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https://www.readbyqxmd.com/read/28081445/bringing-the-dynamic-microbiome-to-life-with-animations
#1
Yoshiki Vázquez-Baeza, Antonio Gonzalez, Larry Smarr, Daniel McDonald, James T Morton, Jose A Navas-Molina, Rob Knight
Our bodies and natural environment contain complex microbial communities, colloquially termed microbiomes. We previously created a web-based application, EMPeror, for visualizing ordinations derived from comparisons of these microbiome communities. We have now improved EMPeror to create interactive animations that connect successive samples to highlight patterns over time.
January 11, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28070282/the-database-of-the-predicts-projecting-responses-of-ecological-diversity-in-changing-terrestrial-systems-project
#2
Lawrence N Hudson, Tim Newbold, Sara Contu, Samantha L L Hill, Igor Lysenko, Adriana De Palma, Helen R P Phillips, Tamera I Alhusseini, Felicity E Bedford, Dominic J Bennett, Hollie Booth, Victoria J Burton, Charlotte W T Chng, Argyrios Choimes, David L P Correia, Julie Day, Susy Echeverría-Londoño, Susan R Emerson, Di Gao, Morgan Garon, Michelle L K Harrison, Daniel J Ingram, Martin Jung, Victoria Kemp, Lucinda Kirkpatrick, Callum D Martin, Yuan Pan, Gwilym D Pask-Hale, Edwin L Pynegar, Alexandra N Robinson, Katia Sanchez-Ortiz, Rebecca A Senior, Benno I Simmons, Hannah J White, Hanbin Zhang, Job Aben, Stefan Abrahamczyk, Gilbert B Adum, Virginia Aguilar-Barquero, Marcelo A Aizen, Belén Albertos, E L Alcala, Maria Del Mar Alguacil, Audrey Alignier, Marc Ancrenaz, Alan N Andersen, Enrique Arbeláez-Cortés, Inge Armbrecht, Víctor Arroyo-Rodríguez, Tom Aumann, Jan C Axmacher, Badrul Azhar, Adrián B Azpiroz, Lander Baeten, Adama Bakayoko, András Báldi, John E Banks, Sharad K Baral, Jos Barlow, Barbara I P Barratt, Lurdes Barrico, Paola Bartolommei, Diane M Barton, Yves Basset, Péter Batáry, Adam J Bates, Bruno Baur, Erin M Bayne, Pedro Beja, Suzan Benedick, Åke Berg, Henry Bernard, Nicholas J Berry, Dinesh Bhatt, Jake E Bicknell, Jochen H Bihn, Robin J Blake, Kadiri S Bobo, Roberto Bóçon, Teun Boekhout, Katrin Böhning-Gaese, Kevin J Bonham, Paulo A V Borges, Sérgio H Borges, Céline Boutin, Jérémy Bouyer, Cibele Bragagnolo, Jodi S Brandt, Francis Q Brearley, Isabel Brito, Vicenç Bros, Jörg Brunet, Grzegorz Buczkowski, Christopher M Buddle, Rob Bugter, Erika Buscardo, Jörn Buse, Jimmy Cabra-García, Nilton C Cáceres, Nicolette L Cagle, María Calviño-Cancela, Sydney A Cameron, Eliana M Cancello, Rut Caparrós, Pedro Cardoso, Dan Carpenter, Tiago F Carrijo, Anelena L Carvalho, Camila R Cassano, Helena Castro, Alejandro A Castro-Luna, Cerda B Rolando, Alexis Cerezo, Kim Alan Chapman, Matthieu Chauvat, Morten Christensen, Francis M Clarke, Daniel F R Cleary, Giorgio Colombo, Stuart P Connop, Michael D Craig, Leopoldo Cruz-López, Saul A Cunningham, Biagio D'Aniello, Neil D'Cruze, Pedro Giovâni da Silva, Martin