keyword
MENU ▼
Read by QxMD icon Read
search

Rob Knight

keyword
https://www.readbyqxmd.com/read/29773078/optimizing-taxonomic-classification-of-marker-gene-amplicon-sequences-with-qiime-2-s-q2-feature-classifier-plugin
#1
Nicholas A Bokulich, Benjamin D Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A Huttley, J Gregory Caporaso
BACKGROUND: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. RESULTS: We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data...
May 17, 2018: Microbiome
https://www.readbyqxmd.com/read/29748586/the-gut-liver-axis-and-the-intersection-with-the-microbiome
#2
REVIEW
Anupriya Tripathi, Justine Debelius, David A Brenner, Michael Karin, Rohit Loomba, Bernd Schnabl, Rob Knight
In the past decade, an exciting realization has been that diverse liver diseases - ranging from nonalcoholic steatohepatitis, alcoholic steatohepatitis and cirrhosis to hepatocellular carcinoma - fall along a spectrum. Work on the biology of the gut-liver axis has assisted in understanding the basic biology of both alcoholic fatty liver disease and nonalcoholic fatty liver disease (NAFLD). Of immense importance is the advancement in understanding the role of the microbiome, driven by high-throughput DNA sequencing and improved computational techniques that enable the complexity of the microbiome to be interrogated, together with improved experimental designs...
May 10, 2018: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29719869/phylogenetic-placement-of-exact-amplicon-sequences-improves-associations-with-clinical-information
#3
Stefan Janssen, Daniel McDonald, Antonio Gonzalez, Jose A Navas-Molina, Lingjing Jiang, Zhenjiang Zech Xu, Kevin Winker, Deborah M Kado, Eric Orwoll, Mark Manary, Siavash Mirarab, Rob Knight
Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith's PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny...
May 2018: MSystems
https://www.readbyqxmd.com/read/29700420/exposure-to-toxic-metals-triggers-unique-responses-from-the-rat-gut-microbiota
#4
Joshua B Richardson, Blair C R Dancy, Cassandra L Horton, Young S Lee, Michael S Madejczyk, Zhenjiang Zech Xu, Gail Ackermann, Gregory Humphrey, Gustavo Palacios, Rob Knight, John A Lewis
Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host's cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals...
April 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29668882/hopanoid-producing-bacteria-in-the-red-sea-include-the-major-marine-nitrite-oxidizers
#5
Jenan J Kharbush, Luke R Thompson, Mohamed Fauzi Haroon, Rob Knight, Lihini I Aluwihare
Hopanoids, including the extended side chain-containing bacteriohopanepolyols (BHPs), are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones (OMZs) suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle...
April 12, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29657969/earth-microbiome-project-and-global-systems-biology
#6
EDITORIAL
Jack A Gilbert, Janet K Jansson, Rob Knight
No abstract text is available yet for this article.
May 2018: MSystems
https://www.readbyqxmd.com/read/29624426/integrated-approaches-to-analyze-big-data-in-the-perinatal-neonatal-space
#7
Rob Knight
No abstract text is available yet for this article.
April 2018: Breastfeeding Medicine: the Official Journal of the Academy of Breastfeeding Medicine
https://www.readbyqxmd.com/read/29577086/katharoseq-enables-high-throughput-microbiome-analysis-from-low-biomass-samples
#8
Jeremiah J Minich, Qiyun Zhu, Stefan Janssen, Ryan Hendrickson, Amnon Amir, Russ Vetter, John Hyde, Megan M Doty, Kristina Stillwell, James Benardini, Jae H Kim, Eric E Allen, Kasthuri Venkateswaran, Rob Knight
Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90...
May 2018: MSystems
https://www.readbyqxmd.com/read/29529084/experimental-chagas-disease-induced-perturbations-of-the-fecal-microbiome-and-metabolome
#9
Laura-Isobel McCall, Anupriya Tripathi, Fernando Vargas, Rob Knight, Pieter C Dorrestein, Jair L Siqueira-Neto
Trypanosoma cruzi parasites are the causative agents of Chagas disease. These parasites infect cardiac and gastrointestinal tissues, leading to local inflammation and tissue damage. Digestive Chagas disease is associated with perturbations in food absorption, intestinal traffic and defecation. However, the impact of T. cruzi infection on the gut microbiota and metabolome have yet to be characterized. In this study, we applied mass spectrometry-based metabolomics and 16S rRNA sequencing to profile infection-associated alterations in fecal bacterial composition and fecal metabolome through the acute-stage and into the chronic stage of infection, in a murine model of Chagas disease...
