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Human gut microbiome

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https://www.readbyqxmd.com/read/29776435/fecal-aliquot-straw-technique-fast-allows-for-easy-and-reproducible-subsampling-assessing-interpersonal-variation-in-trimethylamine-n-oxide-tmao-accumulation
#1
Kymberleigh A Romano, Kimberly A Dill-McFarland, Kazuyuki Kasahara, Robert L Kerby, Eugenio I Vivas, Daniel Amador-Noguez, Pamela Herd, Federico E Rey
BACKGROUND: Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes...
May 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29773876/early-salmonella-typhimurium-infection-in-pigs-disrupts-microbiome-composition-and-functionality-principally-at-the-ileum-mucosa
#2
Héctor Argüello, Jordi Estellé, Sara Zaldívar-López, Ángeles Jiménez-Marín, Ana Carvajal, Mª Asunción López-Bascón, Fiona Crispie, Orla O'Sullivan, Paul D Cotter, Feliciano Priego-Capote, Luis Morera, Juan J Garrido
Salmonella is a major foodborne pathogen which successfully infects animal species for human consumption such as swine. The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, Salmonella infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by Salmonella Typhimurium at three locations: ileum mucosa, ileum content and faeces...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773467/human-microbiome-restoration-and-safety
#3
REVIEW
Eric Banan-Mwine Daliri, Charles Nkufi Tango, Byong H Lee, Deog-Hwan Oh
The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans...
May 9, 2018: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29769378/food-starch-structure-impacts-gut-microbiome-composition
#4
Frederick J Warren, Naoki M Fukuma, Deirdre Mikkelsen, Bernadine M Flanagan, Barbara A Williams, Allan T Lisle, Páraic Ó Cuív, Mark Morrison, Michael J Gidley
Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29765359/comparing-microbiome-sampling-methods-in-a-wild-mammal-fecal-and-intestinal-samples-record-different-signals-of-host-ecology-evolution
#5
Melissa R Ingala, Nancy B Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A Speer, Susan L Perkins
The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29763437/postnatal-colonization-with-human-infant-type-bifidobacterium-species-alters-behavior-of-adult-gnotobiotic-mice
#6
Berkley Luk, Surabi Veeraragavan, Melinda Engevik, Miriam Balderas, Angela Major, Jessica Runge, Ruth Ann Luna, James Versalovic
Accumulating studies have defined a role for the intestinal microbiota in modulation of host behavior. Research using gnotobiotic mice emphasizes that early microbial colonization with a complex microbiota (conventionalization) can rescue some of the behavioral abnormalities observed in mice that grow to adulthood completely devoid of bacteria (germ-free mice). However, the human infant and adult microbiomes vary greatly, and effects of the neonatal microbiome on neurodevelopment are currently not well understood...
2018: PloS One
https://www.readbyqxmd.com/read/29762384/microbial-metabolism-in-the-mammalian-gut-molecular-mechanisms-and-clinical-implications
#7
Anne Hall, James Versalovic
Human intestinal microbes participate actively at the interface of diet, nutrition, and overall health status. These biodiverse communities of microorganisms have a broader metabolic repertoire compared with their host, and they are able to synthesize and degrade substrates that would be otherwise unavailable. In recent years, we have recognized that healthy microbial communities are important for energy harvest and the regulation of body systems outside the digestive tract. Microbial dysbiosis, however, has been implicated in a number of human disorders, including obesity and inflammation...
June 2018: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29762376/microbial-fermentation-of-starch-its-impact-on-the-range-of-acceptable-carbohydrate-intake
#8
Satish C Kalhan
Starch, a major source of carbohydrates in human nutrition, is extensively hydrolyzed in the gastrointestinal tract of children and adults. A small fraction of the ingested starch reaches the cecum and colon where it is fermented by the gut microbiome into short-chain fatty acids (SCFA) and other products. Recent data in humans and in animal models have demonstrated the extensive effects of short-chain fatty acids on whole body energy metabolism, appetite, insulin resistance, fatty acid oxidation, fat accretion, obesity, and diabetes...
