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Human gut microbiome

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https://www.readbyqxmd.com/read/28925886/the-microbiota-gut-brain-axis-in-neuropsychiatric-disorders-pathophysiological-mechanisms-and-novel-treatments
#1
Yong-Ku Kim, Cheolmin Shin
BACKGROUND: The human gut microbiome comprise a huge number of microorganisms with co-evolutionary associations with humans. It has been repeatedly revealed that bidirectional communication exists between the brain and the gut and involves neural, hormonal, and immunological pathways. Evidences from neuroscience researches over the past few years suggest that microbiota is essential for the development and maturation of brain systems that are associated to stress responses. METHOD: This review provides that the summarization of the communication among microbiota, gut and brain and the results of preclinical and clinical studies on gut microbiota used in treatments for neuropsychiatric disorders...
September 15, 2017: Current Neuropharmacology
https://www.readbyqxmd.com/read/28923537/metagenomic-shotgun-sequencing-and-unbiased-metabolomic-profiling-identify-specific-human-gut-microbiota-and-metabolites-associated-with-immune-checkpoint-therapy-efficacy-in-melanoma-patients
#2
Arthur E Frankel, Laura A Coughlin, Jiwoong Kim, Thomas W Froehlich, Yang Xie, Eugene P Frenkel, Andrew Y Koh
This is the first prospective study of the effects of human gut microbiota and metabolites on immune checkpoint inhibitor (ICT) response in metastatic melanoma patients. Whereas many melanoma patients exhibit profound response to ICT, there are fewer options for patients failing ICT-particularly with BRAF-wild-type disease. In preclinical studies, specific gut microbiota promotes regression of melanoma in mice. We therefore conducted a study of the effects of pretreatment gut microbiota and metabolites on ICT Response Evaluation Criteria in Solid Tumors response in 39 metastatic melanoma patients treated with ipilimumab, nivolumab, ipilimumab plus nivolumab (IN), or pembrolizumab (P)...
September 14, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28919884/secretome-of-intestinal-bacilli-a-natural-guard-against-pathologies
#3
REVIEW
Olga N Ilinskaya, Vera V Ulyanova, Dina R Yarullina, Ilgiz G Gataullin
Current studies of human gut microbiome usually do not consider the special functional role of transient microbiota, although some of its members remain in the host for a long time and produce broad spectrum of biologically active substances. Getting into the gastrointestinal tract (GIT) with food, water and probiotic preparations, two representatives of Bacilli class, genera Bacillus and Lactobacillus, colonize epithelium blurring the boundaries between resident and transient microbiota. Despite their minor proportion in the microbiome composition, these bacteria can significantly affect both the intestinal microbiota and the entire body thanks to a wide range of secreted compounds...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28916564/modulation-of-the-gut-microbiome-a-systematic-review-of-the-effect-of-bariatric-surgery
#4
Yan Guo, Zhi-Ping Huang, Chao-Qian Liu, Lin Qi, Yuan Sheng, Da-Jin Zou
OBJECTIVE: Bariatric surgery is recommended for patients with obesity and type 2 diabetes. Recent evidence suggested a strong connection between gut microbiota and bariatric surgery. DESIGN: Systematic review. METHODS: The PubMed and OVID Embase were used and articles concerning bariatric surgery and gut microbiota were screened. The main outcome measures were alterations of gut microbiota after bariatric surgery and correlations between gut microbiota and host metabolism...
September 15, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#5
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28914862/-liver-diseases-the-pathogenetic-role-of-the-gut-microbiome-and-the-potential-of-treatment-for-its-modulation
#6
K A Aitbaev, I T Murkamilov, V V Fomin
The paper gives an update on the role of the gut microbiome (GM) in the development of nonalcoholic fatty liver disease, nonalcoholic steatohepatitis, alcoholic liver disease, liver cirrhosis (LC), and its complications, such as hepatic encephalopathy (HE) and hepatocellular carcinoma (HCC), and discusses the possibilities of its correction with prebiotics, probiotics, synbiotics, antibiotics, and fecal microbiota transplantation (FMT). The pathophysiology of the liver diseases in question demonstrates some common features that are characterized by pathogenic changes in the composition of the gastrointestinal tract microflora, by intestinal barrier impairments, by development of endotoxemia, by increased liver expression of proinflammatory factors, and by development of liver inflammation...
