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https://www.readbyqxmd.com/read/28926920/a-comparative-study-on-the-process-efficiencies-and-microbial-community-structures-of-six-full-scale-wet-and-semi-dry-anaerobic-digesters-treating-food-wastes
#1
Gyuseong Han, Seung Gu Shin, Joonyeob Lee, Juhee Shin, Seokhwan Hwang
The purpose of this study was to investigate the effect of different types of food wastes on the process efficiency and microbial community structures in full-scale anaerobic digesters and to identify parameters that affect these criteria. Six full-scale anaerobic digesters were investigated; three were operated under "wet" condition (total solids TS≤10%), and three were run under "semi-dry" condition (10%≤TS≤20%). Removal efficiency of volatile solids was much higher in the wet digesters (75.2±3.8%) than in the semi-dry digesters (42...
September 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28912524/precise-insertion-and-guided-editing-of-higher-plant-genomes-using-cpf1-crispr-nucleases
#2
Matthew B Begemann, Benjamin N Gray, Emma January, Gina C Gordon, Yonghua He, Haijun Liu, Xingrong Wu, Thomas P Brutnell, Todd C Mockler, Mohammed Oufattole
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based platform that would enable higher efficiencies of precise gene insertion or replacement, we screened the Cpf1 nucleases from Francisella novicida and Lachnospiraceae bacterium ND2006 for their capability to induce targeted gene insertion via homology directed repair. Both nucleases, in the presence of a guide RNA and repairing DNA template flanked by homology DNA fragments to the target site, were demonstrated to generate precise gene insertions as well as indel mutations at the target site in the rice genome...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912020/intestinal-dysbiosis-featuring-abundance-of-ruminococcus-gnavus-associates-with-allergic-diseases-in-infants
#3
Huey-Huey Chua, Hung-Chieh Chou, Ya-Ling Tung, Bor-Luen Chiang, Chien-Chia Liao, Hong-Hsing Liu, Yen-Hsuan Ni
BACKGROUND & AIMS: Dysbiosis of the intestinal microbiota has been associated with development of allergies in infants. However, it is not clear what microbes might contribute to this process. We investigated what microbe(s) might be involved in analyses of infant twins and mice. METHODS: We studied fecal specimens prospectively in a twin cohort (n=30) and age-matched singletons (n=14) born at National Taiwan University Children's Hospital, Taipei, Taiwan, from April 2011 to March 2013...
September 11, 2017: Gastroenterology
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
#4
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/28892041/guide-bound-structures-of-an-rna-targeting-a-cleaving-crispr-cas13a-enzyme
#5
Gavin J Knott, Alexandra East-Seletsky, Joshua C Cofsky, James M Holton, Emeric Charles, Mitchell R O'Connell, Jennifer A Doudna
CRISPR adaptive immune systems protect bacteria from infections by deploying CRISPR RNA (crRNA)-guided enzymes to recognize and cut foreign nucleic acids. Type VI-A CRISPR-Cas systems include the Cas13a enzyme, an RNA-activated RNase capable of crRNA processing and single-stranded RNA degradation upon target-transcript binding. Here we present the 2.0-Å resolution crystal structure of a crRNA-bound Lachnospiraceae bacterium Cas13a (LbaCas13a), representing a recently discovered Cas13a enzyme subtype. This structure and accompanying biochemical experiments define the Cas13a catalytic residues that are directly responsible for crRNA maturation...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28890155/antibiotic-induced-microbiota-perturbation-causes-gut-endocannabinoidome-changes-hippocampal-neuroglial-reorganization-and-depression-in-mice
#6
F Guida, F Turco, M Iannotta, D De Gregorio, I Palumbo, G Sarnelli, A Furiano, F Napolitano, S Boccella, L Luongo, M Mazzitelli, A Usiello, F De Filippis, F A Iannotti, F Piscitelli, D Ercolini, V de Novellis, V Di Marzo, R Cuomo, S Maione
The microbiota-gut-brain axis (MGBA) regulates the reciprocal interaction between chronic inflammatory bowel and psychiatric disorders. This interaction involves multiple pathways that are highly debated. We examined the behavioural, biochemical and electrophysiological alterations, as well as gut microbiota composition in a model of antibiotic-induced experimental dysbiosis. Inflammation of the small intestine was also assessed. Mice were exposed to a mixture of antimicrobials for 2weeks. Afterwards, they received Lactobacillus casei DG (LCDG) or a vehicle for up to 7days via oral gavage...
September 7, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28886218/crispr-cpf1-enables-fast-and-simple-genome-editing-of-saccharomyces-cerevisiae
#7
René Verwaal, Nathalie Buiting-Wiessenhaan, Sacha Dalhuijsen, Johannes A Roubos
Cpf1 represents a novel single RNA-guided CRISPR/Cas endonuclease system suitable for genome editing with distinct features compared to Cas9. We demonstrate the functionality of three Cpf1 orthologues - Acidaminococcus spp. BV3L6 (AsCpf1), Lachnospiraceae bacterium ND2006 (LbCpf1), Francisella novicida U112 (FnCpf1) - for genome editing of Saccharomyces cerevisiae. These Cpf1-based systems enable fast and reliable introduction of donor DNA on the genome using a two plasmid-based editing approach together with linear donor DNA...
