keyword
MENU ▼
Read by QxMD icon Read
search

Rob Knight

keyword
https://www.readbyqxmd.com/read/28735426/diet-versus-phylogeny-a-comparison-of-gut-microbiota-in-captive-colobine-monkey-species
#1
Vanessa L Hale, Chia L Tan, Kefeng Niu, Yeqin Yang, Rob Knight, Qikun Zhang, Duoying Cui, Katherine R Amato
Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza)...
July 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28700459/the-microbiome-in-posttraumatic-stress-disorder-and-trauma-exposed-controls-an-exploratory-study
#2
Sian M J Hemmings, Stefanie Malan-Muller, Leigh L van den Heuvel, Brittany A Demmitt, Maggie A Stanislawski, David G Smith, Adam D Bohr, Christopher E Stamper, Embriette R Hyde, James T Morton, Clarisse A Marotz, Philip H Siebler, Maarten Braspenning, Wim Van Criekinge, Andrew J Hoisington, Lisa A Brenner, Teodor T Postolache, Matthew B McQueen, Kenneth S Krauter, Rob Knight, Soraya Seedat, Christopher A Lowry
OBJECTIVE: Inadequate immunoregulation and elevated inflammation may be risk factors for posttraumatic stress disorder (PTSD), and microbial inputs are important determinants of immunoregulation; however, the association between the gut microbiota and PTSD is unknown. This study investigated the gut microbiome in a South African sample of PTSD-affected individuals and trauma-exposed (TE) controls, to identify potential differences in microbial diversity or microbial community structure...
July 11, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28680968/bacterial-community-composition-and-dynamics-spanning-five-years-in-freshwater-bog-lakes
#3
Alexandra M Linz, Benjamin C Crary, Ashley Shade, Sarah Owens, Jack A Gilbert, Rob Knight, Katherine D McMahon
Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity...
May 2017: MSphere
https://www.readbyqxmd.com/read/28678519/intermittent-hypoxia-and-hypercapnia-accelerate-atherosclerosis-partially-via-trimethylamine-oxide
#4
Jin Xue, Dan Zhou, Orit Poulsen, Toshihiro Imamura, Yu-Hsin Hsiao, Travis H Smith, Atul Malhotra, Pieter Dorrestein, Rob Knight, Gabriel G Haddad
RATIONALE: Obstructive sleep apnea (OSA) is a common disorder characterized by intermittent hypoxia and hypercapnia (IHC) during sleep. OSA has been shown as a risk factor for atherosclerosis but the relation of IHC to induction or progression of atherosclerosis is not well understood. To dissect the mechanisms involved, we compared atherosclerotic formation between two mouse models, i.e., the apolipoprotein E (ApoE) and the low density lipoprotein receptor (Ldlr) deficient mice, with or without IHC exposure...
July 5, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28658209/fine-mapping-inflammatory-bowel-disease-loci-to-single-variant-resolution
#5
Hailiang Huang, Ming Fang, Luke Jostins, Maša Umićević Mirkov, Gabrielle Boucher, Carl A Anderson, Vibeke Andersen, Isabelle Cleynen, Adrian Cortes, François Crins, Mauro D'Amato, Valérie Deffontaine, Julia Dmitrieva, Elisa Docampo, Mahmoud Elansary, Kyle Kai-How Farh, Andre Franke, Ann-Stephan Gori, Philippe Goyette, Jonas Halfvarson, Talin Haritunians, Jo Knight, Ian C Lawrance, Charlie W Lees, Edouard Louis, Rob Mariman, Theo Meuwissen, Myriam Mni, Yukihide Momozawa, Miles Parkes, Sarah L Spain, Emilie Théâtre, Gosia Trynka, Jack Satsangi, Suzanne van Sommeren, Severine Vermeire, Ramnik J Xavier, Rinse K Weersma, Richard H Duerr, Christopher G Mathew, John D Rioux, Dermot P B McGovern, Judy H Cho, Michel Georges, Mark J Daly, Jeffrey C Barrett
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty...
July 13, 2017: Nature
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#6
Alexey V Melnik, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan K Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays, and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
July 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28625159/dna-extraction-for-streamlined-metagenomics-of-diverse-environmental-samples
#7
Clarisse Marotz, Amnon Amir, Greg Humphrey, James Gaffney, Grant Gogul, Rob Knight
A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28607095/reply-to-wang-and-chen-an-ancient-origin-of-magnetotactic-bacteria
#8
Wei Lin, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
No abstract text is available yet for this article.