2017: Terapevticheskiĭ Arkhiv
https://www.readbyqxmd.com/read/28912798/comparative-genomic-analysis-of-the-human-gut-microbiome-reveals-a-broad-distribution-of-metabolic-pathways-for-the-degradation-of-host-synthetized-mucin-glycans-and-utilization-of-mucin-derived-monosaccharides
#7
Dmitry A Ravcheev, Ines Thiele
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense epithelium-attached layer. The outer layer is inhabited by various representatives of the human gut microbiota (HGM). Glycans of the colonic mucus can be used by the HGM as a source of carbon and energy when dietary fibers are not sufficiently available. Both commensals and pathogens can utilize mucin glycans...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28912574/distinct-gut-microbiome-patterns-associate-with-consensus-molecular-subtypes-of-colorectal-cancer
#8
Rachel V Purcell, Martina Visnovska, Patrick J Biggs, Sebastian Schmeier, Frank A Frizelle
Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910638/the-landscape-of-type-vi-secretion-across-human-gut-microbiomes-reveals-its-role-in-community-composition
#9
Adrian J Verster, Benjamin D Ross, Matthew C Radey, Yiqiao Bao, Andrew L Goodman, Joseph D Mougous, Elhanan Borenstein
Although gut microbiome composition is well defined, the mechanisms underlying community assembly remain poorly understood. Bacteroidales possess three genetic architectures (GA1-3) of the type VI secretion system (T6SS), an effector delivery pathway that mediates interbacterial competition. Here we define the distribution and role of GA1-3 in the human gut using metagenomic analysis. We find that adult microbiomes harbor limited effector and cognate immunity genes, suggesting selection for compatibility at the species (GA1 and GA2) and strain (GA3) levels...
September 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28905671/microbiota-derived-uremic-retention-solutes-perpetrators-of-altered-nonrenal-drug-clearance-in-kidney-disease
#10
Alexander J Prokopienko, Thomas D Nolin
Scientific interest in the gut microbiota is increasing due to improved understanding of its implications in human health and disease. In patients with kidney disease, gut microbiota-derived uremic toxins directly contribute to altered nonrenal drug clearance. Microbial imbalances, known as dysbiosis, potentially increase formation of microbiota-derived toxins, and diminished renal clearance leads to toxin accumulation. High concentrations of microbiota-derived toxins such as indoxyl sulfate and p-cresol sulfate perpetrate interactions with drug metabolizing enzymes and transporters, which provides a mechanistic link between increases in drug-related adverse events and dysbiosis in kidney disease...
September 14, 2017: Expert Review of Clinical Pharmacology
https://www.readbyqxmd.com/read/28904999/linking-spatial-structure-and-community-level-biotic-interactions-through-cooccurrence-and-time-series-modeling-of-the-human-intestinal-microbiota
#11
Eric J de Muinck, Knut E A Lundin, Pål Trosvik
The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904997/development-of-inflammatory-bowel-disease-is-linked-to-a-longitudinal-restructuring-of-the-gut-metagenome-in-mice
#12
Thomas Sharpton, Svetlana Lyalina, Julie Luong, Joey Pham, Emily M Deal, Courtney Armour, Christopher Gaulke, Shomyseh Sanjabi, Katherine S Pollard
The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis...
September 2017: MSystems
https://www.readbyqxmd.com/read/28898933/inside-the-guts-of-the-city-urban-induced-alterations-of-the-gut-microbiota-in-a-wild-passerine
#13
Aimeric Teyssier, Lieze Oscar Rouffaer, Noraine Saleh Hudin, Diederik Strubbe, Erik Matthysen, Luc Lens, Joël White
Urbanisation represents one of the most radical forms of terrestrial land use change and has been shown to lead to alterations in ecosystem functioning and community dynamics and changes in individual phenotypic traits. While the recent surge in microbiome studies has brought about a paradigm shift by which individuals cannot truly be considered independently of the bacterial communities they host, the role of gut microbiota in organismal response to human-induced environmental change is still scarcely studied...
September 8, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28894110/omega-3-fatty-acids-correlate-with-gut-microbiome-diversity-and-production-of-n-carbamylglutamate-in-middle-aged-and-elderly-women
#14
Cristina Menni, Jonas Zierer, Tess Pallister, Matthew A Jackson, Tao Long, Robert P Mohney, Claire J Steves, Tim D Spector, Ana M Valdes
Omega-3 fatty acids may influence human physiological parameters in part by affecting the gut microbiome. The aim of this study was to investigate the links between omega-3 fatty acids, gut microbiome diversity and composition and faecal metabolomic profiles in middle aged and elderly women. We analysed data from 876 twins with 16S microbiome data and DHA, total omega-3, and other circulating fatty acids. Estimated food intake of omega-3 fatty acids were obtained from food frequency questionnaires. Both total omega-3and DHA serum levels were significantly correlated with microbiome alpha diversity (Shannon index) after adjusting for confounders (DHA Beta(SE) = 0...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893978/gut-bacteria-from-multiple-sclerosis-patients-modulate-human-t-cells-and-exacerbate-symptoms-in-mouse-models
#15
Egle Cekanaviciute, Bryan B Yoo, Tessel F Runia, Justine W Debelius, Sneha Singh, Charlotte A Nelson, Rachel Kanner, Yadira Bencosme, Yun Kyung Lee, Stephen L Hauser, Elizabeth Crabtree-Hartman, Ilana Katz Sand, Mar Gacias, Yungjiao Zhu, Patrizia Casaccia, Bruce A C Cree, Rob Knight, Sarkis K Mazmanian, Sergio E Baranzini
The gut microbiota regulates T cell functions throughout the body. We hypothesized that intestinal bacteria impact the pathogenesis of multiple sclerosis (MS), an autoimmune disorder of the CNS and thus analyzed the microbiomes of 71 MS patients not undergoing treatment and 71 healthy controls. Although no major shifts in microbial community structure were found, we identified specific bacterial taxa that were significantly associated with MS. Akkermansia muciniphila and Acinetobacter calcoaceticus, both increased in MS patients, induced proinflammatory responses in human peripheral blood mononuclear cells and in monocolonized mice...