September 8, 2017: Yeast
https://www.readbyqxmd.com/read/28883813/a-structural-and-functional-elucidation-of-the-rumen-microbiome-influenced-by-various-diets-and-microenvironments
#8
Simon Deusch, Amélia Camarinha-Silva, Jürgen Conrad, Uwe Beifuss, Markus Rodehutscord, Jana Seifert
The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28874832/antibiotic-induced-perturbations-in-microbial-diversity-during-post-natal-development-alters-amyloid-pathology-in-an-aged-appswe-ps1%C3%AE-e9-murine-model-of-alzheimer-s-disease
#9
Myles R Minter, Reinhard Hinterleitner, Marlies Meisel, Can Zhang, Vanessa Leone, Xiaoqiong Zhang, Paul Oyler-Castrillo, Xulun Zhang, Mark W Musch, Xunuo Shen, Bana Jabri, Eugene B Chang, Rudolph E Tanzi, Sangram S Sisodia
Recent evidence suggests the commensal microbiome regulates host immunity and influences brain function; findings that have ramifications for neurodegenerative diseases. In the context of Alzheimer's disease (AD), we previously reported that perturbations in microbial diversity induced by life-long combinatorial antibiotic (ABX) selection pressure in the APPSWE/PS1ΔE9 mouse model of amyloidosis is commensurate with reductions in amyloid-β (Aβ) plaque pathology and plaque-localised gliosis. Considering microbiota-host interactions, specifically during early post-natal development, are critical for immune- and neuro-development we now examine the impact of microbial community perturbations induced by acute ABX exposure exclusively during this period in APPSWE/PS1ΔE9 mice...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28871246/succession-and-fermentation-products-of-grass-carp-ctenopharyngodon-idellus-hindgut-microbiota-in-response-to-an-extreme-dietary-shift
#10
Yao Tong Hao, Shan Gong Wu, Fan Xiong, Ngoc T Tran, Ivan Jakovlić, Hong Zou, Wen Xiang Li, Gui Tang Wang
Dietary intake affects the structure and function of microbes in host intestine. However, the succession of gut microbiota in response to changes in macronutrient levels during a long period of time remains insufficiently studied. Here, we determined the succession and metabolic products of intestinal microbiota in grass carp (Ctenopharyngodon idellus) undergoing an abrupt and extreme diet change, from fish meal to Sudan grass (Sorghum sudanense). Grass carp hindgut microbiota responded rapidly to the diet shift, reaching a new equilibrium approximately within 11 days...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28861518/butyrate-supplementation-at-high-concentrations-alters-enteric-bacterial-communities-and-reduces-intestinal-inflammation-in-mice-infected-with-citrobacter-rodentium
#11
Janelle A Jiminez, Trina C Uwiera, D Wade Abbott, Richard R E Uwiera, G Douglas Inglis
Butyrate is a short-chain fatty acid by-product of the microbial fermentation of dietary fermentable materials in the large intestine; it is the main energy source for enterocyte regeneration, modulates the enteric microbial community, and contributes to increasing host health via mechanisms that are relatively poorly defined. Limited research has examined the therapeutic potential of butyrate using models of enteric inflammation incited by pathogenic organisms. We used Citrobacter rodentium to incite acute Th1/Th17 inflammation to ascertain the impact of butyrate on the host-microbiota relationship...
July 2017: MSphere
https://www.readbyqxmd.com/read/28856906/effect-of-propionibacterium-acidipropionici-p169-on-the-rumen-and-faecal-microbiota-of-beef-cattle-fed-a-maize-based-finishing-diet
#12
E Azad, N Narvaez, H Derakhshani, A Y Allazeh, Y Wang, T A McAllister, E Khafipour
Direct fed microbial supplementation with lactic acid utilising bacteria (i.e. Propionibacterium acidipropionici P169) has been shown to alleviate the severity of subacute ruminal acidosis in high-grain fed beef cattle. This study was carried out to explore the impact of P169 supplementation on modulating rumen and hindgut microbiota of high-grain fed steers. Seven ruminally-canulated high-grain fed steers were randomly assigned to two treatment groups: control diet (n=3) and the same diet supplemented with P169 added at a rate of 1×10(11) cfu/head/d (n=4)...
August 31, 2017: Beneficial Microbes
https://www.readbyqxmd.com/read/28845459/moderate-exercise-has-limited-but-distinguishable-effects-on-the-mouse-microbiome
#13
Emily V Lamoureux, Scott A Grandy, Morgan G I Langille
The gut microbiome is known to have a complex yet vital relationship with host health. While both exercise and the gut microbiome have been shown to impact human health independently, the direct effects of moderate exercise on the intestinal microbiota remain unclear. In this study, we compared gut microbial diversity and changes in inflammatory markers associated with exercise over an 8-week period in mice that performed either voluntary exercise (VE) (n = 10) or moderate forced exercise (FE) (n = 11) and mice that did not perform any exercise (n = 21)...