June 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28593197/significant-impacts-of-increasing-aridity-on-the-arid-soil-microbiome
#9
Julia W Neilson, Katy Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L Josephson, Rob Knight, Jack A Gilbert, Jay Quade, J Gregory Caporaso, Raina M Maier
Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile...
May 2017: MSystems
https://www.readbyqxmd.com/read/28576788/pigs-unlike-mice-have-two-distinct-colonic-stem-cell-populations-similar-to-humans-that-respond-to-high-calorie-diet-prior-to-insulin-resistance
#10
Venkata Charepalli, Lavanya Reddivari, Sridhar Radhakrishnan, Elisabeth Eriksson, Xia Xiao, Sung Woo Kim, Frank Shen, Matam Vijay-Kumar, Qunhua Li, Vadiraja B Bhat, Rob Knight, Jairam K P Vanamala
Basal colonic crypt stem cells are long lived and play a role in colon homeostasis. Previous evidence has shown that high-calorie diet (HCD) enhances colonic stem cell numbers and expansion of the proliferative zone, an important biomarker for colon cancer. However, it is not clear how HCD drives dysregulation of colon stem cell/colonocyte proliferative kinetics. We used a human-relevant pig model and developed an immunofluorescence technique to detect and quantify colonic stem cells. Pigs (n = 8/group) were provided either standard diet (SD; 5% fat) or HCD (23% fat) for 13 weeks...
June 2, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28539477/bacterial-colonization-and-succession-in-a-newly-opened-hospital
#11
Simon Lax, Naseer Sangwan, Daniel Smith, Peter Larsen, Kim M Handley, Miles Richardson, Kristina Guyton, Monika Krezalek, Benjamin D Shogan, Jennifer Defazio, Irma Flemming, Baddr Shakhsheer, Stephen Weber, Emily Landon, Sylvia Garcia-Houchins, Jeffrey Siegel, John Alverdy, Rob Knight, Brent Stephens, Jack A Gilbert
The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room...
May 24, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28508897/whole-genome-analysis-of-a-schistosomiasis-transmitting-freshwater-snail
#12
Coen M Adema, LaDeana W Hillier, Catherine S Jones, Eric S Loker, Matty Knight, Patrick Minx, Guilherme Oliveira, Nithya Raghavan, Andrew Shedlock, Laurence Rodrigues do Amaral, Halime D Arican-Goktas, Juliana G Assis, Elio Hideo Baba, Olga L Baron, Christopher J Bayne, Utibe Bickham-Wright, Kyle K Biggar, Michael Blouin, Bryony C Bonning, Chris Botka, Joanna M Bridger, Katherine M Buckley, Sarah K Buddenborg, Roberta Lima Caldeira, Julia Carleton, Omar S Carvalho, Maria G Castillo, Iain W Chalmers, Mikkel Christensens, Sandra Clifton, Celine Cosseau, Christine Coustau, Richard M Cripps, Yesid Cuesta-Astroz, Scott F Cummins, Leon di Stephano, Nathalie Dinguirard, David Duval, Scott Emrich, Cédric Feschotte, Rene Feyereisen, Peter FitzGerald, Catrina Fronick, Lucinda Fulton, Richard Galinier, Sandra G Gava, Michael Geusz, Kathrin K Geyer, Gloria I Giraldo-Calderón, Matheus de Souza Gomes, Michelle A Gordy, Benjamin Gourbal, Christoph Grunau, Patrick C Hanington, Karl F Hoffmann, Daniel Hughes, Judith Humphries, Daniel J Jackson, Liana K Jannotti-Passos, Wander de Jesus Jeremias, Susan Jobling, Bishoy Kamel, Aurélie Kapusta, Satwant Kaur, Joris M Koene, Andrea B Kohn, Dan Lawson, Scott P Lawton, Di Liang, Yanin Limpanont, Sijun Liu, Anne E Lockyer, TyAnna L Lovato, Fernanda Ludolf, Vince Magrini, Donald P McManus, Monica Medina, Milind Misra, Guillaume Mitta, Gerald M Mkoji, Michael J Montague, Cesar Montelongo, Leonid L Moroz, Monica C Munoz-Torres, Umar Niazi, Leslie R Noble, Francislon S Oliveira, Fabiano S Pais, Anthony T Papenfuss, Rob Peace, Janeth J Pena, Emmanuel A Pila, Titouan Quelais, Brian J Raney, Jonathan P Rast, David Rollinson, Izinara C Rosse, Bronwyn Rotgans, Edwin J Routledge, Kathryn M Ryan, Larissa L S Scholte, Kenneth B Storey, Martin Swain, Jacob A Tennessen, Chad Tomlinson, Damian L Trujillo, Emanuela V Volpi, Anthony J Walker, Tianfang Wang, Ittiprasert Wannaporn, Wesley C Warren, Xiao-Jun Wu, Timothy P Yoshino, Mohammed Yusuf, Si-Ming Zhang, Min Zhao, Richard K Wilson
Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B...
