cran: PERMANOVA | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0024235

In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs
Cited by: 45
Author(s): Piotr Bielecki, Jacek Puchałka, Melissa L. Wos‐Oxley, Holger Loessner, Justyna Glik, Marek Kawecki, Mariusz Nowak, Burkhard Tümmler, Siegfried Weiß, Vítor A. P. Martins dos Santos
Software Mentions: 3
Published: about 13 years ago

10.3390/cancers12123702

Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank
Cited by: 15
Author(s): Ulrike Wirth, Debora Garzetti, Lara Jochum, Stefanie Spriewald, Florian Kühn, Matthias Ilmer, Serene M. L. Lee, Hanno Nieß, Alexandr V. Bazhin, Joachim Andrassy, Jens Werner, Bärbel Stecher, Tobias S. Schiergens
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers11030309

Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing
Cited by: 35
Author(s): Minji Kwon, Seung‐Woo Seo, Mi Kyung Kim, Dong Ock Lee, Myoung Cheol Lim
Software Mentions: 3
Published: over 5 years ago

10.1016/j.chom.2018.06.011

Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales
Cited by: 124
Author(s): Talia L. Karasov, Juliana Almario, Claudia Friedemann, Wei Ding, Michael Giolai, Darren Heavens, Sonja Kersten, Derek S. Lundberg, Manuela Neumann, Julián Regalado, Richard A. Neher, Eric Kemen, Detlef Weigel
Software Mentions: 3
Published: over 6 years ago

10.1016/j.xcrm.2021.100383

Regorafenib plus toripalimab in patients with metastatic colorectal cancer: a phase Ib/II clinical trial and gut microbiome analysis
Cited by: 45
Author(s): Feng Wang, Ming-Ming He, Yonghong Yao, Xia Zhao, Zhiqiang Wang, Ying Jin, Hongyu Luo, Jibin Li, Fenghua Wang, Miaozhen Qiu, Zhi-Da Lv, De-Shen Wang, Yuhong Li, Dongsheng Zhang, Rui‐Hua Xu
Software Mentions: 3
Published: about 3 years ago

10.1016/j.xcrm.2021.100398

Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia
Cited by: 35
Author(s): Atsushi Ueda, Shoji Shinkai, Hirotsugu Shiroma, Yu Taniguchi, Sayaka Tsuchida, Takahiro Kariya, Tomohiro Kawahara, Yodai Kobayashi, Noriyuki Kohda, Kazunari Ushida, Akihiko Kitamura, Takuji Yamada
Software Mentions: 3
Published: about 3 years ago

10.1186/s13148-021-01110-9

Altered DNA methylation pattern reveals epigenetic regulation of Hox genes in thoracic aortic dissection and serves as a biomarker in disease diagnosis
Cited by: 5
Author(s): Peiru Liu, Jing Zhang, Duo Du, Dandan Zhang, Zelin Jin, Qiu Wan-hua, Xinchen Zhou, Sujun Dong, Mengyu Zhou, Heyu Zhao, Wei Zhang, Jiakang Ma, Song Sun, Weiguo Fu, Yun Liu, Lixin Wang
Software Mentions: 3
Published: over 3 years ago

10.1007/s00784-016-1980-3

The mycobiome of root canal infections is correlated to the bacteriome
Cited by: 52
Author(s): I.F. Persoon, M.J. Buijs, A.R. Özok, Wim Crielaard, Bastiaan P. Krom, Egija Zaura, Bernd W. Brandt
Software Mentions: 3
Published: about 8 years ago

10.14309/ctg.0000000000000191

Gastric Microbiota in a Low–Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions
Cited by: 22
Author(s): Nelson Ndegwa, Alexander Ploner, Anders F. Andersson, Ulrika Zagai, Anna Andréasson, Michael Vieth, Nicholas J. Talley, Lars Agréus, Weimin Ye
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-020-01534-8

Temperature modulates stress response in mainstream anammox reactors
Cited by: 12
Author(s): Robert Niederdorfer, Damian Hausherr, Alejandro Palomo, Jing Wei, Paul Magyar, Barth F. Smets, Adriano Joss, Helmut Bürgmann
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-021-01841-8

Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut
Cited by: 1
Author(s): Christian Diener, Anna C. H. Hoge, Sean M. Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L. Moritz, Susan E. Erdman, Sean M. Gibbons
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-01988-4

The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering
Cited by: 24
Author(s): William L. King, Caylon F. Yates, Jing Guo, Suzanne M. Fleishman, Ryan V. Trexler, Michela Centinari, Terrence H. Bell, David M. Eissenstat
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-020-0822-7

Uncovering diversity and metabolic spectrum of animals in dead zone sediments
Cited by: 16
Author(s): Elias Broman, Stefano Bonaglia, Oleksandr Holovachov, Ugo Marzocchi, Per Hall, Francisco J. A. Nascimento
Software Mentions: 3
Published: over 4 years ago

10.1002/ece3.3121

Disentangling the genetic and morphological structure of Patella candei complex in Macaronesia (NE Atlantic)
Cited by: 10
Author(s): João Faria, Gustavo M. Martins, Alfonso Pita, Pedro A. Ribeiro, Stephen J. Hawkins, Pablo Presa, Ana I. Neto
Software Mentions: 3
Published: over 7 years ago

10.1002/ece3.4170

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea
Cited by: 73
Author(s): Sherlyn Tipayno, Jaak Truu, Sandipan Samaddar, Marika Truu, Jens‐Konrad Preem, Kristjan Oopkaup, Mikk Espenberg, Poulami Chatterjee, Young Kee Kang, Kiyoon Kim, Tongmin Sa
Software Mentions: 3
Published: over 6 years ago

10.1038/s41426-018-0097-y

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia
Cited by: 22
Author(s): Wenkui Dai, Heping Wang, Qian Zhou, Xin Feng, Zhiwei Lü, Dongfang Li, Zhenyu Yang, Yanhong Liu, Yinhu Li, Guoli Xie, Kunling Shen, Yonghong Yang, Yuejie Zheng, Shuai Cheng Li
Software Mentions: 3
Published: over 6 years ago

10.1007/s00267-017-0889-1

Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices
Cited by: 30
Author(s): James C. White, Matthew J. Hill, Melanie A. Bickerton, Paul J. Wood
Software Mentions: 3
Published: over 7 years ago

10.1111/1462-2920.15024

Microbial community development on model particles in the deep sulfidic waters of the Black Sea
Cited by: 9
Author(s): Saara Suominen, Karlijn Doorenspleet, Jaap S. Sinninghe Damsté, Laura Villanueva
Software Mentions: 3
Published: over 4 years ago

10.1111/1462-2920.14913

Extremely halophilic archaeal communities are resilient to short‐term entombment in halite
Cited by: 12
Author(s): Tom J. C. Huby, Dave R. Clark, Boyd A. McKew, Terry J. McGenity
Software Mentions: 3
Published: almost 5 years ago

10.1111/1462-2920.14043

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments
Cited by: 197
Author(s): Stephanie A. Eichorst, Daniela Trojan, Simon Roux, Craig W. Herbold, Thomas Rattei, Dagmar Woebken
Software Mentions: 3
Published: over 6 years ago

10.1111/1462-2920.15232

Putative degraders of low‐density polyethylene‐derived compounds are ubiquitous members of plastic‐associated bacterial communities in the marine environment
Cited by: 14
Author(s): Maria Pinto, Paula Polania Zenner, Teresa M. Langer, Jesse Patrick Harrison, Meinhard Simon, Marta M. Varela, Gerhard J. Herndl
Software Mentions: 3
Published: about 4 years ago

10.1111/1462-2920.14882

Structure and ecological function of the soil microbiome affecting plant–soil feedbacks in the presence of a soil‐borne pathogen
Cited by: 33
Author(s): S. Emilia Hannula, Hui Ma, Juan E. Pérez‐Jaramillo, Ana Pineda, T. Martijn Bezemer
Software Mentions: 3
Published: almost 5 years ago