June 2018: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29761785/discovery-and-characterization-of-a-prevalent-human-gut-bacterial-enzyme-sufficient-for-the-inactivation-of-a-family-of-plant-toxins
#9
Nitzan Koppel, Jordan E Bisanz, Maria-Eirini Pandelia, Peter J Turnbaugh, Emily P Balskus
Although the human gut microbiome plays a prominent role in xenobiotic transformation, most of the genes and enzymes responsible for this metabolism are unknown. Recently, we linked the two-gene 'cardiac glycoside reductase' ( cgr ) operon encoded by the gut Actinobacterium Eggerthella lenta to inactivation of the cardiac medication and plant natural product digoxin. Here, we compared the genomes of 25 E. lenta strains and close relatives, revealing an expanded 8-gene cgr -associated gene cluster present in all digoxin metabolizers and absent in non-metabolizers...
May 15, 2018: ELife
https://www.readbyqxmd.com/read/29761590/the-interaction-of-anti-diabetic-%C3%AE-glucosidase-inhibitors-and-gut-bacteria-%C3%AE-glucosidase
#10
Kemin Tan, Christine Tesar, Rosemarie Wilton, Robert P Jedrzejczak, Andrzej Joachimiak
Carbohydrate hydrolyzing α-glucosidases are commonly found in microorganisms present in the human intestine microbiome. We have previously reported crystal structures of an α-glucosidase from the human gut bacterium Blaubia (Ruminococcus) obeum (Ro-αG1) and its substrate preference/specificity switch. This novel member of the GH31 family is a structural homolog of human intestinal maltase-glucoamylase (MGAM) and sucrase-isomaltase (SI) with a highly conserved active site that is predicted to be common in Ro-αG1 homologs among other species that colonize the human gut...
May 15, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29760467/the-oral-microbiome-bank-of-china
#11
Peng Xian, Zhou Xuedong, Xu Xin, Li Yuqing, Li Yan, Li Jiyao, Su Xiaoquan, Huang Shi, Xu Jian, Liao Ga
The human microbiome project (HMP) promoted further understanding of human oral microbes. However, research on the human oral microbiota has not made as much progress as research on the gut microbiota. Currently, the causal relationship between the oral microbiota and oral diseases remains unclear, and little is known about the link between the oral microbiota and human systemic diseases. To further understand the contribution of the oral microbiota in oral diseases and systemic diseases, a Human Oral Microbiome Database (HOMD) was established in the US...
May 3, 2018: International Journal of Oral Science
https://www.readbyqxmd.com/read/29756574/dietary-protein-and-gut-microbiome-composition-and-function
#12
Jianfei Zhao, Xiaoya Zhang, Hongbin Liu, Michael A Brown, Shiyan Qiao
Dietary protein and its metabolites, amino acids are essential nutrients for human and animals. Accumulated researches revealed that the gut microbiota mediate the crosstalk between protein metabolism and host immune response. Gut microbes are involved in the digestion, absorption, metabolism and transformation process of dietary protein in the gastrointestinal tract. Amino acids can be metabolized into numerous microbial metabolites, and these metabolites participate in various physiological functions related to host health and diseases...
May 14, 2018: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/29756135/microbial-small-molecules-weapons-of-plant-subversion
#13
REVIEW
Ioannis A Stringlis, Hao Zhang, Corné M J Pieterse, Melvin D Bolton, Ronnie de Jonge
Covering: up to 2018Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut...
May 14, 2018: Natural Product Reports
https://www.readbyqxmd.com/read/29755427/16s-rrna-gene-sequencing-for-deciphering-the-colorectal-cancer-gut-microbiome-current-protocols-and-workflows
#14
REVIEW
Muhammad-Afiq Osman, Hui-Min Neoh, Nurul-Syakima Ab Mutalib, Siok-Fong Chin, Rahman Jamal
The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29753695/the-microbiome-in-preterm-birth
#15
REVIEW
Derrick M Chu, Maxim Seferovic, Ryan M Pace, Kjersti M Aagaard
The microbiome is thought to play a role in the maintenance of a healthy pregnancy and thus may either contribute to or protect from preterm birth. Study of the human microbiome has been aided by metagenomic sequencing approaches, providing greater insight into the commensal bacteria that coexist in and on our bodies. The vaginal microbiome has been the most widely studied, though there have been recent efforts to explore the gut, cervical-vaginal, placental and oral microbiomes in the further search of etiologies of preterm birth...