Dallimer, Emmanuel Danquah, Ben Darvill, Jens Dauber, Adrian L V Davis, Jeff Dawson, Claudio de Sassi, Benoit de Thoisy, Olivier Deheuvels, Alain Dejean, Jean-Louis Devineau, Tim Diekötter, Jignasu V Dolia, Erwin Domínguez, Yamileth Dominguez-Haydar, Silvia Dorn, Isabel Draper, Niels Dreber, Bertrand Dumont, Simon G Dures, Mats Dynesius, Lars Edenius, Paul Eggleton, Felix Eigenbrod, Zoltán Elek, Martin H Entling, Karen J Esler, Ricardo F de Lima, Aisyah Faruk, Nina Farwig, Tom M Fayle, Antonio Felicioli, Annika M Felton, Roderick J Fensham, Ignacio C Fernandez, Catarina C Ferreira, Gentile F Ficetola, Cristina Fiera, Bruno K C Filgueiras, Hüseyin K Fırıncıoğlu, David Flaspohler, Andreas Floren, Steven J Fonte, Anne Fournier, Robert E Fowler, Markus Franzén, Lauchlan H Fraser, Gabriella M Fredriksson, Geraldo B Freire, Tiago L M Frizzo, Daisuke Fukuda, Dario Furlani, René Gaigher, Jörg U Ganzhorn, Karla P García, Juan C Garcia-R, Jenni G Garden, Ricardo Garilleti, Bao-Ming Ge, Benoit Gendreau-Berthiaume, Philippa J Gerard, Carla Gheler-Costa, Benjamin Gilbert, Paolo Giordani, Simonetta Giordano, Carly Golodets, Laurens G L Gomes, Rachelle K Gould, Dave Goulson, Aaron D Gove, Laurent Granjon, Ingo Grass, Claudia L Gray, James Grogan, Weibin Gu, Moisès Guardiola, Nihara R Gunawardene, Alvaro G Gutierrez, Doris L Gutiérrez-Lamus, Daniela H Haarmeyer, Mick E Hanley, Thor Hanson, Nor R Hashim, Shombe N Hassan, Richard G Hatfield, Joseph E Hawes, Matt W Hayward, Christian Hébert, Alvin J Helden, John-André Henden, Philipp Henschel, Lionel Hernández, James P Herrera, Farina Herrmann, Felix Herzog, Diego Higuera-Diaz, Branko Hilje, Hubert Höfer, Anke Hoffmann, Finbarr G Horgan, Elisabeth Hornung, Roland Horváth, Kristoffer Hylander, Paola Isaacs-Cubides, Hiroaki Ishida, Masahiro Ishitani, Carmen T Jacobs, Víctor J Jaramillo, Birgit Jauker, F Jiménez Hernández, McKenzie F Johnson, Virat Jolli, Mats Jonsell, S Nur Juliani, Thomas S Jung, Vena Kapoor, Heike Kappes, Vassiliki Kati, Eric Katovai, Klaus Kellner, Michael Kessler, Kathryn R Kirby, Andrew M Kittle, Mairi E Knight, Eva Knop, Florian Kohler, Matti Koivula, Annette Kolb, Mouhamadou Kone, Ádám Kőrösi, Jochen Krauss, Ajith Kumar, Raman Kumar, David J Kurz, Alex S Kutt, Thibault Lachat, Victoria Lantschner, Francisco Lara, Jesse R Lasky, Steven C Latta, William F Laurance, Patrick Lavelle, Violette Le Féon, Gretchen LeBuhn, Jean-Philippe Légaré, Valérie Lehouck, María V Lencinas, Pia E Lentini, Susan G Letcher, Qi Li, Simon A Litchwark, Nick A Littlewood, Yunhui Liu, Nancy Lo-Man-Hung, Carlos A López-Quintero, Mounir Louhaichi, Gabor L Lövei, Manuel Esteban Lucas-Borja, Victor H Luja, Matthew S Luskin, M Cristina MacSwiney G, Kaoru Maeto, Tibor Magura, Neil Aldrin Mallari, Louise A Malone, Patrick K Malonza, Jagoba Malumbres-Olarte, Salvador Mandujano, Inger E Måren, Erika Marin-Spiotta, Charles J Marsh, E J P Marshall, Eliana Martínez, Guillermo Martínez Pastur, David Moreno