bioconductor: phyloseq | Projects

10.1186/s12866-021-02099-0

The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice
Cited by: 41
Author(s): Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, W.H. Wilson Tang, Lee S, Seong‐Tshool Hong, Seungkoo Lee
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.01614

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)
Cited by: 7
Author(s): Pamela M. Smith, Sinéad M. Waters, David A. Kenny, T. M. Boland, J. S. Heffernan, A. K. Kelly
Software Mentions: 5
Published: about 6 years ago

10.3390/microorganisms9051033

Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other
Cited by: 9
Author(s): A. K. Eskov, Aleksei Zverev, Evgeny Abakumov
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9010064

Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap
Cited by: 8
Author(s): Maija Nuppunen-Puputti, Riikka Kietäväinen, Lotta Purkamo, Pauliina Rajala, Merja Itävaara, Ilmo Kukkonen, Malin Bomberg
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2018.01561

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations
Cited by: 16
Author(s): Even Sannes Riiser, Thomas Haverkamp, Ørnulf Borgan, Kjetill S. Jakobsen, Sissel Jentoft, Bastiaan Star
Software Mentions: 5
Published: over 8 years ago

10.1128/mSphere.00308-21

Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds
Cited by: 17
Author(s): Kangpeng Xiao, Yutan Fan, Zhipeng Zhang, Xuejuan Shen, Xiaobing Li, Xianghui Liang, Ran Bi, Yuling Wu, Junqiong Zhai, Jun-Wei Dai, David M. Irwin, Chen Wu, Yongyi Shen
Software Mentions: 5
Published: over 5 years ago

10.1128/mSystems.00132-17

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
Cited by: 18
Author(s): Elin Videvall, Maria Strandh, Anel Engelbrecht, S.W.P. Cloete, Charlie K. Cornwallis
Software Mentions: 5
Published: almost 9 years ago

10.1128/mSphere.00189-17

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder
Cited by: 11
Author(s): Vincent J. Denef, Hunter J. Carrick, Joann F. Cavaletto, Edna Chiang, Thomas H. Johengen, Henry A. Vanderploeg
Software Mentions: 5
Published: over 9 years ago

10.1186/s42523-021-00084-6

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis
Cited by: 5
Author(s): Adrian Muwonge, Anbu K. Karuppannan, Tanja Opriessnig
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9040845

Impact of Chronic Exposure to Sublethal Doses of Glyphosate on Honey Bee Immunity, Gut Microbiota and Infection by Pathogens
Cited by: 29
Author(s): Loreley Castelli, Sofía Balbuena, Belén Branchiccela, Pablo Zunino, Joanito Liberti, Philipp Engel, Karina Antúnez
Software Mentions: 5
Published: over 5 years ago

10.1002/mbo3.1231

Marine biofilms on different fouling control coating types reveal differences in microbial community composition and abundance
Cited by: 16
Author(s): Maria Papadatou, Samuel Robson, Sergey Dobretsov, Joy E. M. Watts, Jennifer Longyear, Maria Salta
Software Mentions: 5
Published: about 5 years ago

10.1002/mbo3.1133

A low‐cost pipeline for soil microbiome profiling
Cited by: 5
Author(s): Anita Bollmann‐Giolai, Michael Giolai, Darren Heavens, Iain C. Macaulay, Jacob G. Malone, Matt Clark
Software Mentions: 5
Published: almost 6 years ago

10.1002/mbo3.681

Do composition and diversity of bacterial communities and abiotic conditions of spring water reflect characteristics of groundwater ecosystems exposed to different agricultural activities?
Cited by: 4
Author(s): Karsten Karczewski, Patricia Göbel, Elisabeth I. Meyer
Software Mentions: 5
Published: over 8 years ago

10.1002/ece3.5789

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species ( Sciurus aberti and S. niger ) living in sympatry
Cited by: 5
Author(s): Andrew Joseph Reed, Jon C. Pigage, Helen K. Pigage, Cody Glickman, Jeremy M. Bono
Software Mentions: 5
Published: almost 7 years ago