March 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29487294/creating-a-3d-microbial-and-chemical-snapshot-of-a-human-habitat
#10
Clifford A Kapono, James T Morton, Amina Bouslimani, Alexey V Melnik, Kayla Orlinsky, Tal Luzzatto Knaan, Neha Garg, Yoshiki Vázquez-Baeza, Ivan Protsyuk, Stefan Janssen, Qiyun Zhu, Theodore Alexandrov, Larry Smarr, Rob Knight, Pieter C Dorrestein
One of the goals of forensic science is to identify individuals and their lifestyle by analyzing the trace signatures left behind in built environments. Here, microbiome and metabolomic methods were used to see how its occupants used an office and to also gain insights into the lifestyle characteristics such as diet, medications, and personal care products of the occupants. 3D molecular cartography, a molecular visualization technology, was used in combination with mass spectrometry and microbial inventories to highlight human-environmental interactions...
February 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29482639/improving-saliva-shotgun-metagenomics-by-chemical-host-dna-depletion
#11
Clarisse A Marotz, Jon G Sanders, Cristal Zuniga, Livia S Zaramela, Rob Knight, Karsten Zengler
BACKGROUND: Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits...
February 27, 2018: Microbiome
https://www.readbyqxmd.com/read/29462950/microbiome-data-accurately-predicts-the-postmortem-interval-using-random-forest-regression-models
#12
Aeriel Belk, Zhenjiang Zech Xu, David O Carter, Aaron Lynne, Sibyl Bucheli, Rob Knight, Jessica L Metcalf
Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is uncertain. The postmortem interval can lead to the identification of the deceased and the validation of witness statements and suspect alibis. Recent research has demonstrated that microbes provide an accurate clock that starts at death and relies on ecological change in the microbial communities that normally inhabit a body and its surrounding environment. Here, we explore how to build the most robust Random Forest regression models for prediction of PMI by testing models built on different sample types (gravesoil, skin of the torso, skin of the head), gene markers (16S ribosomal RNA (rRNA), 18S rRNA, internal transcribed spacer regions (ITS)), and taxonomic levels (sequence variants, species, genus, etc...
February 16, 2018: Genes
https://www.readbyqxmd.com/read/29440750/publisher-correction-enterotypes-in-the-landscape-of-gut-microbial-community-composition
#13
Paul I Costea, Falk Hildebrand, Manimozhiyan Arumugam, Fredrik Bäckhed, Martin J Blaser, Frederic D Bushman, Willem M de Vos, S Dusko Ehrlich, Claire M Fraser, Masahira Hattori, Curtis Huttenhower, Ian B Jeffery, Dan Knights, James D Lewis, Ruth E Ley, Howard Ochman, Paul W O'Toole, Christopher Quince, David A Relman, Fergus Shanahan, Shinichi Sunagawa, Jun Wang, George M Weinstock, Gary D Wu, Georg Zeller, Liping Zhao, Jeroen Raes, Rob Knight, Peer Bork
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
March 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29440415/coprolites-reveal-ecological-interactions-lost-with-the-extinction-of-new-zealand-birds
#14
Alexander P Boast, Laura S Weyrich, Jamie R Wood, Jessica L Metcalf, Rob Knight, Alan Cooper
Over the past 50,000 y, biotic extinctions and declines have left a legacy of vacant niches and broken ecological interactions across global terrestrial ecosystems. Reconstructing the natural, unmodified ecosystems that preceded these events relies on high-resolution analyses of paleoecological deposits. Coprolites are a source of uniquely detailed information about trophic interactions and the behaviors, gut parasite communities, and microbiotas of prehistoric animal species. Such insights are critical for understanding the legacy effects of extinctions on ecosystems, and can help guide contemporary conservation and ecosystem restoration efforts...