Mateos, Margaret M Mayfield, Vicente Mazimpaka, Jennifer L McCarthy, Kyle P McCarthy, Quinn S McFrederick, Sean McNamara, Nagore G Medina, Rafael Medina, Jose L Mena, Estefania Mico, Grzegorz Mikusinski, Jeffrey C Milder, James R Miller, Daniel R Miranda-Esquivel, Melinda L Moir, Carolina L Morales, Mary N Muchane, Muchai Muchane, Sonja Mudri-Stojnic, A Nur Munira, Antonio Muoñz-Alonso, B F Munyekenye, Robin Naidoo, A Naithani, Michiko Nakagawa, Akihiro Nakamura, Yoshihiro Nakashima, Shoji Naoe, Guiomar Nates-Parra, Dario A Navarrete Gutierrez, Luis Navarro-Iriarte, Paul K Ndang'ang'a, Eike L Neuschulz, Jacqueline T Ngai, Violaine Nicolas, Sven G Nilsson, Norbertas Noreika, Olivia Norfolk, Jorge Ari Noriega, David A Norton, Nicole M Nöske, A Justin Nowakowski, Catherine Numa, Niall O'Dea, Patrick J O'Farrell, William Oduro, Sabine Oertli, Caleb Ofori-Boateng, Christopher Omamoke Oke, Vicencio Oostra, Lynne M Osgathorpe, Samuel Eduardo Otavo, Navendu V Page, Juan Paritsis, Alejandro Parra-H, Luke Parry, Guy Pe'er, Peter B Pearman, Nicolás Pelegrin, Raphaël Pélissier, Carlos A Peres, Pablo L Peri, Anna S Persson, Theodora Petanidou, Marcell K Peters, Rohan S Pethiyagoda, Ben Phalan, T Keith Philips, Finn C Pillsbury, Jimmy Pincheira-Ulbrich, Eduardo Pineda, Joan Pino, Jaime Pizarro-Araya, A J Plumptre, Santiago L Poggio, Natalia Politi, Pere Pons, Katja Poveda, Eileen F Power, Steven J Presley, Vânia Proença, Marino Quaranta, Carolina Quintero, Romina Rader, B R Ramesh, Martha P Ramirez-Pinilla, Jai Ranganathan, Claus Rasmussen, Nicola A Redpath-Downing, J Leighton Reid, Yana T Reis, José M Rey Benayas, Juan Carlos Rey-Velasco, Chevonne Reynolds, Danilo Bandini Ribeiro, Miriam H Richards, Barbara A Richardson, Michael J Richardson, Rodrigo Macip Ríos, Richard Robinson, Carolina A Robles, Jörg Römbke, Luz Piedad Romero-Duque, Matthias Rös, Loreta Rosselli, Stephen J Rossiter, Dana S Roth, T'ai H Roulston, Laurent Rousseau, André V Rubio, Jean-Claude Ruel, Jonathan P Sadler, Szabolcs Sáfián, Romeo A Saldaña-Vázquez, Katerina Sam, Ulrika Samnegård, Joana Santana, Xavier Santos, Jade Savage, Nancy A Schellhorn, Menno Schilthuizen, Ute Schmiedel, Christine B Schmitt, Nicole L Schon, Christof Schüepp, Katharina Schumann, Oliver Schweiger, Dawn M Scott, Kenneth A Scott, Jodi L Sedlock, Steven S Seefeldt, Ghazala Shahabuddin, Graeme Shannon, Douglas Sheil, Frederick H Sheldon, Eyal Shochat, Stefan J Siebert, Fernando A B Silva, Javier A Simonetti, Eleanor M Slade, Jo Smith, Allan H Smith-Pardo, Navjot S Sodhi, Eduardo J Somarriba, Ramón A Sosa, Grimaldo Soto Quiroga, Martin-Hugues St-Laurent, Brian M Starzomski, Constanti Stefanescu, Ingolf Steffan-Dewenter, Philip C Stouffer, Jane C Stout, Ayron M Strauch, Matthew J Struebig, Zhimin Su, Marcela Suarez-Rubio, Shinji Sugiura, Keith S Summerville, Yik-Hei Sung, Hari Sutrisno, Jens-Christian Svenning, Tiit Teder, Caragh G Threlfall, Anu Tiitsaar, Jacqui H Todd, Rebecca K Tonietto, Ignasi