10.1128/mSystems.00087-17

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity
Cited by: 43
Author(s): Isabelle Laforest‐Lapointe, Christian Messier, Steven W. Kembel
Software Mentions: 5
Published: almost 9 years ago

10.3390/microorganisms7120598

Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China
Cited by: 24
Author(s): Anyi Hu, Hongjie Wang, Meixian Cao, Abbas Rashid, Mingfeng Li, Chang‐Ping Yu
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2019.00256

Soil Macroinvertebrate Presence Alters Microbial Community Composition and Activity in the Rhizosphere
Cited by: 25
Author(s): Natalie Bray, Jenny Kao‐Kniffin, Serita D. Frey, Timothy J. Fahey, Kyle Wickings
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2020.595555

Antibiotic Treatment for Chronic Rhinosinusitis: Prescription Patterns and Associations With Patient Outcome and the Sinus Microbiota
Cited by: 16
Author(s): Christian A Lux, Brett Wagner Mackenzie, James Johnston, Melissa Zoing, Kristi Biswas, Michael W. Taylor, Richard Douglas
Software Mentions: 5
Published: almost 6 years ago

10.1128/mBio.00311-19

Gut Microbiota and Phytoestrogen-Associated Infertility in Southern White Rhinoceros
Cited by: 32
Author(s): Candace L. Williams, Alexis R. Ybarra, Ashley N. Meredith, Barbara S. Durrant, Christopher W. Tubbs
Software Mentions: 5
Published: over 7 years ago

10.1128/mBio.02637-20

Seed-Derived Microbial Colonization of Wild Emmer and Domesticated Bread Wheat ( Triticum dicoccoides and T. aestivum ) Seedlings Shows Pronounced Differences in Overall Diversity and Composition
Cited by: 34
Author(s): Ezgi Özkurt, M. Amine Hassani, Uğur Sesiz, Sven Künzel, Tal Dagan, Hakan Özkan, Eva H. Stukenbrock
Software Mentions: 5
Published: almost 6 years ago

10.3390/toxics9090215

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice
Cited by: 4
Author(s): Karen Chiu, Shah Tauseef Bashir, Lei Gao, Jessica Gutiérrez, María R C de Godoy, Jenny Drnevich, Christopher J. Fields, Isaac Cann, Jodi A. Flaws, Romana A. Nowak
Software Mentions: 5
Published: about 5 years ago

10.1264/jsme2.ME20153

Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2020.00966

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Kristina Ulrich, Regina Becker, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2018.00031

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes
Cited by: 37
Author(s): Kevin D’hoe, Lorenza Conterno, Francesca Fava, Gwen Falony, Sara Vieira-Silva, Joan Vermeiren, Kieran Tuohy, Jeroen Raes
Software Mentions: 5
Published: over 8 years ago

10.3390/microorganisms8060944

Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
Cited by: 48
Author(s): Ahmed Abdelfattah, Susan R. Whitehead, Dumitru Macarisin, Jia Liu, Erik Burchard, Shiri Freilich, Christopher Dardick, Samir Droby, Michael Wisniewski
Software Mentions: 5
Published: over 6 years ago

10.3390/ani9110970

Enzymatically Digested Food Waste Altered Fecal Microbiota But Not Meat Quality and Carcass Characteristics of Growing-Finishing Pigs
Cited by: 2
Author(s): Cynthia Jinno, Perot Saelao, Elizabeth A. Maga, Arthur S. King, Dan Morash, Steven M. Zicari, Xiang Yang, Yanhong Liu
Software Mentions: 5
Published: almost 7 years ago

