering from depression experience significant mood, anxiety, and cognitive symptoms. Currently, most antidepressants work by altering neurotransmitter activity in the brain to improve these symptoms. However, in the last decade, research has revealed an extensive bidirectional communication network between the gastrointestinal tract and the central nervous system, referred to as the "gut-brain axis." Advances in this field have linked psychiatric disorders to changes in the microbiome, making it a potential target for novel antidepressant treatments...
2017: Annals of General Psychiatry
https://www.readbyqxmd.com/read/28235986/-fecal-microbiota-transplantation
#3
C Lübbert, B Salzberger, J Mössner
The human intestinal microbiome has important metabolic and immunological functions for the host and is part of the defense against pathogens in the gastrointestinal tract. Antibiotics, probiotics, dietary measures, such as prebiotics, and the relatively newly established method of fecal microbiota transplantation (FMT, also known as fecal microbiome transfer) all influence the intestinal microbiome. The FMT procedure comprises the transmission of fecal microorganisms from a healthy donor into the gastrointestinal tract of a patient...
February 24, 2017: Der Internist
https://www.readbyqxmd.com/read/28230052/unraveling-the-processes-shaping-mammalian-gut-microbiomes-over-evolutionary-time
#4
Mathieu Groussin, Florent Mazel, Jon G Sanders, Chris S Smillie, Sébastien Lavergne, Wilfried Thuiller, Eric J Alm
Whether mammal-microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary shifts have affected the distribution of different gut bacterial lineages and did so on vastly different bacterial phylogenetic resolutions. Diet mostly influences the acquisition of ancient and large microbial lineages. Conversely, correlation with host phylogeny is mostly seen among more recently diverged bacterial lineages, consistent with processes operating at similar timescales to host evolution...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28229114/the-trier-social-stress-test-principles-and-practice
#5
REVIEW
Andrew P Allen, Paul J Kennedy, Samantha Dockray, John F Cryan, Timothy G Dinan, Gerard Clarke
Researchers interested in the neurobiology of the acute stress response in humans require a valid and reliable acute stressor that can be used under experimental conditions. The Trier Social Stress Test (TSST) provides such a testing platform. It induces stress by requiring participants to make an interview-style presentation, followed by a surprise mental arithmetic test, in front of an interview panel who do not provide feedback or encouragement. In this review, we outline the methodology of the TSST, and discuss key findings under conditions of health and stress-related disorder...
February 2017: Neurobiology of Stress
https://www.readbyqxmd.com/read/28228596/antimicrobials-from-human-skin-commensal-bacteria-protect-against-staphylococcus-aureus-and-are-deficient-in-atopic-dermatitis
#6
Teruaki Nakatsuji, Tiffany H Chen, Saisindhu Narala, Kimberly A Chun, Aimee M Two, Tong Yun, Faiza Shafiq, Paul F Kotol, Amina Bouslimani, Alexey V Melnik, Haythem Latif, Ji-Nu Kim, Alexandre Lockhart, Keli Artis, Gloria David, Patricia Taylor, Joanne Streib, Pieter C Dorrestein, Alex Grier, Steven R Gill, Karsten Zengler, Tissa R Hata, Donald Y M Leung, Richard L Gallo
The microbiome can promote or disrupt human health by influencing both adaptive and innate immune functions. We tested whether bacteria that normally reside on human skin participate in host defense by killing Staphylococcus aureus, a pathogen commonly found in patients with atopic dermatitis (AD) and an important factor that exacerbates this disease. High-throughput screening for antimicrobial activity against S. aureus was performed on isolates of coagulase-negative Staphylococcus (CoNS) collected from the skin of healthy and AD subjects...
February 22, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28225785/betel-nut-chewing-oral-premalignant-lesions-and-the-oral-microbiome
#7
Brenda Y Hernandez, Xuemei Zhu, Marc T Goodman, Robert Gatewood, Paul Mendiola, Katrina Quinata, Yvette C Paulino
Oral cancers are attributed to a number of causal agents including tobacco, alcohol, human papillomavirus (HPV), and areca (betel) nut. Although betel nut chewing has been established as an independent cause of oral cancer, the mechanisms of carcinogenesis are poorly understood. An investigation was undertaken to evaluate the influence of betel nut chewing on the oral microbiome and oral premalignant lesions. Study participants were recruited from a dental clinic in Guam. Structured interviews and oral examinations were performed...