10.1186/s40793-021-00383-0

Changes in the root-associated bacteria of sorghum are driven by the combined effects of salt and sorghum development
Cited by: 17
Author(s): Yukun Gao, Jianghui Cui, Ge Ren, Wei Shilin, Yang Puyuan, Congpei Yin, Liang Hongkai, Chang Jin-hua
Software Mentions: 3
Published: over 3 years ago

10.1186/s40793-019-0347-1

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
Cited by: 58
Author(s): Hyun S. Gweon, Liam P. Shaw, Jeremy Swann, Nicola De Maio, Manal AbuOun, René Niehus, Alasdair T. M. Hubbard, Michael J. Bowes, Mark Bailey, Tim Peto, Sarah Hoosdally, A Sarah Walker, Robert Sebra, Derrick W. Crook, Muna F. Anjum, Daniel S. Read, Nicole Stoesser
Software Mentions: 3
Published: about 5 years ago

10.1007/s11356-018-3765-5

Inter-species and inter-colony differences in elemental concentrations in eggshells of sympatrically nesting great cormorants Phalacrocorax carbo and grey herons Ardea cinerea
Cited by: 2
Author(s): Dariusz Jakubas, Ignacy Kitowski, Dariusz Wiącek, Szymon Bzoma
Software Mentions: 3
Published: about 6 years ago

10.1111/eva.12658

Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods
Cited by: 30
Author(s): Camille Lavoie, Maxime Courcelle, Baptise Redivo, Nicolas Derôme
Software Mentions: 3
Published: over 6 years ago

10.1007/s10493-018-0314-3

Response of soil mites (Acari, Mesostigmata) to long-term Norway spruce plantation along a mountain stream
Cited by: 10
Author(s): Jacek Kamczyc, Maciej Skorupski, Marcin K. Dyderski, Anna Gazda, Mariusz Hachułka, Paweł Horodecki, Izabela Kałucka, Marek Malicki, Remigiusz Pielech, Michał Smoczyk, Sylwia Wierzcholska, Andrzej M. Jagodziński
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.9227.2

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
Cited by: 86
Author(s): Javier Ramiro-García, Gerben D. A. Hermes, Christos Giatsis, Detmer Sipkema, Erwin G. Zoetendal, Peter J. Schaap, Hauke Smidt
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.27502.2

Inter-site and interpersonal diversity of salivary and tongue microbiomes, and the effect of oral care tablets
Cited by: 2
Author(s): Hugo Maruyama, Ayako Masago, Takayuki Nambu, Chiho Mashimo, Kazuya Takahashi, Toshinori Okinaga
Software Mentions: 3
Published: over 3 years ago

10.1093/femsec/fiaa163

Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure
Cited by: 19
Author(s): Ragnhild Inderberg Vestrum, Kari J.K. Attramadal, Ôlav Vadstein, Madeleine S. Gundersen, Ingrid Bakke
Software Mentions: 3
Published: over 4 years ago

10.1093/femsec/fiaa082

Vegetation type determines spore deposition within a forest–agricultural mosaic landscape
Cited by: 19
Author(s): Miguel Á. Redondo, Anna Berlin, Johanna Boberg, Jonàs Oliva
Software Mentions: 3
Published: over 4 years ago

10.1093/femsec/fiab022

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils
Cited by: 39
Author(s): Sunil Mundra, O. Janne Kjønaas, Luis Morgado, Anders K. Krabberød, Yngvild Ransedokken, Håvard Kauserud
Software Mentions: 3
Published: almost 4 years ago

10.1093/femsec/fix117

Assessing effects of the entomopathogenic fungus Metarhizium brunneum on soil microbial communities in Agriotes spp. biological pest control
Cited by: 25
Author(s): Johanna Mayerhofer, Sonja Eckard, Martin Hartmann, Giselher Grabenweger, Franco Widmer, Adrian Leuchtmann, Jürg Enkerli
Software Mentions: 3
Published: about 7 years ago