10.1038/s42003-020-01477-0

Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models
Cited by: 9
Author(s): Nirosh D. Aluthge, Wesley A Tom, Alison Bartenslager, Thomas E. Burkey, Phillip S. Miller, Kelly D. Heath, Craig Kreikemeier-Bower, Hatem Kittana, Robert Schmaltz, Amanda E. Ramer‐Tait, Samodha C. Fernando
Software Mentions: 5
Published: almost 6 years ago

10.3390/microorganisms8030404

Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica
Cited by: 13
Author(s): Maria Monteiro, Mafalda S. Baptista, Joana Séneca, Luı́s Torgo, Charles K. Lee, S. Craig Cary, Catarina Magalhães
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-98549-w

Effect of functional oils or probiotics on performance and microbiota profile of newly weaned piglets
Cited by: 4
Author(s): Alexandre Maciel Vieira, Amanda Pires Sessin, Tatiany Aparecida Teixeira Soratto, Paula Gabriela da Silva Pires, Kátia Maria Cardinal, Glauber Wagner, Lucélia Hauptli, André Luís Ferreira Lima, Fabiano Dahlke, Diego Peres Netto, Priscila de Oliveira Moraes
Software Mentions: 5
Published: about 5 years ago

10.1002/ece3.7434

Tree diversity and functional leaf traits drive herbivore‐associated microbiomes in subtropical China
Cited by: 1
Author(s): Yang Li, Douglas Chesters, Ming‐Qiang Wang, Tesfaye Wubet, Andreas Schuldt, Perttu Anttonen, Pengfei Guo, Jing‐Ting Chen, Qianxiong Zhou, Nai‐Li Zhang, Keping Ma, Helge Bruelheide, Chunsheng Wu, Chao‐Dong Zhu
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2021.683685

Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries
Cited by: 13
Author(s): Vivianne Cruz de Jesus, Mohd Wasif Khan, Betty-Anne Mittermuller, Kangmin Duan, Pingzhao Hu, Robert J Schroth, Prashen Chelikani
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-02372-y

Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Cited by: 9
Author(s): Fatemeh Ostadhossein, Parikshit Moitra, Esra Altun, Debapriya Dutta, Dinabandhu Sar, Indu Tripathi, Shih Hsuan Hsiao, Valeriya Kravchuk, Shuming Nie, Dipanjan Pan
Software Mentions: 5
Published: over 5 years ago

10.3390/microorganisms9030641

A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome
Cited by: 4
Author(s): Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Ignacio Cabrera-Aguilera, Isaac Almendros, Ramón Farré, David Gozal, Núria Farré, Toni Gabaldón
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.00481

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
Cited by: 40
Author(s): Gregory Bonito, Gian Maria Niccolò Benucci, Khalid Hameed, Deborah Weighill, Piet Jones, Ko‐Hsuan Chen, Daniel Jacobson, Christopher W. Schadt, Rytas Vilgalys
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-021-97619-3

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps)
Cited by: 13
Author(s): Kleopatra Leontidou, Despoina Vokou, Anna Sandionigi, Antonia Bruno, Maria Lazarina, Johannes De Groeve, Mingai Li, Claudio Varotto, Matteo Girardi, Andrea Galimberti, Alessandro Cristofori
Software Mentions: 5
Published: about 5 years ago

10.3390/microorganisms8071073

Maturational Changes Alter Effects of Dietary Phytase Supplementation on the Fecal Microbiome in Fattening Pigs
Cited by: 7
Author(s): Barbara U. Metzler‐Zebeli, Jutamat Klinsoda, Julia Vötterl, Doris Verhovsek
Software Mentions: 5
Published: about 6 years ago

10.1016/j.cmet.2020.03.003

Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells
Cited by: 247
Author(s): Elizabeth C. Rosser, Christopher Piper, Diana E. Matei, Paul A. Blair, André F. Rendeiro, Michael Orford, Dagmar Alber, Thomas Krausgruber, Diego Catalán, Nigel Klein, Jessica Manson, Ignat Drozdov, Christoph Bock, Lucy R. Wedderburn, Simon Eaton, Claudia Mauri
Software Mentions: 5
Published: over 6 years ago

