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Human gut microbiome

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https://www.readbyqxmd.com/read/27911317/alzheimer-s-disease-histological-and%C3%A2-behavioral-manifestations-in%C3%A2-transgenic-mice-correlate-with%C3%A2-specific%C3%A2-gut-microbiome-state
#1
Liang Shen, Lu Liu, Hong-Fang Ji
Alzheimer's disease (AD) is a neurodegenerative brain disease and is the most common form of dementia. In recent years, many studies indicated the association of gut microbiota changes with metabolic diseases. However, the gut microbiota of AD has not been investigated. The present study aims to compare the gut microbiota in APP/PS1 transgenic mice of AD and C57/Bl6 wild-type (WT) mice by pyrosequencing the V3 and V4 regions of the bacterial 16S ribosomal RNA genes. The 3-, 6-, and 8-month-old APP/PS1 and WT mice were used to explore the effects of age on the gut microbiota...
November 28, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910783/recent-advances-and-challenges-in-studies-of-control-of-cancer-stem-cells-and-the-gut-microbiome-by-the-trametes-derived-polysaccharopeptide-psp-review
#2
Joseph M Wu, Barbara B Doonan, Tze-Chen Hsieh, Qingyao Yang, Xiao-Tong Yang, Ming-Tat Ling
The medicinal mushroom Trametes versicolor has been well recognized for its activity in maintaining the general health of the population and in managing and treating human diseases in various cultures. Its use has been recently gaining acceptance and popularity in Western countries. The reported health benefits of T. versicolor led to a search for the identity of its bioactive ingredients. These efforts have resulted in the isolation of the polysaccharopeptide PSP from cultured mycelia of strain Cov-1, which expresses large amounts of PSP...
2016: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/27907005/intraluminal-flagellin-differentially-contributes-to-gut-dysbiosis-and-systemic-inflammation-following-burn-injury
#3
Logan Grimes, Allie Doyle, Aaron L Miller, Richard B Pyles, Gabor Olah, Csaba Szabo, Sarah Hoskins, Tonyia Eaves-Pyles
Burn injury is associated with a loss of gut barrier function, resulting in systemic dissemination of gut-derived bacteria and their products. The bacterial protein and TLR5 agonist, flagellin, induces non-specific innate immune responses. Because we detected flagellin in the serum of burn patients, we investigated whether gut-derived flagellin was a primary or secondary contributor to intestinal dysfunction and systemic inflammation following burn injury. The apical surface of polarized human intestinal epithelial cells (IECs), Caco-2BBe, were exposed to 50 or 500 ng of purified flagellin and 1 x 105 of an intestinal E...
2016: PloS One
https://www.readbyqxmd.com/read/27904735/urinary-metabolomics-of-young-italian-autistic-children-supports-abnormal-tryptophan-and-purine-metabolism
#4
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/27900395/microbiome-and-metabolic-disease-revisiting-the-bacterial-phylum-bacteroidetes
#5
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/27898428/beneficial-effects-of-a-dietary-weight-loss-intervention-on-human-gut-microbiome-diversity-and-metabolism-are-not-sustained-during-weight-maintenance
#6
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
#7
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/27895265/gut-homeostasis-microbial-dysbiosis-and-opioids
#8
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
#9
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/27892936/influence-of-early-life-exposure-host-genetics-and-diet-on-the-mouse-gut-microbiome-and-metabolome
#10
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
#11
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
#12
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/27883264/mucosa-associated-biohydrogenating-microbes-protect-the-simulated-colon-microbiome-from-stress-associated-with-high-concentrations-of-poly-unsaturated-fat
#13
Rosemarie De Weirdt, Emma Hernandez-Sanabria, Veerle Fievez, Eva Mees, Annelies Geirnaert, Florence Van Herreweghen, Ramiro Vilchez-Vargas, Pieter Van den Abbeele, Ruy Jauregui, Dietmar H Pieper, Bruno Vlaeminck, Tom Van de Wiele
Polyunsaturated fatty acids (PUFAs) may affect colon microbiome homeostasis by exerting (specific) antimicrobial effects and/or interfering with mucosal biofilm formation at the gut mucosal interface. We used standardized batch incubations and the Mucosal-Simulator of the Human Microbial Intestinal Ecosystem (M-SHIME) to show the in vitro luminal and mucosal effects of the main PUFA in the Western diet, linoleic acid (LA). High concentrations of LA were found to decrease butyrate production and Faecalibacterium prausnitzii numbers dependent on LA biohydrogenation to vaccenic acid (VA) and stearic acid (SA)...
