cran: PERMANOVA | Projects | Ecosyste.ms: Papers

10.3390/nu13041141

Adherence to a Supplemented Mediterranean Diet Drives Changes in the Gut Microbiota of HIV-1-Infected Individuals
Cited by: 11
Author(s): Roque Pastor-Ibáñez, Juan Blanco-Heredia, Florencia Etcheverry, Sonsoles Sánchez-Palomino, Francisco Díez-Fuertes, Rosa Casas, María A Navarrete-Muñoz, Sara Castro‐Barquero, Claudia Lucero, Irene Fernández, Lorna Leal, José María Sánchez Benito, Marc Noguera-Julián, Roger Paredes, Norma Rallón, Ramón Estruch, David Torrents, Felipe García
Software Mentions: 2
Published: over 5 years ago

10.3390/nu11030664

Procyanidin—Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro
Cited by: 39
Author(s): Carine Le Bourvellec, Priscilla Bagano Vilas Boas, Pascale Lepercq, Sophie Comtet-Marre, Pauline Auffret, Philippe Ruiz, Raoul Bott, Cathérine M.G.C. Renard, Claire Dufour, Jean‐Marc Chatel, Pascale Mosoni
Software Mentions: 2
Published: over 7 years ago

10.3390/nu13030713

Multiple Selection Criteria for Probiotic Strains with High Potential for Obesity Management
Cited by: 16
Author(s): Jeanne Alard, Benoît Cudennec, Denise Boutillier, Véronique Peucelle, Amandine Descat, Raphael Decoin, Sarah Kuylle, Amin Jablaoui, Moez Rhimi, Isabelle Wolowczuk, Bruno Pot, Anne Tailleux, Emmanuelle Maguin, Sophie Holowacz, Corinne Grangette
Software Mentions: 2
Published: over 5 years ago

10.3390/nu12082193

Dynamics of Structural and Functional Changes in Gut Microbiota during Treatment with a Microalgal β-Glucan, Paramylon and the Impact on Gut Inflammation
Cited by: 12
Author(s): Harrison B. Taylor, Radhika Gudi, Robert R. Brown, Chenthamarakshan Vasu
Software Mentions: 2
Published: about 6 years ago

10.3390/nu13041066

Analysis of the Gut Mycobiome in Adult Patients with Type 1 and Type 2 Diabetes Using Next-Generation Sequencing (NGS) with Increased Sensitivity—Pilot Study
Cited by: 14
Author(s): Dominika Salamon, Agnieszka Sroka-Oleksiak, Artur Gurgul, Zbigniew Arent, Magdalena Szopa, Małgorzata Bulanda, Maciej Małecki, Tomasz Gosiewski
Software Mentions: 2
Published: over 5 years ago

10.3390/nu11030547

Human Gut Microbiome Response Induced by Fermented Dairy Product Intake in Healthy Volunteers
Cited by: 50
Author(s): Olesya Volokh, Natalia Klimenko, Yulia Berezhnaya, Alexander Tyakht, Polina Nesterova, Anna Popenko, Dmitry Alexeev
Software Mentions: 2
Published: over 7 years ago

10.3390/nu12020373

Dietary Synbiotic Supplementation Protects Barrier Integrity of Hepatocytes and Liver Sinusoidal Endothelium in a Mouse Model of Chronic-Binge Ethanol Exposure
Cited by: 16
Author(s): Yingchun Han, Bryan Glueck, David Shapiro, Aaron W. Miller, Sanjoy Roychowdhury, Gail Cresci
Software Mentions: 2
Published: over 6 years ago

10.3390/nu8110684

Dietary Gluten-Induced Gut Dysbiosis Is Accompanied by Selective Upregulation of microRNAs with Intestinal Tight Junction and Bacteria-Binding Motifs in Rhesus Macaque Model of Celiac Disease
Cited by: 46
Author(s): Mahesh Mohan, Cheryl-Emiliane T. Chow, Caitlin N. Ryan, Luisa Chan, Jason Dufour, Pyone P. Aye, James Blanchard, Charles P. Moehs, Karol Sestak
Software Mentions: 2
Published: almost 10 years ago