Torre, Béla Tóthmérész, Teja Tscharntke, Edgar C Turner, Jason M Tylianakis, Marcio Uehara-Prado, Nicolas Urbina-Cardona, Denis Vallan, Adam J Vanbergen, Heraldo L Vasconcelos, Kiril Vassilev, Hans A F Verboven, Maria João Verdasca, José R Verdú, Carlos H Vergara, Pablo M Vergara, Jort Verhulst, Massimiliano Virgilio, Lien Van Vu, Edward M Waite, Tony R Walker, Hua-Feng Wang, Yanping Wang, James I Watling, Britta Weller, Konstans Wells, Catrin Westphal, Edward D Wiafe, Christopher D Williams, Michael R Willig, John C Z Woinarski, Jan H D Wolf, Volkmar Wolters, Ben A Woodcock, Jihua Wu, Joseph M Wunderle, Yuichi Yamaura, Satoko Yoshikura, Douglas W Yu, Andrey S Zaitsev, Juliane Zeidler, Fasheng Zou, Ben Collen, Rob M Ewers, Georgina M Mace, Drew W Purves, Jörn P W Scharlemann, Andy Purvis
The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3...
January 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28011012/intestinal-adaptation-in-proximal-and-distal-segments-two-epithelial-responses-diverge-after-intestinal-separation
#3
Kathy A Schall, Kathleen A Holoyda, Mubina Isani, Christopher Schlieve, Tasha Salisbury, Thien Khuu, Justine W Debelius, Rex A Moats, Harvey A Pollack, Ching-Ling Lien, Kathryn Fowler, Xiaogang Hou, Rob Knight, Tracy C Grikscheit
BACKGROUND: In short bowel syndrome, luminal factors influence adaptation in which the truncated intestine increases villus lengths and crypt depths to increase nutrient absorption. No study has evaluated the effect of adaptation within the distal intestine after intestinal separation. We evaluated multiple conditions, including Igf1r inhibition, in proximal and distal segments after intestinal resection to evaluate the epithelial effects of the absence of mechanoluminal stimulation. METHODS: Short bowel syndrome was created in adult male zebrafish by performing a proximal stoma with ligation of the distal intestine...
December 20, 2016: Surgery
https://www.readbyqxmd.com/read/27993177/diets-high-in-resistant-starch-increase-plasma-levels-of-trimethylamine-n-oxide-a-gut-microbiome-metabolite-associated-with-cvd-risk
#4
Nathalie Bergeron, Paul T Williams, Regina Lamendella, Nastaran Faghihnia, Alyssa Grube, Xinmin Li, Zeneng Wang, Rob Knight, Janet K Jansson, Stanley L Hazen, Ronald M Krauss
Production of trimethylamine-N-oxide (TMAO), a biomarker of CVD risk, is dependent on intestinal microbiota, but little is known of dietary conditions promoting changes in gut microbial communities. Resistant starches (RS) alter the human microbiota. We sought to determine whether diets varying in RS and carbohydrate (CHO) content affect plasma TMAO levels. We also assessed postprandial glucose and insulin responses and plasma lipid changes to diets high and low in RS. In a cross-over trial, fifty-two men and women consumed a 2-week baseline diet (41 percentage of energy (%E) CHO, 40 % fat, 19 % protein), followed by 2-week high- and low-RS diets separated by 2-week washouts...