November 24, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27881416/metagenomics-of-two-severe-foodborne-outbreaks-provides-diagnostic-signatures-and-signs-of-co-infection-not-attainable-by-traditional-methods
#14
Andrew D Huang, Chengwei Luo, Angela Pena-Gonzalez, Michael R Weigand, Cheryl Tarr, Konstantinos T Konstantinidis
: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based, culture-independent approaches such as shotgun metagenomics could sidestep these limitations, and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27872611/hypocholesterolemic-and-prebiotic-effects-of-a-whole-grain-oat-based-granola-breakfast-cereal-in-a-cardio-metabolic-at-risk-population
#15
Michael L Connolly, Xenofon Tzounis, Kieran M Tuohy, Julie A Lovegrove
Meta-analyses of randomized controlled trials (RTC) have confirmed the hypocholesterolaemic effect of oats and oat based fibers. However, the mechanisms by which oats or oat fractions lower cholesterol is not totally clear. Recognizing the important role of the gut microbiome in metabolism and metabolic disease risk, we examined the impact of whole grain oat Granola (WGO) on the human gut microbiota and cardio-metabolic risk factors using a randomized crossover dietary intervention in at risk individuals (ClinicalTrials...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27871802/probiotic-normalization-of-candida-albicans-in-schizophrenia-a-randomized-placebo-controlled-longitudinal-pilot-study
#16
Emily G Severance, Kristin L Gressitt, Cassie R Stallings, Emily Katsafanas, Lucy A Schweinfurth, Christina L G Savage, Maria B Adamos, Kevin M Sweeney, Andrea E Origoni, Sunil Khushalani, Faith B Dickerson, Robert H Yolken
The molecules and pathways of the gut-brain axis represent new targets for developing methods to diagnose and treat psychiatric disorders. Manipulation of the gut microbiome with probiotics may be a therapeutic strategy with the potential to relieve gastrointestinal (GI) comorbidities and improve psychiatric symptoms. Candida albicans and Saccharomyces cerevisiae, commensal yeast species, can be imbalanced in the unhealthy human microbiome, and these fungal exposures were previously found elevated in schizophrenia...
November 18, 2016: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/27871240/abo-antigen-and-secretor-statuses-are-not-associated-with-gut-microbiota-composition-in-1-500-twins
#17
Emily R Davenport, Julia K Goodrich, Jordana T Bell, Tim D Spector, Ruth E Ley, Andrew G Clark
BACKGROUND: Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such factor is the ABO antigen. This molecule is not only expressed on the surface of red blood cells, but is also secreted from mucosal surfaces in individuals containing an intact FUT2 gene (secretors)...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27869789/genome-guided-design-of-a-defined-mouse-microbiota-that-confers-colonization-resistance-against-salmonella-enterica-serovar-typhimurium
#18
Sandrine Brugiroux, Markus Beutler, Carina Pfann, Debora Garzetti, Hans-Joachim Ruscheweyh, Diana Ring, Manuel Diehl, Simone Herp, Yvonne Lötscher, Saib Hussain, Boyke Bunk, Rüdiger Pukall, Daniel H Huson, Philipp C Münch, Alice C McHardy, Kathy D McCoy, Andrew J Macpherson, Alexander Loy, Thomas Clavel, David Berry, Bärbel Stecher
Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S...
November 21, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27867199/candida-albicans-cell-type-switching-and-functional-plasticity-in-the-mammalian-host
#19
Suzanne M Noble, Brittany A Gianetti, Jessica N Witchley
Candida albicans is a ubiquitous commensal of the mammalian microbiome and the most prevalent fungal pathogen of humans. A cell-type transition between yeast and hyphal morphologies in C. albicans was thought to underlie much of the variation in virulence observed in different host tissues. However, novel yeast-like cell morphotypes, including opaque(a/α), grey and gastrointestinally induced transition (GUT) cell types, were recently reported that exhibit marked differences in vitro and in animal models of commensalism and disease...
November 21, 2016: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/27866909/unsaturated-fatty-acid-synthesis-in-the-gastric-pathogen-helicobacter-pylori-proceeds-via-a-backtracking-mechanism
#20
Hongkai Bi, Lei Zhu, Jia Jia, Liping Zeng, John E Cronan
Helicobacter pylori is a Gram-negative bacterium that inhabits the upper gastrointestinal tract in humans, and the presence of this pathogen in the gut microbiome increases the risk of peptic ulcers and stomach cancer. H. pylori depends on unsaturated fatty acid (UFA) biosynthesis for maintaining membrane structure and function. Although some of the H. pylori enzymes involved in UFA biosynthesis are functionally homologous with the enzymes found in Escherichia coli, we show here that an enzyme HP0773, now annotated as FabX, uses an unprecedented backtracking mechanism to not only dehydrogenate decanoyl-acyl carrier protein (ACP) in a reaction that parallels that of acyl-CoA dehydrogenase, the first enzyme of the fatty acid β-oxidation cycle, but also isomerizes trans-2-decenoyl-ACP to cis-3-decenoyl-ACP, the key UFA synthetic intermediate...
November 16, 2016: Cell Chemical Biology
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