February 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29438507/bacterial-density-rather-than-diversity-correlates-with-hatching-success-across-different-avian-species
#15
Juan Manuel Peralta-Sánchez, Antonio Manuel Martín-Platero, Laura Wegener-Parfrey, Manuel Martínez-Bueno, Sonia Rodríguez-Ruano, José Antonio Navas-Molina, Yoshiki Vázquez-Baeza, David Martín-Gálvez, Manuel Martín-Vivaldi, Juan Diego Ibáñez-Álamo, Rob Knight, Juan José Soler
Bacterial communities within avian nests are considered an important determinant of egg viability, potentially selecting for traits that confer embryos with protection against trans-shell infection. A high bacterial density on the eggshell increases hatching failure, whether this effect could be due to changes in bacterial community or just a general increase in bacterial density. We explored this idea using intra- and interspecific comparisons of the relationship between hatching success and eggshell bacteria characterized by culture and molecular techniques (fingerprinting and high-throughput sequencing)...
March 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29435495/correction-for-morton-et-al-uncovering-the-horseshoe-effect-in-microbial-analyses
#16
James T Morton, Liam Toran, Anna Edlund, Jessica L Metcalf, Christian Lauber, Rob Knight
[This corrects the article DOI: 10.1128/mSystems.00166-16.].
January 2018: MSystems
https://www.readbyqxmd.com/read/29429588/expanding-our-understanding-of-the-role-of-the-microbiome-in-health-and-disease
#17
EDITORIAL
Rob Knight
No abstract text is available yet for this article.
November 2017: Archives of Medical Research
https://www.readbyqxmd.com/read/29407287/overview-and-systematic-review-of-studies-of-microbiome-in-schizophrenia-and-bipolar-disorder
#18
REVIEW
Tanya T Nguyen, Tomasz Kosciolek, Lisa T Eyler, Rob Knight, Dilip V Jeste
Schizophrenia and bipolar disorder are among the leading causes of disability, morbidity, and mortality worldwide. In addition to being serious mental illnesses, these disorders are associated with considerable systemic physiological dysfunction, including chronic inflammation and elevated oxidative stress. The advent of sophisticated sequencing techniques has led to a growing interest in the potential role of gut microbiota in human health and disease. Advances in this area have transformed our understanding of a number of medical conditions and have generated a new perspective suggesting that gut microbiota might be involved in the development and maintenance of brain/mental health...
April 2018: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/29406516/corrigendum-minimum-information-about-a-single-amplified-genome-misag-and-a-metagenome-assembled-genome-mimag-of-bacteria-and-archaea
#19
Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, Adam R Rivers, Emiley A Eloe-Fadrosh, Susannah G Tringe, Natalia N Ivanova, Alex Copeland, Alicia Clum, Eric D Becraft, Rex R Malmstrom, Bruce Birren, Mircea Podar, Peer Bork, George M Weinstock, George M Garrity, Jeremy A Dodsworth, Shibu Yooseph, Granger Sutton, Frank O Glöckner, Jack A Gilbert, William C Nelson, Steven J Hallam, Sean P Jungbluth, Thijs J G Ettema, Scott Tighe, Konstantinos T Konstantinidis, Wen-Tso Liu, Brett J Baker, Thomas Rattei, Jonathan A Eisen, Brian Hedlund, Katherine D McMahon, Noah Fierer, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi, Gene W Tyson, Christian Rinke, Alla Lapidus, Folker Meyer, Pelin Yilmaz, Donovan H Parks, A Murat Eren, Lynn Schriml, Jillian F Banfield, Philip Hugenholtz, Tanja Woyke
No abstract text is available yet for this article.
February 6, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29404425/gut-microbiota-offers-universal-biomarkers-across-ethnicity-in-inflammatory-bowel-disease-diagnosis-and-infliximab-response-prediction
#20
Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, Amnon Amir, Antonio González, Anupriya Tripathi, Minhu Chen, Gary D Wu, Rob Knight, Hongwei Zhou, Ye Chen
Gut microbiota dysbiosis contributes to the onset and perpetuation of inflammatory bowel disease (IBD). Given that gut microbiotas vary across geography and ethnicity, it remains obscure whether any universal microbial signatures for IBD diagnosis and prognosis evaluation exist irrespective of populations. Here we profiled the fecal microbiota of a series of Chinese IBD patients and combined them with two Western IBD cohorts, PRISM and RISK, for meta-analyses. We found that the gut microbial alteration patterns in IBD are similar among Chinese and Westerners...
January 2018: MSystems
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"