10.1016/j.foodhyd.2019.06.006

Changes in stool frequency following chicory inulin consumption, and effects on stool consistency, quality of life and composition of gut microbiota
Cited by: 31
Author(s): Anthony Watson, David Houghton, Peter Avery, Christopher J. Stewart, Elaine E. Vaughan, P Meyer, Minse J.J. de Bos Kuil, P.J.M. Weijs, Kirsten Brandt
Software Mentions: 3
Published: about 5 years ago

10.3390/foods10020362

Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage
Cited by: 16
Author(s): Aurélien Maillet, Pauline Denojean, Agnès Bouju-Albert, Erwan Scaon, Sébastien Leuillet, Xavier Dousset, Emmanuel Jaffrès, Jérôme Combrisson, Hervé Prévost
Software Mentions: 3
Published: almost 4 years ago

10.3390/foods10092040

Impact of Plant-Based Meat Alternatives on the Gut Microbiota of Consumers: A Real-World Study
Cited by: 36
Author(s): Miguel Toribio-Mateas, Adri Bester, Natalia Klimenko
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2016.00476

Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin
Cited by: 76
Author(s): Francesco Paolo Mancuso, Sofie D’hondt, Anne Willems, Laura Airoldi, Olivier De Clerck
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2018.01998

Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)
Cited by: 14
Author(s): Margaret Mars Brisbin, Lisa Y. Mesrop, Mary M. Grossmann, Satoshi Mitarai
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.674556

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping
Cited by: 13
Author(s): Barbara Pivato, Amélie Semblat, Thibault Guégan, Samuel Jacquiod, Juliette Martin, Florence Deau, Nathalie Moutier, Christophe Lecomte, Judith Burstin, Philippe Lemanceau
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.02096

Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition
Cited by: 52
Author(s): Gulnaz T. Javan, Sheree J. Finley, Tasia M. Smith, Joselyn Miller, Jeremy E. Wilkinson
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2015.00729

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability
Cited by: 16
Author(s): Kathleen Merritt Brannen-Donnelly, Annette Summers Engel
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2018.02203

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics
Cited by: 9
Author(s): Pedro Milet Meirelles, Ana Carolina Soares, Louisi Souza de Oliveira, Luciana Leomil, Luciana Appolinario, Ronaldo B. Francini‐Filho, Rodrigo L. Moura, Renato Tenan de Barros Almeida, Paulo S. Salomon, Gilberto M. Amado‐Filho, Ricardo Henrique Krüger, Eduardo Siegle, Diogo A. Tschoeke, Isao Kudo, Sayaka Mino, Tomoo Sawabe, Cristiane C. Thompson, Fabiano L. Thompson
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2020.01772

Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai–Tibetan Lakes
Cited by: 15
Author(s): Jiangen Huang, Jian Yang, Hongchen Jiang, Geng Wu, Wen Li, Beichen Wang, Haiyi Xiao, Jibin Han
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.01758

Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity
Cited by: 17
Author(s): Marta Agostinelli, Michelle Cleary, Juan A. Martín, Benedicte Riber Albrectsen, Johanna Witzell
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.03226

Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities
Cited by: 10
Author(s): Laurence J. Clarke, Léonie Suter, Robert A. King, Andrew Bissett, Bruce E. Deagle
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2019.01743

Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group
Cited by: 27
Author(s): Liliane Costa Conteville, Joseli Oliveira-Ferreira, Ana Carolina Paulo Vicente
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.00930

Water Treatment Effect, Microbial Community Structure, and Metabolic Characteristics in a Field-Scale Aquaculture Wastewater Treatment System
Cited by: 17
Author(s): Zhifei Li, Ermeng Yu, Kai Zhang, Wangbao Gong, Yun Xia, Jingjing Tian, Guangjun Wang, Jun Xie
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.02836

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System
Cited by: 45
Author(s): Jennifer Bachmann, Tabea Heimbach, Christiane Hassenrück, Gérmán A. Kopprio, Morten Hvitfeldt Iversen, Hans Peter Grossart, Astrid Gärdes
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2021.647089