2017: PloS One
https://www.readbyqxmd.com/read/28223683/metataxonomics-reveal-vultures-as-a-reservoir-for-clostridium-perfringens
#8
Xiangli Meng, Shan Lu, Jing Yang, Dong Jin, Xiaohong Wang, Xiangning Bai, Yumeng Wen, Yiting Wang, Lina Niu, Changyun Ye, Ramon Rosselló-Móra, Jianguo Xu
The Old World vulture may carry and spread pathogens for emerging infections since they feed on the carcasses of dead animals and participate in the sky burials of humans, some of whom have died from communicable diseases. Therefore, we studied the precise fecal microbiome of the Old World vulture with metataxonomics, integrating the high-throughput sequencing of almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons in tandem with the operational phylogenetic unit (OPU) analysis strategy...
February 22, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28222117/two-dynamic-regimes-in-the-human-gut-microbiome
#9
Sean M Gibbons, Sean M Kearney, Chris S Smillie, Eric J Alm
The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Prior work on gut microbial time series has largely focused on autoregressive models (e.g. Lotka-Volterra). However, we show that most of the variance in microbial time series is non-autoregressive. In addition, we show how community state-clustering is flawed when it comes to characterizing within-host dynamics and that more continuous methods are required. Most organisms exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities and abundant taxa were largely shared across individuals...
February 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28220542/the-gut-microbiome-in-human-neurological-disease-a-review
#10
REVIEW
Helen Tremlett, Kylynda C Bauer, Silke Appel-Cresswell, Brett B Finlay, Emmanuelle Waubant
Almost half the cells and 1% of the unique genes found in our bodies are human, the rest are from microbes; predominantly bacteria, archaea, fungi, and viruses. These microorganisms collectively form the human microbiota, with most colonizing the gut. Recent technological advances, open access data-libraries, and application of high throughput sequencing have allowed these microbes to be identified and their contribution to neurological health examined. Emerging evidence links perturbations in the gut microbiota to neurological disease, including disease risk, activity, and progression...
February 21, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28219830/gut-microbiome-based-medical-methodologies-for-early-stage-disease-prevention
#11
REVIEW
Jing-Zhang Wang, Wen-Tao Du, Yan-Li Xu, Shu-Zhen Cheng, Zhi-Jun Liu
Recent advancements highlight the important role of gut microbiome in human health. However, a variety of endogenous and exogenous factors, such as genes, foods, drugs, environmental pollutions, oxidative stress, etc., may interfere with the gut microbiome in vivo and increase risks of digestive system diseases, cardiovascular diseases, neurological diseases, obesity, diabetes, cancers, and so on. Abundant discoveries listed in this work support that changes in the composition of the gut microbiome may be potentially used as sensitive early-stage diagnostic biomarkers and that the gut microbiome could be a promising therapeutic target for systemic prevention of multiple human diseases...
February 20, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28217698/questions-and-challenges-associated-with-studying-the-microbiome-of-the-urinary-tract
#12
REVIEW
Yige Bao, Kait F Al, Ryan M Chanyi, Samantha Whiteside, Malcom Dewar, Hassan Razvi, Gregor Reid, Jeremy P Burton
Urologists are typically faced with clinical situations for which the microbiome may have been a contributing factor. Clinicians have a good understanding regarding the role of bacteria related to issues such as antibiotic resistance; however, they generally have a limited grasp of how the microbiome may relate to urological issues. The largest part of the human microbiome is situated in the gastrointestinal tract, and though this is mostly separated from the urinary system, bacterial dissemination and metabolic output by this community is thought to have a significant influence on urological conditions...
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28217695/gut-microbiome-and-chronic-prostatitis-chronic-pelvic-pain-syndrome
#13
REVIEW
Hans C Arora, Charis Eng, Daniel A Shoskes
Analysis of the human microbiome continues to reveal new and previously unrealized associations between microbial dysbiosis and disease. Novel approaches to bacterial identification using culture-independent methods allow practitioners to discern the presence of alterations in the taxa and diversity of the microbiome and identify correlations with disease processes. While some of these diseases that have been extensively studied are well-defined in their etiology and treatment methods (colorectal cancer), others have provided much more significant challenges in both diagnosis and treatment...