10.3390/s20216281

An Automated Pipeline for Image Processing and Data Treatment to Track Activity Rhythms of Paragorgia arborea in Relation to Hydrographic Conditions
Cited by: 15
Author(s): Ander Zuazo, Jordi Grinyó, Vanesa López-Vázquez, E. A. Rodríguez, Corrado Costa, Luciano Ortenzi, Sascha Flögel, Javier Valencia, Simone Marini, Guosong Zhang, Henning Wehde, Jacopo Aguzzi
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-020-0784-5

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system
Cited by: 40
Author(s): Yaron Krotman, Timur Yergaliyev, Rivka Alexander Shani, Yosef Avrahami, Amir Szitenberg
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-018-0510-8

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism
Cited by: 146
Author(s): Sarah Just, Stanislas Mondot, Josef Ecker, Katrin Wegner, Eva Rath, Laura Gau, Theresa Streidl, Geneviève Héry-Arnaud, Sinah Schmidt, Till Robin Lesker, Valentin Bieth, Andreas Dunkel, Till Strowig, Thomas G. Hofmann, Dirk Haller, Gerhard Liebisch, Philippe Gérard, Sascha Rohn, Patricia Lepage, Thomas Clavel
Software Mentions: 2
Published: about 8 years ago

10.1186/s40168-017-0327-x

Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine
Cited by: 17
Author(s): Xuejian Xiong, Elise S. Bales, Diana Ir, Charles E. Robertson, James L. McManaman, Daniel N. Frank, John Parkinson
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-016-0151-8

Composition and dynamics of the respiratory tract microbiome in intubated patients
Cited by: 129
Author(s): Brendan J Kelly, Ize Imai, Kyle Bittinger, Alice Laughlin, Barry D. Fuchs, Frederic D. Bushman, Ronald G. Collman
Software Mentions: 2
Published: over 10 years ago

10.1186/s40168-020-00899-6

Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria
Cited by: 60
Author(s): Bastian Seelbinder, Jiarui Chen, Sascha Brunke, Ruben Vazquez-Uribe, Rakesh Santhaman, Anne-Christin Meyer, Felipe Senne de Oliveira Lino, Ka-Fai Chan, Daniel Loos, Lejla Imamovic, Chi‐Ching Tsang, Rex Pui-kin Lam, Siddharth Sridhar, Kang Kang, Bernhard Hube, Patrick Chiu-Yat Woo, Morten Otto Alexander Sommer, Gianni Panagiotou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-019-0699-1

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle
Cited by: 189
Author(s): Fuyong Li, Changxi Li, Yanhong Chen, Junhong Liu, Chunyan Zhang, Barry Irving, Carolyn Fitzsimmons, Graham Plastow, Le Luo Guan
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-021-01028-7

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation
Cited by: 88
Author(s): Daotong Li, Yao Feng, Mi Tian, Junfu Ji, Xiaosong Hu, Fang Chen
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-017-0270-x

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
Cited by: 75
Author(s): Sonny T. M. Lee, Stacy A. Kahn, Tom O. Delmont, Alon Shaiber, Özcan C. Esen, Nathaniel Hubert, Hilary G. Morrison, Dionysios A. Antonopoulos, David T. Rubin, A. Murat Eren
Software Mentions: 2
Published: over 9 years ago

10.1186/s40168-018-0451-2

Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers
Cited by: 291
Author(s): Zhenwei Dai, Olabisi Oluwabukola Coker, Geicho Nakatsu, William Ka Kei Wu, Liuyang Zhao, Zigui Chen, Francis K.L. Chan, Karsten Kristiansen, Joseph J.Y. Sung, Sunny H. Wong, Jun Yu
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-018-0587-0

Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice
Cited by: 128
Author(s): Kanakaraju Kaliannan, Ruairi C. Robertson, Kiera Murphy, Catherine Stanton, Chao Kang, Bin Wang, Lei Hao, Atul K. Bhan, Jing Kang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-017-0326-y

Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis
Cited by: 38
Author(s): Cornelia Gottschick, Zhi-Luo Deng, Marius Vital, Clarissa Masur, Christoph Abels, Dietmar H. Pieper, Manfred Rohde, Werner Mendling, Irene Wagner‐Döbler
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-020-00983-x

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota
Cited by: 8
Author(s): Ryan A. Blaustein, Lisa Marie Michelitsch, A. Glawe, Hansung Lee, Stefanie Huttelmaier, Nancy Hellgeth, Sarah Ben Maamar, Erica M. Hartmann
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-020-00810-3

Lung function and microbiota diversity in cystic fibrosis
Cited by: 115
Author(s): Leah Cuthbertson, Alan W. Walker, Anna Oliver, Geraint B. Rogers, Damian W. Rivett, Thomas H. Hampton, Alix Ashare, J. Stuart Elborn, Anthony De Soyza, Mary Carroll, Lucas R. Hoffman, Clare Lanyon, Samuel M. Moskowitz, George A. O’Toole, Julian Parkhill, Paul J. Planet, Charlotte C. Tenebäck, Michael Tunney, Jonathan B. Zuckerman, Kenneth D. Bruce, Christopher J. van der Gast
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-017-0366-3

Normalization of the microbiota in patients after treatment for colonic lesions
Cited by: 53
Author(s): Marc A. Sze, Nielson T. Baxter, Mack T. Ruffin, Mary A.M. Rogers, Patrick D. Schloss
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-021-01118-6

Plant developmental stage drives the differentiation in ecological role of the maize microbiome
Cited by: 120
Author(s): Chao Xiong, Brajesh K. Singh, Ji‐Zheng He, Yong Han, Peipei Li, Li-Hua Wan, Guo-Zhong Meng, Si-Yi Liu, Juntao Wang, Chuanfa Wu, An‐Hui Ge, Limei Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/s40168-021-01032-x

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils
Cited by: 62
Author(s): Yuanyuan Bao, Jan Dolfing, Zhiying Guo, Ruirui Chen, Meng Wu, Zhongpei Li, Xiangui Lin, Youzhi Feng
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-019-0726-2

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities
Cited by: 49
Author(s): Xuanping Tan, Taejung Chung, Yi Chen, Dumitru Macarisin, Luke F. LaBorde, Jasna Kovač
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-021-01138-2

Disease-induced changes in plant microbiome assembly and functional adaptation
Cited by: 116
Author(s): Min Gao, Chao Xiong, Cheng Gao, Clement K. M. Tsui, Mengmeng Wang, Xin Zhou, Aimin Zhang, Lei Cai
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-018-0497-1

Network hubs in root-associated fungal metacommunities
Cited by: 94
Author(s): Hirokazu Toju, Akifumi S. Tanabe, Hirotoshi Sato
Software Mentions: 2
Published: about 8 years ago

10.1186/s40168-018-0416-5

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia
Cited by: 88
Author(s): Bruce A. Rosa, Taniawati Supali, Lincoln Gankpala, Yenny Djuardi, Erliyani Sartono, Yanjiao Zhou, Kerstin Fischer, John Martin, Rahul Tyagi, Fatorma K. Bolay, Peter U. Fischer, Maria Yazdanbakhsh, Makedonka Mitreva
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-020-00908-8

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
Cited by: 30
Author(s): Aaron McKenna, Umer Zeeshan Ijaz, Carmel Kelly, Mark Linton, William T. Sloan, Brian D. Green, Ursula Lavery, Nick Dorrell, Brendan W. Wren, Anne Richmond, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-020-00913-x

Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status
Cited by: 57
Author(s): Jordi Mayneris‐Perxachs, María Arnoriaga-Rodríguez, D. Luque-Córdoba, Feliciano Priego‐Capote, Vicente Pérez‐Brocal, Andrés Moya, Aurelijus Burokas, Rafaël Maldonado, José Manuel Fernández-Real
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40168-017-0252-z

Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status
Cited by: 112
Author(s): Jôice Dias Corrêa, Débora Cerqueira Calderaro, Gilda Aparecida Ferreira, Santuza Maria Souza de Mendonça, Gabriel R. Fernandes, E. Xiao, Antônio Lúcio Teixeira, Eugene J. Leys, Dana T. Graves, Tarcı́lia Aparecida Silva
Software Mentions: 2
Published: over 9 years ago

10.1186/s40168-018-0525-1

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion
Cited by: 69
Author(s): Késia Silva Lourenço, Afnan Khalil Ahmad Suleiman, Agata Pijl, Johannes A. van Veen, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 2
Published: about 8 years ago

10.1186/s40168-019-0727-1

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia
Cited by: 124
Author(s): Juan E. Pérez‐Jaramillo, Mattias de Hollander, Camilo A. Ramírez, Rodrigo Mendes, Jos M. Raaijmakers, Víctor J. Carrión
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-018-0448-x

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults
Cited by: 146
Author(s): Xiaozhou Fan, Brandilyn A. Peters, Eric J. Jacobs, Susan M. Gapstur, Mark P. Purdue, Neal D. Freedman, Alexander V. Alekseyenko, Jing Wu, Liying Yang, Zhiheng Pei, Richard B. Hayes, Jiyoung Ahn
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-021-01034-9

Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data
Cited by: 14
Author(s): Zhengyi Zhu, Glen A. Satten, Caroline Mitchell, Yi‐Juan Hu
Software Mentions: 2
Published: about 5 years ago

10.1186/s40168-020-00833-w

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions
Cited by: 55
Author(s): Stien Beirinckx, Tom Viaene, Annelies Haegeman, Jane Debode, Fien Amery, Sophie Vandenabeele, Hilde Nelissen, Dirk Inzé, Raúl Y. Tito, Jeroen Raes, Caroline De Tender, Sofie Goormachtig
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-018-0478-4

Gut microbiota in experimental murine model of Graves’ orbitopathy established in different environments may modulate clinical presentation of disease
Cited by: 52
Author(s): Giulia Masetti, Sajad Moshkelgosha, Hedda-Luise Köhling, Danila Covelli, J. Paul Banga, Utta Berchner‐Pfannschmidt, Mareike Horstmann, Salvador Díaz‐Cano, Gina-Eva Goertz, Sue Plummer, Anja Eckstein, Marian Ludgate, Filippo Biscarini, Julian R. Marchesi
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-021-01066-1

Synergistic action of the gut microbiota in environmental RNA interference in a leaf beetle
Cited by: 27
Author(s): Letian Xu, Shijing Xu, Liuwei Sun, Yiqiu Zhang, Jing Luo, Ralph Bock, Jiang Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/s40168-017-0381-4

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease
Cited by: 90
Author(s): Alexa A. Pragman, Tianmeng Lyu, Joshua A. Baller, Trevor Gould, Rosemary F. Kelly, Cavan Reilly, Richard E. Isaacson, Chris H. Wendt
Software Mentions: 2
Published: over 8 years ago

10.3390/microorganisms8060936

A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)
Cited by: 19
Author(s): Claudia Leoni, Mariateresa Volpicella, Bruno Fosso, Caterina Manzari, Elisabetta Piancone, Maria C.G. Dileo, Erika Arcadi, Michail M. Yakimov, Graziano Pesole, Luigi R. Ceci
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.11057

DNA metabarcoding of zooplankton communities: species diversity and seasonal variation revealed by 18S rRNA and COI
Cited by: 5
Author(s): Lina Zhao, Xue Zhang, Mingang Xu, Ying Mao, Yuan Huang
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.8735