Bacterial Communities Associated With Four Blooming Scyphozoan Jellyfish: Potential Species-Specific Consequences for Marine Organisms and Humans Health
Cited by: 7
Author(s): Saijun Peng, Hao Wu, Yongxue Li, Lei Wang, Tingting Sun, Jianmin Zhao, Zhibao Dong
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2020.00745

Gross N2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices
Cited by: 7
Author(s): Chang Yin, Xiaoping Fan, Guochao Yan, Hao Chen, Mujun Ye, Liang Ni, Hongxia Peng, Ran Wei, Yanfang Zhao, Tingqiang Li, Steve Wakelin, Yongchao Liang
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.01518

Fecal Microbiome Data Distinguish Liver Recipients With Normal and Abnormal Liver Function From Healthy Controls
Cited by: 18
Author(s): Haifeng Lü, Zhigang Ren, Ang Li, Hua Zhang, Shaoyan Xu, Jianwen Jiang, Lin Zhou, Qi Ling, Baohong Wang, Guangying Cui, Xinhua Chen, Shusen Zheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2018.01926

Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites
Cited by: 20
Author(s): Rhea Lumactud, Roberta R. Fulthorpe
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2015.01438

Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary
Cited by: 63
Author(s): Thomas C. Jeffries, Maria Luiza Schmitz Fontes, Donald D. Harrison, Virginie Van-Dongen-Vogels, Bradley D. Eyre, Peter J. Ralph, Justin R. Seymour
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2018.01562

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea
Cited by: 17
Author(s): Christoffer Berner, Mireia Bertos‐Fortis, Jarone Pinhassi, Catherine Legrand
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.02360

Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period
Cited by: 51
Author(s): Preethi Balan, Yap Seng Chong, Shivshankar Umashankar, Sanjay Swarup, Wong Mun Loke, Violeta Lopez, Hong He, Chaminda Jayampath Seneviratne
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2016.00092

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil
Cited by: 52
Author(s): François Thomas, Aurélie Cébron
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2019.01534

Effects of Hardwood Biochar on Methane Production, Fermentation Characteristics, and the Rumen Microbiota Using Rumen Simulation
Cited by: 35
Author(s): Rebecca Teoh, Eleonora Caro, Devin B. Holman, Stephen Joseph, S. J. Meale, Alex V. Chaves
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2015.00746

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils
Cited by: 19
Author(s): C. Ryan Penton, Derek St. Louis, Amanda Pham, James R. Cole, Liyou Wu, Yiqi Luo, E. A. G. Schuur, Jizhong Zhou, James M. Tiedje
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2018.02023

Vertical Distribution of Microbial Eukaryotes From Surface to the Hadal Zone of the Mariana Trench
Cited by: 34
Author(s): Zhimeng Xu, Min Wang, Wenxue Wu, Yifan Li, Qian Liu, Yuye Han, Hongbing Shao, Andrew McMinn, Hongbin Liu
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.572212

Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits
Cited by: 7
Author(s): Wang Shi, Robert Walker, Marcus Schicklberger, Peter Nico, Patricia Fox, Ulaş Karaöz, Romy Chakraborty, Eoin L. Brodie
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2018.00076

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques
Cited by: 29
Author(s): Anna Gałązka, Jarosław Grządziel
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2019.00212

Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life
Cited by: 9
Author(s): Aurélie Allemann, Julia G. Kraemer, Insa Korten, Kathryn Ramsey, Carmen Casaulta, Daniel Wüthrich, Alban Ramette, Andrea Endimiani, Philipp Latzin, Markus Hilty
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmicb.2015.01532

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients
Cited by: 22
Author(s): Tom V. Joss, Catherine Burke, Bernard Hudson, Aaron E. Darling, Martin Forer, Dagmar Alber, Ian G. Charles, Nicholas W. Stow
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2020.592248

Gut Microbial Dysbiosis and Plasma Metabolic Profile in Individuals With Vitiligo
Cited by: 19
Author(s): Qingrong Ni, Zhubiao Ye, Yinghan Wang, Jianru Chen, Weigang Zhang, Cuiling Ma, Kai Li, Yu Liu, Ling Liu, Zheyi Han, Tianwen Gao, Zhe Jian, Shuli Li, Chunying Li
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.539921

Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff
Cited by: 18
Author(s): Rachelle E. Beattie, Aditya Bandla, Sanjay Swarup, Krassimira R. Hristova
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2021.723649

Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues
Cited by: 5
Author(s): William L. King, Mirjam Kaestli, Nachshon Siboni, Anna Padovan, Keith A. Christian, David K. Mills, Justin R. Seymour, Karen S. Gibb
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2016.01533

Coupling Bacterioplankton Populations and Environment to Community Function in Coastal Temperate Waters
Cited by: 13
Author(s): Sachia J. Traving, Mikkel Bentzon-Tilia, Helle Knudsen-Leerbeck, Mustafa Mantikçi, Jørgen L.S. Hansen, Colin A. Stedmon, Helle Sørensen, Stiig Markager, Lasse Riemann
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.02614

Profiling of Protein Degraders in Cultures of Human Gut Microbiota
Cited by: 67
Author(s): Alberto Amaretti, Caterina Gozzoli, Marta Simone, Stefano Raimondi, Lucia Righini, Vicente Pérez‐Brocal, Rodrigo García-López, Andrés Moya, Maddalena Rossi
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2017.02670

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity
Cited by: 44
Author(s): Bing Huang, Chun Wen Chang, Chih-Wei Huang, Jian Gao, Pei Chun Liao
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2021.667832

Nasal and Fecal Microbiota and Immunoprofiling of Infants With and Without RSV Bronchiolitis
Cited by: 8
Author(s): Claudio Alba, Marina Aparicio, Felipe González‐Martínez, María-Isabel González-Sánchez, Jimena Pérez-Moreno, Blanca Toledo del Castillo, Juan Miguel Díaz Rodríguez, Rosa Rodríguez‐Fernández, Leónides Fernández
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2018.02606

Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach
Cited by: 36
Author(s): Valerie De Anda, Icoquih Zapata‐Peñasco, Jazmín Blaz, Augusto César Poot-Hernández, Bruno Contreras‐Moreira, Marcos González-Laffitte, Niza Gámez-Tamariz, Maribel Hernández-Rosales, Luis E. Eguiarte, Valeria Souza
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2018.01752

Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC)
Cited by: 61
Author(s): David J. Smith, Jayamary Divya Ravichandar, Sunit Jain, Dale W. Griffin, Hongbin Yu, Qian Tan, James B. Thissen, Terry C. Lusby, Patrick Nicoll, Sarah Shedler, Paul Martinez, Alejandro Zarur Osorio, Jason A. Lechniak, Samuel Choi, Kayleen Sabino, Kathryn Iverson, Luisa Chan, Crystal Jaing, John W. McGrath
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2019.02576

Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale
Cited by: 23
Author(s): Zhimin Zhang, Dapeng Li, Weigang Xu, Rong Tang, Li Li
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.586050

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial
Cited by: 13
Author(s): Robin Raveau, Joël Fontaine, Mohamed Hijri, Anissa Lounès-Hadj Sahraoui
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2018.01815

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios
Cited by: 63
Author(s): Yingying Ni, Teng Yang, Kaoping Zhang, Congcong Shen, Haiyan Chu
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2020.615659

Regional Diversity of Maritime Antarctic Soil Fungi and Predicted Responses of Guilds and Growth Forms to Climate Change
Cited by: 13
Author(s): Kevin K. Newsham, Marie L. Davey, D. W. Hopkins, Paul G. Dennis
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2021.642587

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria
Cited by: 18
Author(s): Tessa E. Reid, Vanessa Nessner Kavamura, Maïder Abadie, Adriana Torres-Ballesteros, Mark Pawlett, Ian M. Clark, J. Arthur Harris, Tim H. Mauchline
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2019.01661

Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland
Cited by: 22
Author(s): Wen Tian, Hongmei Wang, Xiang Xiao, Ruicheng Wang, Ying Xu
Software Mentions: 3
Published: over 5 years ago

