Read by QxMD icon Read

Rob Knight

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 12, 2018: PLoS Neglected Tropical Diseases
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
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
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
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.
February 13, 2018: Nature Microbiology
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
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)...
February 9, 2018: FEMS Microbiology Ecology
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
Rob Knight
No abstract text is available yet for this article.
February 8, 2018: Archives of Medical Research
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...
January 31, 2018: Journal of Psychiatric Research
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
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
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
Emily R Davenport, Jon G Sanders, Se Jin Song, Katherine R Amato, Andrew G Clark, Rob Knight
The trillions of microbes living in the gut-the gut microbiota-play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity's near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations...
December 27, 2017: BMC Biology
Qi Guo, Stephen Burgess, Constance Turman, Manjeet K Bolla, Qin Wang, Michael Lush, Jean Abraham, Kristiina Aittomäki, Irene L Andrulis, Carmel Apicella, Volker Arndt, Myrto Barrdahl, Javier Benitez, Christine D Berg, Carl Blomqvist, Stig E Bojesen, Bernardo Bonanni, Judith S Brand, Hermann Brenner, Annegien Broeks, Barbara Burwinkel, Carlos Caldas, Daniele Campa, Federico Canzian, Jenny Chang-Claude, Stephen J Chanock, Suet-Feung Chin, Fergus J Couch, Angela Cox, Simon S Cross, Cezary Cybulski, Kamila Czene, Hatef Darabi, Peter Devilee, W Ryan Diver, Alison M Dunning, Helena M Earl, Diana M Eccles, Arif B Ekici, Mikael Eriksson, D Gareth Evans, Peter A Fasching, Jonine Figueroa, Dieter Flesch-Janys, Henrik Flyger, Susan M Gapstur, Mia M Gaudet, Graham G Giles, Gord Glendon, Mervi Grip, Jacek Gronwald, Lothar Haeberle, Christopher A Haiman, Per Hall, Ute Hamann, Susan Hankinson, Jaana M Hartikainen, Alexander Hein, Louise Hiller, Frans B Hogervorst, Bernd Holleczek, Maartje J Hooning, Robert N Hoover, Keith Humphreys, David J Hunter, Anika Hüsing, Anna Jakubowska, Arja Jukkola-Vuorinen, Rudolf Kaaks, Maria Kabisch, Vesa Kataja, Julia A Knight, Linetta B Koppert, Veli-Matti Kosma, Vessela N Kristensen, Diether Lambrechts, Loic Le Marchand, Jingmei Li, Annika Lindblom, Sara Lindström, Jolanta Lissowska, Jan Lubinski, Mitchell J Machiela, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Federik Marme, John W M Martens, Catriona McLean, Primitiva Menéndez, Roger L Milne, Anna Marie Mulligan, Taru A Muranen, Heli Nevanlinna, Patrick Neven, Sune F Nielsen, Børge G Nordestgaard, Janet E Olson, Jose I A Perez, Paolo Peterlongo, Kelly-Anne Phillips, Christopher J Poole, Katri Pylkäs, Paolo Radice, Nazneen Rahman, Thomas Rüdiger, Anja Rudolph, Elinor J Sawyer, Fredrick Schumacher, Petra Seibold, Caroline Seynaeve, Mitul Shah, Ann Smeets, Melissa C Southey, Rob A E M Tollenaar, Ian Tomlinson, Helen Tsimiklis, Hans-Ulrich Ulmer, Celine Vachon, Ans M W van den Ouweland, Laura J Van't Veer, Hans Wildiers, Walter Willett, Robert Winqvist, M Pilar Zamora, Georgia Chenevix-Trench, Thilo Dörk, Douglas F Easton, Montserrat García-Closas, Peter Kraft, John L Hopper, Wei Zheng, Marjanka K Schmidt, Paul D P Pharoah
Background: There is increasing evidence that elevated body mass index (BMI) is associated with reduced survival for women with breast cancer. However, the underlying reasons remain unclear. We conducted a Mendelian randomization analysis to investigate a possible causal role of BMI in survival from breast cancer. Methods: We used individual-level data from six large breast cancer case-cohorts including a total of 36 210 individuals (2475 events) of European ancestry...
December 1, 2017: International Journal of Epidemiology
Venkatakrishna R Jala, Paramahamsa Maturu, Sobha R Bodduluri, Elangovan Krishnan, Steven Mathis, Krishnaprasad Subbarao, Min Wang, Alfred B Jenson, Mary L Proctor, Eric C Rouchka, Rob Knight, Bodduluri Haribabu
Inflammation and infection are key promoters of colon cancer but the molecular interplay between these events is largely unknown. Mice deficient in leukotriene B4 receptor1 (BLT1) are protected in inflammatory disease models of arthritis, asthma and atherosclerosis. In this study, we show that BLT1-/- mice when bred onto a spontaneous tumor (ApcMin/+ ) model displayed an increase in the rate of intestinal tumor development and mortality. A paradoxical increase in inflammation in the tumors from the BLT1- / - ApcMin/+ mice is coincidental with defective host response to infection...
2017: Oncoimmunology
Aura Raulo, Lasse Ruokolainen, Avery Lane, Katherine Amato, Rob Knight, Steven Leigh, Rebecca Stumpf, Bryan White, Karen E Nelson, Andrea L Baden, Stacey R Tecot
Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time...
March 2018: Journal of Animal Ecology
Lingjing Jiang, Amnon Amir, James T Morton, Ruth Heller, Ery Arias-Castro, Rob Knight
Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold...
November 2017: MSystems
Shabnam Shalapour, Xue-Jia Lin, Ingmar N Bastian, John Brain, Alastair D Burt, Alexander A Aksenov, Alison F Vrbanac, Weihua Li, Andres Perkins, Takaji Matsutani, Zhenyu Zhong, Debanjan Dhar, Jose A Navas-Molina, Jun Xu, Rohit Loomba, Michael Downes, Ruth T Yu, Ronald M Evans, Pieter C Dorrestein, Rob Knight, Christopher Benner, Quentin M Anstee, Michael Karin
This corrects the article DOI: 10.1038/nature24302.
December 21, 2017: Nature
Andrew Jahoda, Richard Hastings, Chris Hatton, Sally-Ann Cooper, Dave Dagnan, Ruiqi Zhang, Alex McConnachie, Nicola McMeekin, Kim Appleton, Rob Jones, Katie Scott, Lauren Fulton, Rosie Knight, Dawn Knowles, Chris Williams, Andrew Briggs, Ken MacMahon, Helen Lynn, Ian Smith, Gail Thomas, Craig Melville
BACKGROUND: Psychological therapies are first-line interventions for depression, but existing provision is not accessible for many adults with intellectual disabilities. We investigated the clinical and cost-effectiveness of a behavioural activation intervention (BeatIt) for people with intellectual disabilities and depression. BeatIt was compared with a guided self-help intervention (StepUp). METHODS: We did a multicentre, single-blind, randomised, controlled trial with follow-up at 4 months and 12 months after randomisation...
December 2017: Lancet Psychiatry
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"