Contemporary diets of walruses in Bristol Bay, Alaska suggest temporal variability in benthic community structure
Cited by: 6
Author(s): John M. Maniscalco, Alan M. Springer, Katrina L. Counihan, Tuula E. Hollmén, Helen Aderman, Moses Toyukak
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.10184

Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing
Cited by: 11
Author(s): Alaa Emara Rabee, Robert J. Forster, Chijioke O. Elekwachi, Ebrahim A. Sabra, Mebarek Lamara
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.10715

Taxonomic, functional and expression analysis of viral communities associated with marine sponges
Cited by: 9
Author(s): Mary Nguyen, Bernd Wemheuer, Patrick W. Laffy, Nicole S. Webster, Torsten Thomas
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.1911

Largest global shark biomass found in the northern Galápagos Islands of Darwin and Wolf
Cited by: 43
Author(s): Pelayo Salinas de León, David Acuña-Marrero, Etienne Rastoin, Alan M. Friedlander, Mary K. Donovan, Enric Sala
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.7526

Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China
Cited by: 12
Author(s): Tianyu Liang, Guang Yang, Yunxia Ma, Quan‐Hong Yao, Yongxiang Ma, Hao Ma, Yang Hu, Ying Yang, Shaoxiong Wang, Yiyong Pan, Gangtie Li
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.2455

Does regional diversity recover after disturbance? A field experiment in constructed ponds
Cited by: 7
Author(s): Lauren Michelle Woods, Elizabeth G. Biro, Muxi Yang, Kevin G. Smith
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.2444

Genetic signatures of ecological diversity along an urbanization gradient
Cited by: 67
Author(s): Ryan P. Kelly, James L. O’Donnell, Natalie Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist, Gregory D. Williams
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.11675

Where three snail species attach while emersed in relation to heterogenous substrate temperatures underneath intertidal boulders
Cited by: 1
Author(s): Nathan Janetzki, Kirsten Benkendorff, Peter G. Fairweather
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.11532

Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species
Cited by: 7
Author(s): Bárbara Santos, Molly C. Bletz, Joana Sabino‐Pinto, Walter Cocca, Jean Francois Solofoniaina Fidy, Karen Freeman, Sven Kuenzel, Serge H. Ndriantsoa, Jean Noël, Tsanta Rakotonanahary, Miguel Vences, Angelica Crottini
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.4441

Benthic macrofaunal structure and secondary production in tropical estuaries on the Eastern Marine Ecoregion of Brazil
Cited by: 29
Author(s): Lorena B Bissoli, Ângelo F. Bernardino
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.10103

The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef
Cited by: 5
Author(s): Alexis Enrique Medina-Valmaseda, Rosa E. Rodríguez-Martínez, Lorenzo Álvarez‐Filip, Eric Jordán-Dahlgren, Paul Blanchon
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.4885

Urbanization alters small rodent community composition but not abundance
Cited by: 6
Author(s): Jessica Noemi Alvarez Guevara, Becky A. Ball
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.9591

Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis
Cited by: 24
Author(s): Xiang Li, Zewen Li, Yan He, Pan Li, Hongwei Zhou, Nianyi Zeng
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.7376

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location
Cited by: 4
Author(s): Yunshi Li, Xiukun Wu, Wanfu Wang, Minghao Wang, Changming Zhao, Tuo Chen, Guangxiu Lu, Wei Zhang, Shi-Weng Li, Huaizhe Zhou, Minghui Wu, Ruiqi Yang, Gaosen Zhang
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.3202

Endosymbiont interference and microbial diversity of the Pacific coast tick,Dermacentor occidentalis, in San Diego County, California
Cited by: 49
Author(s): Nikos Gurfield, Saran Grewal, S Lynnie, Pedro J. Torres, Scott T. Kelley
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.3125