10.1186/s42523-021-00080-w

The skin microbiome of Xenopus laevis and the effects of husbandry conditions
Cited by: 7
Author(s): Maya Z. Piccinni, Joy E. M. Watts, Marie Fourny, Matthew Guille, Samuel Robson
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers12030628

tRNA Queuosine Modification Enzyme Modulates the Growth and Microbiome Recruitment to Breast Tumors
Cited by: 35
Author(s): Jilei Zhang, Rong Lü, Yongguo Zhang, Żaneta Matuszek, Wen Zhang, Yinglin Xia, Tao Pan, Jun Sun
Software Mentions: 5
Published: over 6 years ago

10.1007/s00248-019-01412-9

Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature
Cited by: 32
Author(s): Jonas Frankel-Bricker, Michael Song, Maia J. Benner, Sarah Schaack
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0243609

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data
Cited by: 6
Author(s): Yi An Chen, Jonguk Park, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Attayeb Mohsen, Koji Hosomi, Kumpei Tanisawa, Harumi Ohno, Kana Konishi, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-021-94761-w

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica
Cited by: 3
Author(s): Lavinia Iancu, Iulia Roxana Angelescu, Victoria Ioana Paun, Carlos Henríquez‐Castillo, Paris Lavín, Cristina Purcărea
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2017.00655

Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Cited by: 66
Author(s): Guillermo Marcial, Amanda Ford, Michael J. Haller, Salvador A. Gezan, Natalie A. Harrison, David Cai, Julie Meyer, Daniel J. Perry, Mark A. Atkinson, Clive Wasserfall, Timothy J. Garrett, Claudio F. González, Todd M. Brusko, Wendy J. Dahl, Graciela L. Lorca
Software Mentions: 5
Published: over 9 years ago

10.3389/fmicb.2020.00582

Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes
Cited by: 12
Author(s): Sainur Samad, Hyo‐Jung Lee, Sławek Cerbin, Marion Meima-Franke, Paul L. E. Bodelier
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-84497-y

Gut microbiota resilience in horse athletes following holidays out to pasture
Cited by: 15
Author(s): Núria Mach, Léa Lansade, David Bars-Cortina, Sophie Dhorne–Pollet, Aline Foury, Marie‐Pierre Moisan, Alice Ruet
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.5228

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats
Cited by: 51
Author(s): Melissa R. Ingala, Daniel J. Becker, Jacob Bak Holm, Karsten Kristiansen, Nancy B. Simmons
Software Mentions: 5
Published: over 7 years ago

10.3390/microorganisms9071374

The Microbiome Associated with the Reef Builder Neogoniolithon sp. in the Eastern Mediterranean
Cited by: 2
Author(s): Shany Gefen-Treves, Alexander Bartholomäus, Fabian Horn, Adam Boleslaw Zaborowski, Dan Tchernov, Dirk Wagner, Aharon Oren, Aaron Kaplan
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.01429

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient
Cited by: 72
Author(s): Nadine Praeg, Harald Pauli, Paul Illmer
Software Mentions: 5
Published: over 7 years ago

10.1111/ele.13082

Linking phytoplankton community metabolism to the individual size distribution
Cited by: 20
Author(s): Daniel Padfield, Angus Buckling, Ruth Warfield, Chris D. Lowe, Gabriel Yvon‐Durocher
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 7 years ago

10.3390/microorganisms9081711

Microbial Shift in the Enteric Bacteriome of Coral Reef Fish Following Climate-Driven Regime Shifts
Cited by: 6
Author(s): Marie-Charlotte Cheutin, Sébastien Villéger, Christina C. Hicks, James P. W. Robinson, Nicholas A. J. Graham, Clémence Marconnet, Claudia Ximena Ortiz Restrepo, Yvan Bettarel, Thierry Bouvier, Jean‐Christophe Auguet
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2020.01075

Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System
Cited by: 18
Author(s): Linta Reji, Bradley B. Tolar, Francisco P. Chávez, Christopher A. Francis
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2019.02883

Diversity-Stability Dynamics of the Amphibian Skin Microbiome and Susceptibility to a Lethal Viral Pathogen
Cited by: 37
Author(s): Xavier A. Harrison, Stephen J. Price, Kevin Hopkins, William T. M. Leung, Chris Sergeant, Trenton W. J. Garner
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-020-80557-x

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)
Cited by: 33
Author(s): Esteban Góngora, Kyle H. Elliott, Lyle G. Whyte
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcimb.2019.00339

Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses
Cited by: 17
Author(s): Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, Marcos Pérez‐Losada
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-020-68933-z

Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing
Cited by: 14
Author(s): Daisuke Tanaka, So Fujiyoshi, Fumito Maruyama, Motoshi Goto, Shinichi Koyama, Jun-ichi Kanatani, Junko Isobe, Masanori Watahiki, Akihiro Sakatoku, Shigehiro Kagaya, Shōgo Nakamura
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-66178-4

Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis
Cited by: 5
Author(s): Shoichi Fukui, Shimpei Morimoto, Kunihiro Ichinose, Shota Nakashima, Hiroshi Ishimoto, Atsuko Hara, Tomoyuki Kakugawa, Noriho Sakamoto, Yoshika Tsuji, Toshiyuki Aramaki, Tomohiro Koga, Shin‐ya Kawashiri, Naoki Iwamoto, Mami Tamai, Hideki Nakamura, Tomoki Origuchi, Yukitaka Ueki, Shino Suzuki, Hiroshi Mukae, Atsushi Kawakami
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-69317-z

Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis
Cited by: 46
Author(s): Osvaldo Bogado Pascottini, Sabrina J. Van Schyndel, J. F. W. Sprícigo, Joyce D. Rousseau, J. Scott Weese, S.J. LeBlanc
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-65329-x

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase
Cited by: 9
Author(s): Max‐Bernhard Ballhausen, Rebecca E. Hewitt, Matthias C. Rillig
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-020-03838-2

Selected abstracts of “Bioinformatics: from Algorithms to Applications 2020” conference
Cited by: 3
Author(s): Robert J. Moore, Michael Barnathan, Brian Fristensky, Yán Li, Greg Knowles, Paul Gardner-Stephen, Angelo Bueti, Peter Anderson, Jianguang Qin, Andrew S. Ball
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2021.631244

Unravelling the Importance of Diazotrophy in Corals – Combined Assessment of Nitrogen Assimilation, Diazotrophic Community and Natural Stable Isotope Signatures
Cited by: 6
Author(s): Vanessa N. Bednarz, Jeroen A. J. M. van de Water, Renaud Grover, Jean‐François Maguer, Maoz Fine, Christine Ferrier‐Pagès
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-66028-3

Sward type alters the relative abundance of members of the rumen microbial ecosystem in dairy cows
Cited by: 7
Author(s): Pamela M. Smith, Daniel Enríquez-Hidalgo, Deirdre Hennessy, Matthew S. McCabe, David A. Kenny, A. K. Kelly, Sinéad M. Waters
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-70249-x

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Cited by: 5
Author(s): Tereza Matějková, Petra Hájková, Romana Stopková, Michał Stanko, Jean‐François Martin, Jakub Kreisinger, Pavel Stopka
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-57798-x

Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort
Cited by: 8
Author(s): Sabrina Rodriguez‐Campos, Ana Rostaher, Lena Zwickl, Nina Fischer, Isabelle Brodard, Sara Vidal, Bernd W. Brandt, Claude Favrot, Vincent Perreten
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.548618