July 2017: MSystems
https://www.readbyqxmd.com/read/28840077/engineering-crispr-cpf1-crrnas-and-mrnas-to-maximize-genome-editing-efficiency
#14
Bin Li, Weiyu Zhao, Xiao Luo, Xinfu Zhang, Chenglong Li, Chunxi Zeng, Yizhou Dong
Cpf1, a type-V CRISPR-Cas effector endonuclease, exhibits gene-editing activity in human cells through a single RNA-guided approach. Here, we report the design and assessment of an array of 42 types of engineered Acidaminococcus sp. Cpf1 (AsCpf1) CRISPR RNAs (crRNAs) and 5 types of AsCpf1 mRNAs, and show that the top-performing modified crRNA (cr3'5F, containing five 2'-fluoro ribose at the 3' termini) and AsCpf1 mRNA (full ψ-modification) improved gene-cutting efficiency by, respectively, 127% and 177%, with respect to unmodified crRNA and plasmid-encoding AsCpf1...
May 2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/28822545/effects-of-the-dose-and-viability-of-saccharomyces-cerevisiae-2-ruminal-fermentation-performance-of-lactating-dairy-cows-and-correlations-between-ruminal-bacteria-abundance-and-performance-measures
#15
Y Jiang, I M Ogunade, K G Arriola, M Qi, D Vyas, C R Staples, A T Adesogan
This study examined effects of the dose and viability of supplemented Saccharomyces cerevisiae yeast strain YE1496 on ruminal fermentation and performance of lactating dairy cows. A second objective was to examine correlations between ruminal bacteria abundance and performance measures. Four ruminally cannulated lactating cows (284 ± 18 days in milk) were assigned randomly to 1 of 4 treatment sequences in a 4 × 4 Latin square experimental design using four 21-d experimental periods. Cows were fed a nonacidotic total mixed ration comprising 22...
August 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28808547/patterns-of-seasonality-and-group-membership-characterize-the-gut-microbiota-in-a-longitudinal-study-of-wild-verreaux-s-sifakas-propithecus-verreauxi
#16
Andrea Springer, Claudia Fichtel, Gabriel A Al-Ghalith, Flávia Koch, Katherine R Amato, Jonathan B Clayton, Dan Knights, Peter M Kappeler
The intestinal microbiota plays a major role in host development, metabolism, and health. To date, few longitudinal studies have investigated the causes and consequences of microbiota variation in wildlife, although such studies provide a comparative context for interpreting the adaptive significance of findings from studies on humans or captive animals. Here, we investigate the impact of seasonality, diet, group membership, sex, age, and reproductive state on gut microbiota composition in a wild population of group-living, frugi-folivorous primates, Verreaux's sifakas (Propithecus verreauxi)...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28781234/structural-basis-for-the-canonical-and-non-canonical-pam-recognition-by-crispr-cpf1
#17
Takashi Yamano, Bernd Zetsche, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu, Osamu Nureki
The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM...
August 17, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28761933/insights-into-butyrate-production-in-a-controlled-fermentation-system-via-gene-predictions
#18
S Esquivel-Elizondo, Z E Ilhan, E I Garcia-Peña, R Krajmalnik-Brown
Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2)...
July 2017: MSystems
https://www.readbyqxmd.com/read/28757346/development-of-an-xbp1-agonist-hlj2-as-a-potential-therapeutic-agent-for-ulcerative-colitis
#19
HaiJing Zhang, ZhiHui Zhang, GuangMing Song, XiaoNan Tang, HuaChen Song, AnJun Deng, WenJie Wang, LianQiu Wu, Hailin Qin
There is a severe lack of effective treatments for ulcerative colitis (UC), a recurrent and intractable inflammatory bowel disease. The identification of valid targets and new drugs is an urgent need. In this study, we identified the XBP-1 agonist HLJ2 as a promising treatment candidate. In an in vivo mouse model of DSS-induced colitis, HLJ2 decreased weight loss, colon contracture, disease activity index (DAI), colon mucosa damage index (CMDI) and histopathological index (HI). HLJ2 also decreased myeloperoxidase (MPO) activity and reduced production of the inflammatory cytokines TNF-α, IL-1β, and IL-6...
July 28, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28741995/merdimonas-faecis-gen-nov-sp-nov-isolated-from-human-faeces
#20
Boram Seo, Ju Eun Yoo, Yung Mi Lee, GwangPyo Ko
A strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31T, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4-2.1×0.5-0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31T formed a distinct phylogenetic lineage that reflects a new genus within Clostridium cluster XIVa in the family Lachnospiraceae, with highest similarity to Eubacterium contortum DSM 3982T (94...
July 26, 2017: International Journal of Systematic and Evolutionary Microbiology
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