Variegated tropical landscapes conserve diverse dung beetle communities
Cited by: 29
Author(s): Cristiane Maria Queiroz da Costa, Victor Hugo Fonseca Oliveira, Rafaella Maciel, Wallace Beiroz, Vanesca Korasaki, Júlio Louzada
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.4178

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise
Cited by: 40
Author(s): Taha Soliman, Sung‐Yin Yang, Tomoko Yamazaki, Holger Jenke‐Kodama
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.5649

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing
Cited by: 24
Author(s): Zhifang Zhou, Guanghui Ling, Ning Ding, Zhe Xun, Ce Zhu, Hong Hua, Xiaochi Chen
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.4653

Soft-bottom fishes and spatial protection: findings from a temperate marine protected area
Cited by: 11
Author(s): Inês Sousa, Jorge M. S. Gonçalves, Joachim Claudet, Rui Coelho, Emanuel João Gonçalves, Karim Erzini
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.4809

A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fishPycnodus(Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy
Cited by: 7
Author(s): John Joseph Cawley, Giuseppe Marramà, Giorgio Carnevale, Jürgen Kriwet
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.10905

Depression of the soil arbuscular mycorrhizal fungal community by the canopy gaps in a Japanese cedar (Cryptomeria japonica) plantation on Lushan Mountain, subtropical China
Cited by: 4
Author(s): Guiwu Zou, Yuanqiu Liu, Fansen Kong, Liqin Liao, Guanghua Deng, Jiang Xue, Junhuo Cai, Wei Liu
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.1936

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity
Cited by: 50
Author(s): Georg Steinert, Michael W. Taylor, Peter Deines, Rachel L. Simister, Nicole J. de Voogd, Michael Hoggard, Peter J. Schupp
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.2853

Identifying zooplankton community changes between shallow and upper-mesophotic reefs on the Mesoamerican Barrier Reef, Caribbean
Cited by: 10
Author(s): Dominic A. Andradi‐Brown, Catherine E. I. Head, Dan A. Exton, Christina L. Hunt, Alicia Hendrix, Erika Gress, Alex D. Rogers
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.8550

Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata
Cited by: 16
Author(s): Kaho H. Tisthammer, Zac H. Forsman, Robert J. Toonen, Robert H. Richmond
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.1110

Not all jellyfish are equal: isotopic evidence for inter- and intraspecific variation in jellyfish trophic ecology
Cited by: 44
Author(s): Nicholas E.C. Fleming, Chris Harrod, Jason Newton, Jonathan D. R. Houghton
Software Mentions: 2
Published: about 11 years ago

10.7717/peerj.5754

Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China
Cited by: 10
Author(s): Song Gu, Xingjun Guo, Yuetong Cai, Zehui Zhang, Shuai Wu, Xin Li, Huihui Zhang, Wei Yang
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0039634

Habitat Specialization in Tropical Continental Shelf Demersal Fish Assemblages
Cited by: 86
Author(s): Ben Fitzpatrick, Euan S. Harvey, Andrew Heyward, Emily Twiggs, Jamie Colquhoun
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0077704

The Importance of Vertical and Horizontal Dimensions of the Sediment Matrix in Structuring Nematodes Across Spatial Scales
Cited by: 14
Author(s): Danilo Cândido Vieira, Gustavo Fonseca
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0137778

Edge Effects along a Seagrass Margin Result in an Increased Grazing Risk on Posidonia australis Transplants
Cited by: 9
Author(s): John Statton, Samuel Gustin-Craig, Kingsley W. Dixon, Gary A. Kendrick
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0112942

Müllerian Mimicry as a Result of Codivergence between Velvet Ants and Spider Wasps
Cited by: 15
Author(s): Juanita Rodríguez, James P. Pitts, Carol D. von Dohlen, Joseph S. Wilson
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0208852

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem
Cited by: 47
Author(s): Eneas Aguirre‐von‐Wobeser, Jorge Rocha, Lori R. Shapiro, Mayra de la Torre
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0180859