September 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28891224/smv1-an-extremely-stable-thermophilic-virus-platform-for-nanoparticle-trafficking-in-the-mammalian-gi-tract
#16
Kristine B Uldahl, Seth T Walk, Stephen C Olshefsky, Mark J Young, Xu Peng
AIMS: analysis of the stability and safety of Sulfolobus monocaudavirus 1 (SMV1) during passage through the mammalian GI tract. METHODS AND RESULTS: A major challenge of using nano-vectors to target gut microbiome is their survival during passage through the extremely acidic and proteolytic environment of the mammalian GI tract. Here we investigated the thermo-acidophilic archaeal virus SMV1 as a candidate therapeutic nano-vector for the distal mammalian GI tract microbiome...
September 11, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28891140/other-helicobacters-gastric-and-gut-microbiota
#17
REVIEW
Christelle Péré-Védrenne, Bram Flahou, Mun Fai Loke, Armelle Ménard, Jamuna Vadivelu
The current article is a review of the most important and relevant literature published in 2016 and early 2017 on non-Helicobacter pylori Helicobacter infections in humans and animals, as well as interactions between H. pylori and the microbiota of the stomach and other organs. Some putative new Helicobacter species were identified in sea otters, wild boars, dogs, and mice. Many cases of Helicobacter fennelliae and Helicobacter cinaedi infection have been reported in humans, mostly in immunocompromised patients...
September 2017: Helicobacter
https://www.readbyqxmd.com/read/28887729/intestinal-microbiome-gut-brain-axis-and-irritable-bowel-syndrome
#18
REVIEW
Gabriele Moser, Camille Fournier, Johannes Peter
Psychological comorbidity is highly present in irritable bowel syndrome (IBS). Recent research points to a role of intestinal microbiota in visceral hypersensitivity, anxiety, and depression. Increased disease reactivity to psychological stress has been described too. A few clinical studies have attempted to identify features of dysbiosis in IBS. While animal studies revealed strong associations between stress and gut microbiota, studies in humans are rare. This review covers the most important studies on intestinal microbial correlates of psychological and clinical features in IBS, including stress, anxiety, and depression...
September 8, 2017: Wiener Medizinische Wochenschrift
https://www.readbyqxmd.com/read/28887570/the-salivary-microbiome-is-consistent-between-subjects-and-resistant-to-impacts-of-short-term-hospitalization
#19
Damien J Cabral, Jenna I Wurster, Myrto E Flokas, Michail Alevizakos, Michelle Zabat, Benjamin J Korry, Aislinn D Rowan, William H Sano, Nikolaos Andreatos, R Bobby Ducharme, Philip A Chan, Eleftherios Mylonakis, Beth Burgwyn Fuchs, Peter Belenky
In recent years, a growing amount of research has begun to focus on the oral microbiome due to its links with health and systemic disease. The oral microbiome has numerous advantages that make it particularly useful for clinical studies, including non-invasive collection, temporal stability, and lower complexity relative to other niches, such as the gut. Despite recent discoveries made in this area, it is unknown how the oral microbiome responds to short-term hospitalization. Previous studies have demonstrated that the gut microbiome is extremely sensitive to short-term hospitalization and that these changes are associated with significant morbidity and mortality...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28884091/alterations-of-the-gut-microbiome-in-hypertension
#20
Qiulong Yan, Yifang Gu, Xiangchun Li, Wei Yang, Liqiu Jia, Changming Chen, Xiuyan Han, Yukun Huang, Lizhe Zhao, Peng Li, Zhiwei Fang, Junpeng Zhou, Xiuru Guan, Yanchun Ding, Shaopeng Wang, Muhammad Khan, Yi Xin, Shenghui Li, Yufang Ma
Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing...
2017: Frontiers in Cellular and Infection Microbiology
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