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28217694/probiotics-for-prevention-of-urinary-stones
#14
John C Lieske
BACKGROUND: Urinary supersaturation is one key determinant of calcium oxalate (CaOx) urinary stone formation, and urinary excretions of oxalate and citrate are two key determinants. Each is influenced by gastrointestinal processes. METHODS: Open label and randomized placebo studies have examined the effect of oral probiotic preparations on urinary supersaturation and oxalate excretion. Cross sectional studies in humans have studied the association of Oxalobacter formigenes colonization status and urinary oxalate excretion and prevalence of urinary stones...
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28217692/preface-to-the-human-microbiome-in-urologic-health-and-disease
#15
Daniel A Shoskes, Jill A Macoska
No abstract text is available yet for this article.
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28216014/the-conserved-phylogeny-of-blood-microbiome
#16
Malay Bhattacharyya, Tuhin Ghosh, Sujit Shankar, Namrata Tomar
The proliferation and intensification of diseases have forced every researcher to take actions for a robust understanding of the organisms. This demands deep knowledge about the cells and tissues in an organ and its entire surroundings, more precisely the microbiome community which involves viruses, bacteria, archaea, among others. They play an important role in the function of our body, and act both as a deterrent as well as shelter for diseases. Therefore, it is pertinent to study the relation within the microbiome in a human body...
February 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28214542/several-hpept1-transported-drugs-are-substrates-of-the-escherichia-coli-proton-coupled-oligopeptide-transporter-ydgr
#17
Bala K Prabhala, Nanda G Aduri, Mazhar Iqbal, Moazur Rahman, Michael Gajhede, Paul R Hansen, Osman Mirza
Proton-dependent oligopeptide transporters (POTs) are secondary active transporters found in all kingdoms of life. POTs utilize the proton electrochemical gradient for the uptake of nutrient dipeptides and tripeptides. The human POT hPepT1 is known to transport a number of drugs. As part of ongoing studies on substrate specificities of POTs from Escherichia coli, our aim in this study was to investigate whether bacterial POTs could also transport these drugs. For this, we selected the common orally administered drugs sulpiride, bestatin, valacyclovir, ampicillin and oseltamivir, that are all transported by hPepT1...
February 16, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28214389/synthesis-of-lacto-n-tetraose
#18
Kelly M Craft, Steven D Townsend
Human milk oligosaccharides (HMOs) are the third largest macromolecular component of breast milk and offer infants numerous health benefits, most of which stem from the development of a healthy microbiome. Characterization, quantification, and chemical derivatization of HMOs remains a frontier issue in glycobiology due to the challenge of isolating appreciable quantities of homogenous HMOs from breast milk. Herein, we report the synthesis of the human milk tetrasaccharide lacto-N-tetraose (LNT). LNT is ubiquitous in human breast milk as it is a core structure common to longer-chain HMOs and many glycolipids...
February 11, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28214100/nlrp6-a-multifaceted-innate-immune-sensor
#19
REVIEW
Maayan Levy, Hagit Shapiro, Christoph A Thaiss, Eran Elinav
NLRP6, a member of the nucleotide-binding domain, leucine-rich repeat-containing (NLR) innate immune receptor family, regulates inflammation and host defense against microorganisms. Similar to other NLRs, NLRP6 not only participates in inflammasome formation, but is also involved in nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling regulation and facilitation of gastrointestinal antiviral effector functions. Additionally, NLRP6 contributes to the regulation of mucus secretion and antimicrobial peptide production, thereby impacting intestinal microbial colonization and associated microbiome-related infectious, autoinflammatory, metabolic, and neoplastic diseases...
February 14, 2017: Trends in Immunology
https://www.readbyqxmd.com/read/28212267/effects-of-dietary-yogurt-on-the-healthy-human-gastrointestinal-gi-microbiome
#20
Daniel J Lisko, G Patricia Johnston, Carl G Johnston
The gastrointestinal (GI) tract performs key functions that regulate the relationship between the host and the microbiota. Research has shown numerous benefits of probiotic intake in the modulation of immune responses and human metabolic processes. However, unfavorable attention has been paid to temporal changes of the microbial composition and diversity of the GI tract. This study aimed to investigate the effects of yogurt consumption on the GI microbiome bacteria community composition, structure and diversity during and after a short-term period (42 days)...
February 15, 2017: Microorganisms
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