December 2016: British Journal of Nutrition
https://www.readbyqxmd.com/read/27986704/comparison-of-collection-methods-for-fecal-samples-in-microbiome-studies
#5
Emily Vogtmann, Jun Chen, Amnon Amir, Jianxin Shi, Christian C Abnet, Heidi Nelson, Rob Knight, Nicholas Chia, Rashmi Sinha
Prospective cohort studies are needed to assess the relationship between the fecal microbiome and human health and disease. To evaluate fecal collection methods, we determined technical reproducibility, stability at ambient temperature, and accuracy of 5 fecal collection methods (no additive, 95% ethanol, RNAlater Stabilization Solution, fecal occult blood test cards, and fecal immunochemical test tubes). Fifty-two healthy volunteers provided fecal samples at the Mayo Clinic in Rochester, Minnesota, in 2014...
December 16, 2016: American Journal of Epidemiology
https://www.readbyqxmd.com/read/27940910/antibiotic-discovery-is-a-walk-in-the-park
#6
Louis-Félix Nothias, Rob Knight, Pieter C Dorrestein
No abstract text is available yet for this article.
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27912057/gut-microbiota-regulate-motor-deficits-and-neuroinflammation-in-a-model-of-parkinson-s-disease
#7
Timothy R Sampson, Justine W Debelius, Taren Thron, Stefan Janssen, Gauri G Shastri, Zehra Esra Ilhan, Collin Challis, Catherine E Schretter, Sandra Rocha, Viviana Gradinaru, Marie-Francoise Chesselet, Ali Keshavarzian, Kathleen M Shannon, Rosa Krajmalnik-Brown, Pernilla Wittung-Stafshede, Rob Knight, Sarkis K Mazmanian
The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27849584/lifestyle-chemistries-from-phones-for-individual-profiling
#8
Amina Bouslimani, Alexey V Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available. Here, we develop an approach to translate chemistries recovered from personal objects such as phones into a lifestyle sketch of the owner, using mass spectrometry and informatics approaches. Our results show that phones' chemistries reflect a personalized lifestyle profile...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27822557/migraines-are-correlated-with-higher-levels-of-nitrate-nitrite-and-nitric-oxide-reducing-oral-microbes-in-the-american-gut-project-cohort
#9
Antonio Gonzalez, Embriette Hyde, Naseer Sangwan, Jack A Gilbert, Erik Viirre, Rob Knight
Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822553/mockrobiota-a-public-resource-for-microbiome-bioinformatics-benchmarking
#10
Nicholas A Bokulich, Jai Ram Rideout, William G Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J Gregory Caporaso
Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822543/the-oral-and-skin-microbiomes-of-captive-komodo-dragons-are-significantly-shared-with-their-habitat
#11
Embriette R Hyde, Jose A Navas-Molina, Se Jin Song, Jordan G Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R Mendelson, Valerie J McKenzie, Jack A Gilbert, Rob Knight
Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822526/preservation-methods-differ-in-fecal-microbiome-stability-affecting-suitability-for-field-studies
#12
Se Jin Song, Amnon Amir, Jessica L Metcalf, Katherine R Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight
Immediate freezing at -20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods-95% ethanol, FTA cards, and the OMNIgene Gut kit-can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates...
May 2016: MSystems
https://www.readbyqxmd.com/read/27822524/from-sample-to-multi-omics-conclusions-in-under-48-hours
#13
Robert A Quinn, Jose A Navas-Molina, Embriette R Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J Minich, Alexey V Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C Dorrestein, Rob Knight
Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology...
March 2016: MSystems
https://www.readbyqxmd.com/read/27822521/geography-and-location-are-the-primary-drivers-of-office-microbiome-composition
#14
John Chase, Jennifer Fouquier, Mahnaz Zare, Derek L Sonderegger, Rob Knight, Scott T Kelley, Jeffrey Siegel, J Gregory Caporaso
In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices...