April 9, 2018: Best Practice & Research. Clinical Obstetrics & Gynaecology
https://www.readbyqxmd.com/read/29751733/intestinal-absorption-of-fructose
#16
Ronaldo P Ferraris, Jun-Yong Choe, Chirag R Patel
Increased understanding of fructose metabolism, which begins with uptake via the intestine, is important because fructose now constitutes a physiologically significant portion of human diets and is associated with increased incidence of certain cancers and metabolic diseases. New insights in our knowledge of intestinal fructose absorption mediated by the facilitative glucose transporter GLUT5 in the apical membrane and by GLUT2 in the basolateral membrane are reviewed. We begin with studies related to structure as well as ligand binding, then revisit the controversial proposition that apical GLUT2 is the main mediator of intestinal fructose absorption...
May 11, 2018: Annual Review of Nutrition
https://www.readbyqxmd.com/read/29751049/increased-butyrate-priming-in-the-gut-stalls-microbiome-associated-gastrointestinal-inflammation-and-hepatic-metabolic-reprogramming-in-a-mouse-model-of-gulf-war-illness
#17
Ratanesh Kumar Seth, Diana Kimono, Firas Alhasson, Sutapa Sarkar, Muayad Albadrani, Stephen K Lasley, Ronnie Horner, Patricia Janulecewicz, Mitzi Nagarkatti, Prakash Nagarkatti, Kimberly Sullivan, Saurabh Chatterjee
Most of the associated pathologies in Gulf War Illness (GWI) have been ascribed to chemical and pharmaceutical exposures during the war. Since an increased number of veterans complain of gastrointestinal (GI), neuroinflammatory and metabolic complications as they age and there are limited options for a cure, the present study was focused to assess the role of butyrate, a short chain fatty acid for attenuating GWI-associated GI and metabolic complications. Results in a GWI-mouse model of permethrin and pyridostigmine bromide (PB) exposure showed that oral butyrate restored gut homeostasis and increased GPR109A receptor copies in the small intestine (SI)...
May 8, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29750437/green-tea-liquid-consumption-alters-the-human-intestinal-and-oral-microbiome
#18
Xiaojie Yuan, Yong Long, Zhaohua Ji, Jie Gao, Ting Fu, Min Yan, Lei Zhang, Haixia Su, Weilu Zhang, Xiaohui Wen, Zhongshu Pu, Hui Chen, Yufei Wang, Xu Gu, Binyuan Yan, Kanakaraju Kaliannan, Zhongjun Shao
SCOPE: GTPs exerts anti-CRC activity. The intestinal microbiota and intestinal colonization by bacteria of oral origin has been implicated in colorectal carcinogenesis. GT modulates the composition of mouse gut microbiota harmonious with anticancer activity. Therefore, we investigated the effect of GTL consumption on the gut and oral microbiome in healthy volunteers (n = 12). METHODS AND RESULTS: 16S sequencing and PICRUSt analysis of both fecal and saliva samples (collected before intervention, after 2 weeks of GTL (400 ml/day) and after a washout period of one week) in healthy volunteers showed changes in microbial diversity and core microbiota and difference in clear classification (PLS-DA)...
May 11, 2018: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29750384/effects-of-moderate-voluntary-ethanol-consumption-on-the-rat-and-human-gut-microbiome
#19
Kassi L Kosnicki, Jerrold C Penprase, Patricia Cintora, Pedro J Torres, Greg L Harris, Susan M Brasser, Scott T Kelley
Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans...
May 11, 2018: Addiction Biology
https://www.readbyqxmd.com/read/29750272/gut-microbial-diversity-is-associated-with-lower-arterial-stiffness-in-women
#20
Cristina Menni, Chihung Lin, Marina Cecelja, Massimo Mangino, Maria Luisa Matey-Hernandez, Louise Keehn, Robert P Mohney, Claire J Steves, Tim D Spector, Chang-Fu Kuo, Phil Chowienczyk, Ana M Valdes
Aims: The gut microbiome influences metabolic syndrome (MetS) and inflammation and is therapeutically modifiable. Arterial stiffness is poorly correlated with most traditional risk factors. Our aim was to examine whether gut microbial composition is associated with arterial stiffness. Methods and results: We assessed the correlation between carotid-femoral pulse wave velocity (PWV), a measure of arterial stiffness, and gut microbiome composition in 617 middle-aged women from the TwinsUK cohort with concurrent serum metabolomics data...
May 9, 2018: European Heart Journal
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