10.3389/fvets.2016.00002

Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity
Cited by: 204
Author(s): Anne Ballou, Rizwana Ali, Mary Mendoza, J. Christopher Ellis, Hosni M. Hassan, W. J. Croom, Matthew D. Koci
Software Mentions: 3
Published: almost 9 years ago

10.3389/fvets.2020.00331

Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase
Cited by: 9
Author(s): Bishnu Adhikari, Se‐Ran Jun, Young Min Kwon, Aaron S. Kiess, Pratima Adhikari
Software Mentions: 3
Published: over 4 years ago

10.3389/fvets.2021.692521

Oral Vaccination Reduces the Effects of Lawsonia intracellularis Challenge on the Swine Small and Large Intestine Microbiome
Cited by: 2
Author(s): Fernando Leite, Brittanie Winfield, Elizabeth A. Miller, Bonnie Weber, Timothy J. Johnson, Fred Sylvia, Erika Vasquez, Fábio A. Vannucci, Dana Beckler, Richard E. Isaacson
Software Mentions: 3
Published: over 3 years ago

10.3389/fvets.2020.596933

Comprehensive Survey of the Litter Bacterial Communities in Commercial Turkey Farms
Cited by: 7
Author(s): Bishnu Adhikari, Guillermo Téllez–Isaías, Tieshan Jiang, Brian Wooming, Young Min Kwon
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12983-021-00427-8

Multiple phenotypic traits as triggers of host attacks towards ant symbionts: body size, morphological gestalt, and chemical mimicry accuracy
Cited by: 10
Author(s): Christoph von Beeren, Adrian Brückner, Philipp O. Hoenle, Bryan Ospina-Jara, Daniel J. C. Kronauer, Nico Blüthgen
Software Mentions: 3
Published: about 3 years ago

10.1111/1365-2435.12977

Cumulative stress restricts niche filling potential of habitat‐forming kelps in a future climate
Cited by: 20
Author(s): Nathan G. King, David Wilcockson, Richard Webster, Dan A. Smale, Laura Sophie Hoelters, Pippa J. Moore
Software Mentions: 3
Published: about 7 years ago

10.1016/j.funeco.2016.05.007

Biocontrol agent Fusarium oxysporum f.sp. strigae has no adverse effect on indigenous total fungal communities and specific AMF taxa in contrasting maize rhizospheres
Cited by: 15
Author(s): Judith Zimmermann, Mary K. Musyoki, Georg Cadisch, Frank Rasche
Software Mentions: 3
Published: about 8 years ago

10.3390/genes11080904

The Gut Microbiota Profile in Children with Prader–Willi Syndrome
Cited by: 17
Author(s): Ye Peng, Qiming Tan, Shima Afhami, Edward C. Deehan, Suisha Liang, Marie G. Gantz, Lucila Triador, Karen Madsen, Jens Walter, Hein Min Tun, Andrea M. Haqq
Software Mentions: 3
Published: over 4 years ago

10.3390/genes11091105

Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
Cited by: 44
Author(s): Astrid P. Heikema, Deborah Horst-Kreft, Stefan A. Boers, Rick Jansen, Saskia Hiltemann, Willem de Koning, Robert Kraaij, Maria A. J. de Ridder, Chantal B. van Houten, Louis Bont, Andrew Stubbs, John P. Hays
Software Mentions: 3
Published: about 4 years ago

10.3390/genes11111380

Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method
Cited by: 8
Author(s): Tasha M. Santiago-Rodríguez, Aaron Garoutte, Emmase Adams, Waleed Nasser, Matthew C. Ross, Alex La Reau, Zachariah Henseler, Tonya Ward, Dan Knights, Joseph F. Petrosino, Emily B. Hollister
Software Mentions: 3
Published: about 4 years ago

10.1186/gb-2013-14-1-r4

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
Cited by: 354
Author(s): Falk Hildebrand, Thi Loan Anh Nguyen, Brigitta M. N. Brinkman, Roberto Garcia Yunta, Bénédicte Cauwe, Peter Vandenabeele, Adrian Liston, Jeroen Raes
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-019-1807-z

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny
Cited by: 49
Author(s): Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony L. Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andrés Gómez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh, Rob Knight
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-021-02418-8