March 2016: MSystems
https://www.readbyqxmd.com/read/27822518/improved-bacterial-16s-rrna-gene-v4-and-v4-5-and-fungal-internal-transcribed-spacer-marker-gene-primers-for-microbial-community-surveys
#15
William Walters, Embriette R Hyde, Donna Berg-Lyons, Gail Ackermann, Greg Humphrey, Alma Parada, Jack A Gilbert, Janet K Jansson, J Gregory Caporaso, Jed A Fuhrman, Amy Apprill, Rob Knight
Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5' end, allowing for a range of different 3' primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene...
January 2016: MSystems
https://www.readbyqxmd.com/read/27822515/open-source-sequence-clustering-methods-improve-the-state-of-the-art
#16
Evguenia Kopylova, Jose A Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J Gregory Caporaso, Rob Knight
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE...
January 2016: MSystems
https://www.readbyqxmd.com/read/27786218/let-researchers-try-new-paths
#17
COMMENT
Tolu Oni, Fabio Sciarrino, Gerardo Adesso, Rob Knight
No abstract text is available yet for this article.
27, 2016: Nature
https://www.readbyqxmd.com/read/27760558/tiny-microbes-enormous-impacts-what-matters-in-gut-microbiome-studies
#18
Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight
Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions. The presentation of quantitative effect sizes in addition to P values will improve our ability to perform meta-analysis and to evaluate potentially relevant biological effects...
October 19, 2016: Genome Biology
https://www.readbyqxmd.com/read/27756413/fat-and-vitamin-intakes-during-pregnancy-have-stronger-relations-with-a-pro-inflammatory-maternal-microbiota-than-does-carbohydrate-intake
#19
Siddhartha Mandal, Keith M Godfrey, Daniel McDonald, Will V Treuren, Jørgen V Bjørnholt, Tore Midtvedt, Birgitte Moen, Knut Rudi, Rob Knight, Anne Lise Brantsæter, Shyamal D Peddada, Merete Eggesbø
BACKGROUND: Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited. Modulation of the composition of the microbiota in pregnant women is especially important as maternal microbes are transferred during delivery and initiate the colonization process in the infant. We studied the associations between intake of specific dietary nutrients during pregnancy and gut microbiota composition...
October 19, 2016: Microbiome
https://www.readbyqxmd.com/read/27732780/mass-spectrometry-based-visualization-of-molecules-associated-with-human-habitats
#20
Daniel Petras, Louis-Félix Nothias, Robert A Quinn, Theodore Alexandrov, Nuno Bandeira, Amina Bouslimani, Gabriel Castro-Falcón, Liangyu Chen, Tam Dang, Dimitrios J Floros, Vivian Hook, Neha Garg, Nicole Hoffner, Yike Jiang, Clifford A Kapono, Irina Koester, Rob Knight, Christopher A Leber, Tie-Jun Ling, Tal Luzzatto-Knaan, Laura-Isobel McCall, Aaron P McGrath, Michael J Meehan, Jonathan K Merritt, Robert H Mills, Jamie Morton, Sonia Podvin, Ivan Protsyuk, Trevor Purdy, Kendall Satterfield, Stephen Searles, Sahil Shah, Sarah Shires, Dana Steffen, Margot White, Jelena Todoric, Robert Tuttle, Aneta Wojnicz, Valerie Sapp, Fernando Vargas, Jin Yang, Chao Zhang, Pieter C Dorrestein
The cars we drive, the homes we live in, the restaurants we visit, and the laboratories and offices we work in are all a part of the modern human habitat. Remarkably, little is known about the diversity of chemicals present in these environments and to what degree molecules from our bodies influence the built environment that surrounds us and vice versa. We therefore set out to visualize the chemical diversity of five built human habitats together with their occupants, to provide a snapshot of the various molecules to which humans are exposed on a daily basis...
November 15, 2016: Analytical Chemistry
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