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome
Cited by: 31
Author(s): Marion Engel, David Endesfelder, Brigitte Schloter-Hai, Susanne Kublik, Michael S. Granitsiotis, Pierà Boschetto, Mariarita Stendardo, Imre Barta, Balázs Döme, Jean‐François Deleuze, Anne Boland, Joachim Müller–Quernheim, Antje Prasse, Tobias Welte, Jens M. Hohlfeld, Deepak Subramanian, David Parr, Marta Gut, Timm Greulich, Andreas Rembert Koczulla, Adam Nowiński, Dorota Górecka, Dave Singh, Sumit Gupta, Christopher E. Brightling, Harald Hoffmann, Marion Frankenberger, Thomas P. Hofer, Dorothe Burggraf, Marion Heiß-Neumann, Loems Ziegler-Heitbrock, Michael Schloter, Wolfgang zu Castell
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0195967

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout
Cited by: 18
Author(s): Omolola C. Betiku, Carl J. Yeoman, T. Gibson Gaylord, Benjamin Americus, Sarah K. Olivo, G. C. Duff, Wendy M. Sealey
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0202863

Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover
Cited by: 6
Author(s): Omar Valencia‐Méndez, Fabián Alejandro Rodríguez‐Zaragoza, Luis E. Calderón-Aguilera, Omár Domínguez-Domínguez, Andrés López‐Pérez
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0207703

The influence of depth and a subsea pipeline on fish assemblages and commercially fished species
Cited by: 29
Author(s): Todd Bond, Julian C. Partridge, Michael D. Taylor, Tim F. Cooper, Dianne L. McLean
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0141373

Hybridization between Yellowstone Cutthroat Trout and Rainbow Trout Alters the Expression of Muscle Growth-Related Genes and Their Relationships with Growth Patterns
Cited by: 5
Author(s): Carl O. Ostberg, Dorothy M. Chase, Lorenz Hauser
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0192772

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption
Cited by: 79
Author(s): Jeremiah J. Minich, Megan M. Morris, Matt Brown, Michael P. Doane, Matthew S. Edwards, Todd P. Michael, Elizabeth A. Dinsdale
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0223026

The responses of extracellular enzyme activities and microbial community composition under nitrogen addition in an upland soil
Cited by: 37
Author(s): Sami Ullah, Chao Ai, Shaohui Huang, Jiajia Zhang, Jia Liu, Jinlong Ma, Wei Zhou, Ping He
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0234830

Climate gradients, and patterns of biodiversity and biotic homogenization in urban residential yards
Cited by: 5
Author(s): Elizabeth A. Bergey, Benjamin E. Whipkey
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0233065

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host
Cited by: 6
Author(s): M. A. Stephens, Daniel J. Gage
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0145191

Warming and Elevated CO2 Interact to Drive Rapid Shifts in Marine Community Production
Cited by: 17
Author(s): Cascade J. B. Sorte, Matthew E. S. Bracken
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0077527

Availability of Ectomycorrhizal Fungi to Black Spruce above the Present Treeline in Eastern Labrador
Cited by: 19
Author(s): Laura Reithmeier, Gavin Kernaghan
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0123943

Passive Acoustic Monitoring of the Temporal Variability of Odontocete Tonal Sounds from a Long-Term Marine Observatory
Cited by: 18
Author(s): Tzu‐Hao Lin, Hon‐Tsen Yu, Chi‐Fang Chen, Lien‐Siang Chou
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0123216

Sinonasal Microbiome Sampling: A Comparison of Techniques
Cited by: 47
Author(s): Ahmed Bassiouni, Edward John Cleland, Alkis J. Psaltis, Sarah Vreugde, Peter‐John Wormald
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0250975

Genomics of Staphylococcus aureus ocular isolates
Cited by: 9
Author(s): William L. Johnson, Michael B. Sohn, Samantha M. Taffner, Payel Chatterjee, Paul M. Dunman, Nicole Pecora, Rachel A. F. Wozniak
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0186929

DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem
Cited by: 56
Author(s): Eglė Jakubavičiūtė, Ulf Bergström, Johan Eklöf, Quiterie Haenel, Sarah J. Bourlat
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0038073

Organic Farming and Landscape Structure: Effects on Insect-Pollinated Plant Diversity in Intensively Managed Grasslands
Cited by: 48
Author(s): Eileen F. Power, Daniel L. Kelly, Jane C. Stout
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0184611

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems
Cited by: 54
Author(s): Dipak Sharma‐Poudyal, Daniel Schlatter, Chuntao Yin, Scot H. Hulbert, T. C. Paulitz
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0229259

Kelp forests at the end of the earth: 45 years later
Cited by: 34
Author(s): Alan M. Friedlander, Enric Ballesteros, Tom W. Bell, Jennifer E. Caselle, Claudio Campagna, Whitney Goodell, Mathias Hüne, Alex Muñoz, Pelayo Salinas‐de‐León, Enric Sala, Paul K. Dayton
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0167405

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach
Cited by: 47
Author(s): Véronique Gourmelon, Laurent Maggia, Jeff R. Powell, Sarah Gigante, Sara Hortal, Claire Gueunier, Kelly Letellier, Fabian Carriconde
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0052448

Growth Attenuation with Developmental Schedule Progression in Embryos and Early Larvae of Sterechinus neumayeri Raised under Elevated CO2
Cited by: 39
Author(s): Pauline C. Yu, Mary A. Sewell, Paul G. Matson, Emily B. Rivest, Lydia Kapsenberg, Gretchen E. Hofmann
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0202278

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health
Cited by: 40
Author(s): Kathrin Beyer, Egija Zaura, Bernd W. Brandt, M.J. Buijs, Johan G. Brun, Wim Crielaard, Anne Isine Bolstad
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0115798

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem
Cited by: 10
Author(s): Ximei Zhang, Albert Barberán, Xinghua Zhu, Guangming Zhang, Xingguo Han
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0245995

Rebamipide ameliorates indomethacin-induced small intestinal damage and proton pump inhibitor-induced exacerbation of this damage by modulation of small intestinal microbiota
Cited by: 8
Author(s): Tetsuya Tanigawa, Toshio Watanabe, Akira Higashimori, Sunao Shimada, Hiroyuki Kitamura, Takuya Kuzumoto, Yuji Nadatani, Koji Otani, Shusei Fukunaga, Shuhei Hosomi, Fumio Tanaka, Noriko Kamata, Yasuaki Nagami, Koichi Taira, Masatsugu Shiba, Wataru Suda, Masahira Hattori, Yasuhiro Fujiwara
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0208327

Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi
Cited by: 13
Author(s): Loganathan Ponnusamy, Alexandra C Willcox, R. Michael Roe, Silas A. Davidson, Piyada Linsuwanon, Anthony L. Schuster, Allen L. Richards, Steven R. Meshnick, Charles S. Apperson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0251499

Trophic ecology of yellowtail rockfish (Sebastes flavidus) during a marine heat wave off central California, USA
Cited by: 3
Author(s): Jennifer A. Chiu, Joseph J. Bizzarro, Richard M. Starr
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0136157

Impacts of Rotational Grazing on Soil Carbon in Native Grass-Based Pastures in Southern Australia
Cited by: 41
Author(s): Jonathan Sanderman, Reseigh Jodie, Michael Wurst, Young Mary-Anne, Jenet Austin
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0178559

Distribution and diversity of aquatic macroinvertebrate assemblages in a semi-arid region earmarked for shale gas exploration (Eastern Cape Karoo, South Africa)
Cited by: 28
Author(s): Annah Mabidi, Matthew S. Bird, Renzo Perissinotto
Software Mentions: 2
Published: about 9 years ago

Projects: cran: PERMANOVA

Science Score: 85/100

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Papers Mentioning PERMANOVA 6,292