2dFDR: a new approach to confounder adjustment substantially increases detection power in omics association studies
Cited by: 2
Author(s): Sangyoon Yi, Xianyang Zhang, Lu Yang, Jinyan Huang, Yuanhang Liu, Chen Wang, Daniel J. Schaid, Jun Chen
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-016-0290-3

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions
Cited by: 255
Author(s): Nielson T. Baxter, Mack T. Ruffin, Mary A.M. Rogers, Patrick D. Schloss
Software Mentions: 3
Published: over 8 years ago

10.1186/s13073-016-0368-y

Potential contribution of the uterine microbiome in the development of endometrial cancer
Cited by: 211
Author(s): Marina Walther-Antonio, Jun Chen, Francesco Multinu, Alexis N. Hokenstad, Tammy J. Distad, Elizabeth Cheek, Gary L. Keeney, Douglas J. Creedon, Heidi Nelson, Andrea Mariani, Nicholas Chia
Software Mentions: 3
Published: about 8 years ago

10.1186/s13073-020-00758-x

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans
Cited by: 18
Author(s): Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt, Georg K. Gerber
Software Mentions: 3
Published: over 4 years ago

10.1016/j.geoderma.2020.114474

Mineral–nutrient relationships in African soils assessed using cluster analysis of X-ray powder diffraction patterns and compositional methods
Cited by: 22
Author(s): Benjamin Butler, Javier Palarea‐Albaladejo, Keith D. Shepherd, Kamau M. Nyambura, Erick K. Towett, Andrew Sila, S. J. Hillier
Software Mentions: 3
Published: about 4 years ago

10.1186/s13742-015-0086-1

Evaluating a multigene environmental DNA approach for biodiversity assessment
Cited by: 118
Author(s): Alexei J. Drummond, Richard D. Newcomb, Thomas R. Buckley, Donghua Xie, Andrew Dopheide, Benjamin C. M. Potter, Joseph Heled, Howard A. Ross, Leah Tooman, Stefanie Grosser, Duckchul Park, Nicholas J. Demetras, Mark I. Stevens, James C. Russell, Sandra Anderson, Anna Carter, Nicola J. Nelson
Software Mentions: 3
Published: about 9 years ago

10.1080/19490976.2020.1788898

TH1 cell-inducing Escherichia coli strain identified from the small intestinal mucosa of patients with Crohn’s disease
Cited by: 35
Author(s): Shiho Nagayama, Tomonori Yano, Koji Atarashi, Takeshi Tanoue, Mariko Sekiya, Yasutoshi Kobayashi, Hirotsugu Sakamoto, Kouichi Miura, Keijiro Sunada, Takaaki Kawaguchi, Satoru Morita, Kayoko Sugita, Seiko Narushima, Nicolas Barnich, Jun Isayama, Yuko Kiridooshi, Atsushi Shiota, Wataru Suda, Masahira Hattori, Hironori Yamamoto, Kenya Honda
Software Mentions: 3
Published: over 4 years ago

10.1080/19490976.2020.1862027

Changes in IgA-targeted microbiota following fecal transplantation for recurrent Clostridioides difficile infection
Cited by: 11
Author(s): Kelsey E. Huus, Marcin Frankowski, Maja Pučić‐Baković, Frano Vučković, Gordan Lauc, Benjamin H. Mullish, Julian R. Marchesi, Tanya Monaghan, Dina Kao, B. Brett Finlay
Software Mentions: 3
Published: almost 4 years ago

10.1080/19490976.2020.1830699

Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice
Cited by: 5
Author(s): Wenjun Liu, Zheng Sun, Castello Ma, Jiachao Zhang, Chenchen Ma, Yinjian Zhao, Hong Wei, Shi Huang, Heping Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-32529-5

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments
Cited by: 60
Author(s): Man Kit Cheung, Carmen Wong, Ka Hou Chu, Hoi Shan Kwan
Software Mentions: 3
Published: about 6 years ago

Projects: cran: PERMANOVA

Papers Mentioning PERMANOVA 6,292