May 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28506317/changes-in-microbial-ecology-after-fecal-microbiota-transplantation-for-recurrent-c-difficile-infection-affected-by-underlying-inflammatory-bowel-disease
#13
Sahil Khanna, Yoshiki Vazquez-Baeza, Antonio González, Sophie Weiss, Bradley Schmidt, David A Muñiz-Pedrogo, John F Rainey, Patricia Kammer, Heidi Nelson, Michael Sadowsky, Alexander Khoruts, Stefan L Farrugia, Rob Knight, Darrell S Pardi, Purna C Kashyap
BACKGROUND: Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28494234/an-elegan-t-screen-for-drug-microbe-interactions
#14
Alison Vrbanac, Justine W Debelius, Lingjing Jiang, James T Morton, Pieter Dorrestein, Rob Knight
Microbes affect drug responses, but mechanisms remain elusive. Two papers in Cell exploit C. elegans to infer anticancer drug mechanisms. Through high-throughput screens of drug-microbe-host interactions, García-González et al. (2017) and Scott et al. (2017) determine that bacterial metabolism underpins fluoropyrimidine cytotoxicity, providing a paradigm for unraveling bacterial mechanisms in drug metabolism.
May 10, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28492366/digitizing-mass-spectrometry-data-to-explore-the-chemical-diversity-and-distribution-of-marine-cyanobacteria-and-algae
#15
Tal Luzzatto-Knaan, Neha Garg, Mingxun Wang, Evgenia Glukhov, Yao Peng, Gail Ackermann, Amnon Amir, Brendan M Duggan, Sergey Ryazanov, Lena Gerwick, Rob Knight, Theodore Alexandrov, Nuno Bandeira, William H Gerwick, Pieter C Dorrestein
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes...
May 11, 2017: ELife
https://www.readbyqxmd.com/read/28428981/correction-for-gonzalez-et-al-migraines-are-correlated-with-higher-levels-of-nitrate-nitrite-and-nitric-oxide-reducing-oral-microbes-in-the-american-gut-project-cohort
#16
Antonio Gonzalez, Embriette Hyde, Naseer Sangwan, Jack A Gilbert, Erik Viirre, Rob Knight
[This corrects the article DOI: 10.1128/mSystems.00105-16.].
March 2017: MSystems
https://www.readbyqxmd.com/read/28421042/mosquito-microbiome-dynamics-a-background-for-prevalence-and-seasonality-of-west-nile-virus
#17
Eva Novakova, Douglas C Woodhams, Sonia M Rodríguez-Ruano, Robert M Brucker, Jonathan W Leff, Amin Maharaj, Amnon Amir, Rob Knight, James Scott
Symbiotic microbial communities augment host phenotype, including defense against pathogen carriage and infection. We sampled the microbial communities in 11 adult mosquito host species from six regions in southern Ontario, Canada over 3 years. Of the factors examined, we found that mosquito species was the largest driver of the microbiota, with remarkable phylosymbiosis between host and microbiota. Seasonal shifts of the microbiome were consistently repeated over the 3-year period, while region had little impact...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28405197/mass-spectrometry-based-molecular-3d-cartography-of-plant-metabolites
#18
Dimitrios J Floros, Daniel Petras, Clifford A Kapono, Alexey V Melnik, Tie-Jun Ling, Rob Knight, Pieter C Dorrestein
Plants play an essential part in global carbon fixing through photosynthesis and are the primary food and energy source for humans. Understanding them thoroughly is therefore of highest interest for humanity. Advances in DNA and RNA sequencing and in protein and metabolite analysis allow the systematic description of plant composition at the molecular level. With imaging mass spectrometry, we can now add a spatial level, typically in the micrometer-to-centimeter range, to their compositions, essential for a detailed molecular understanding...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28375652/the-microbiome-and-human-biology
#19
Rob Knight, Chris Callewaert, Clarisse Marotz, Embriette R Hyde, Justine W Debelius, Daniel McDonald, Mitchell L Sogin
Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries...
March 20, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28366290/microbiome-tools-for-forensic-science
#20
REVIEW
Jessica L Metcalf, Zhenjiang Z Xu, Amina Bouslimani, Pieter Dorrestein, David O Carter, Rob Knight
Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system...
March 30, 2017: Trends in Biotechnology
keyword
keyword
47118
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"