Microbiome in Healthy Women Between Two Districts With Different Air Quality Index
Cited by: 8
Author(s): Yinhua Wu, Zujin Wang, Yu Zhang, Li-Ming Ruan, Ang Li, Xiaoyan Liu
Software Mentions: 5
Published: almost 6 years ago

10.3390/microorganisms8060906

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature
Cited by: 23
Author(s): Francisco Luis Massello, Chia Sing Chan, Kok Gan Chan, Kian Mau Goh, Edgardo R. Donati, María Sofía Urbieta
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2019.00496

Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities
Cited by: 6
Author(s): Pengfei Liu, Melanie Klose, Ralf Conrad
Software Mentions: 5
Published: over 7 years ago

10.1093/ajcn/nqab077

Associations of healthy food choices with gut microbiota profiles
Cited by: 33
Author(s): Kari K. Koponen, Aaro Salosensaari, Matti O. Ruuskanen, Aki S. Havulinna, Satu Männistö, Pekka Jousilahti, Joonatan Palmu, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Jon G. Sanders, Guillaume Méric, Susan Cheng, Michael Inouye, Mohit Jain, Teemu J. Niiranen, Liisa Valsta, Rob Knight, Veikko Salomaa
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-019-53623-2

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome
Cited by: 41
Author(s): Shijie Deng, Heidi M.-L. Wipf, Grady Pierroz, Theodore K. Raab, Rajnish Khanna, Devin Coleman‐Derr
Software Mentions: 5
Published: almost 7 years ago

10.3389/fmicb.2018.02121

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils
Cited by: 48
Author(s): Miguel Semedo, Bongkeun Song, Tavis Sparrer, R. Phillips
Software Mentions: 5
Published: about 8 years ago

10.1186/s12936-021-03624-2

Development of a new barcode-based, multiplex-PCR, next-generation-sequencing assay and data processing and analytical pipeline for multiplicity of infection detection of Plasmodium falciparum
Cited by: 2
Author(s): Rebecca Mitchell, Zhansong Zhou, Mili Sheth, Sheila B. Sergent, Michael Frace, Vishal Nayak, Bin Hu, John E. Gimnig, Feiko ter Kuile, Kim A. Lindblade, Laurence Slutsker, Mary J. Hamel, Meghna Desai, Kephas Otieno, Simon Kariuki, Ýmir Vigfússon, Ya Ping Shi
Software Mentions: 5
Published: over 5 years ago

10.1186/s42523-020-00058-0

Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides
Cited by: 1
Author(s): Bianca R. P. Brown, Joaquin C. B. Nunez, David M. Rand
Software Mentions: 5
Published: almost 6 years ago

10.1186/s40635-021-00398-4

Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis
Cited by: 8
Author(s): Nora S. Wolff, Max C. Jacobs, W. Joost Wiersinga, Floor Hugenholtz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0248654

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems
Cited by: 17
Author(s): Árpád Szilágyi, Attila Bodor, Norbert Tolvai, Kornél L. Kovács, László Bodai, Roland Wirth, Zoltán Bagi, Ágnes Szepesi, Viktória Markó, Balázs Kakuk, Naila Bounedjoum, Gábor Rákhely
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.02244

Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract
Cited by: 115
Author(s): Julie Meyer, Jessy Castellanos-Gell, Greta S. Aeby, Claudia C. Häse, Blake Ushijima, Valerie J. Paul
Software Mentions: 5
Published: about 7 years ago

10.3390/life11030246

Postoperative Complications Are Associated with Long-Term Changes in the Gut Microbiota Following Colorectal Cancer Surgery
Cited by: 7
Author(s): Felix C. F. Schmitt, Martin Schneider, William Mathejczyk, Markus A. Weigand, Jane C. Figueiredo, Christopher I. Li, David Shibata, Erin M. Siegel, Adetunji T. Toriola, Cornelia M. Ulrich, Alexis Ulrich, Sébastien Boutin, Biljana Gigic
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-64393-7

Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study
Cited by: 13
Author(s): Manuela de Oliveira Ramalho, Christophe Duplais, Jérôme Orivel, Alain Déjean, Joshua C. Gibson, Andrew V. Suarez, Corrie S. Moreau
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-021-04106-7

EzMAP: Easy Microbiome Analysis Platform
Cited by: 0
Author(s): Gnanendra Shanmugam, Song Hee Lee, Junhyun Jeon
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0215497

Gut microbiota features associated with Clostridioides difficile colonization in puppies
Cited by: 15
Author(s): Alexander S. F. Berry, Brendan J Kelly, Denise Barnhart, Douglas G. Kelly, Daniel P. Beiting, Robert N. Baldassano, Laurel E. Redding
Software Mentions: 5
Published: about 7 years ago

10.3390/insects10110391

Do Host Plant and Associated Ant Species Affect Microbial Communities in Myrmecophytes?
Cited by: 5
Author(s): Mario X. Ruiz-González, Céline Leroy, Alain Déjean, Hervé Gryta, Patricia Jargeat, Angelo D. Armijos Carrión, Jérôme Orivel
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0238764

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes
Cited by: 24
Author(s): Sahar Radwan, Darby Gilfillan, Bridget Eklund, Hend M. Radwan, Nagwan Galal El Menofy, Justin Lee, Marylee Kapuscinski, Zaid Abdo
Software Mentions: 5
Published: about 6 years ago

10.3390/microorganisms8020308

The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems
Cited by: 206
Author(s): Jesse R. Willis, Toni Gabaldón
Software Mentions: 5
Published: over 6 years ago

10.3390/brainsci11081085

Maternal Immune Activation Causes Social Behavior Deficits and Hypomyelination in Male Rat Offspring with an Autism-Like Microbiota Profile
Cited by: 29
Author(s): Gilbert Lee, Yen Kuang Lin, Jing Lai, Yu Chun Lo, Yu Yang, Syuan You Ye, Chia-Jung Lee, Ching Chiung Wang, Yung Hsiao Chiang, Sung Hui Tseng
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0194131

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata
Cited by: 55
Author(s): Antonino Malacrinò, Orlando Campolo, Raúl F. Medina, Vincenzo Palmeri
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2020.596589

The Transition From Stochastic to Deterministic Bacterial Community Assembly During Permafrost Thaw Succession
Cited by: 24
Author(s): Stacey J. Doherty, Robyn A. Barbato, A. Stuart Grandy, W. Kelley Thomas, Sylvain Monteux, Ellen Dorrepaal, Margareta Johansson, Jessica G. Ernakovich
Software Mentions: 5
Published: almost 6 years ago

10.3390/microorganisms9051054

Microbial Sharing between Pediatric Patients and Therapy Dogs during Hospital Animal-Assisted Intervention Programs
Cited by: 7
Author(s): Kathryn R. Dalton, Kathy Ruble, Laurel E. Redding, Daniel O. Morris, Noel T. Mueller, Roland J. Thorpe, Jacqueline Agnew, Karen C. Carroll, Paul J. Planet, Ronald C. Rubenstein, Allen Chen, Elizabeth A. Grice, Meghan F. Davis
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2020.01541

Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida)
Cited by: 15
Author(s): Justyna J. Hampel, Mark J. McCarthy, Sanni L. Aalto, Silvia E. Newell
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0243395

The applicability of forensic time since death estimation methods for buried bodies in advanced decomposition stages
Cited by: 21
Author(s): Stefan Pittner, Valentina Bugelli, M. Eric Benbow, Bianca Ehrenfellner, Angela Zissler, Carlo Pietro Campobasso, Roelof‐Jan Oostra, Maurice C. G. Aalders, Richard Zehner, Lena Lutz, Fabio Monticelli, Christian Staufer, Katharina Helm, Vilma Pinchi, Joseph P. Receveur, Janine Geißenberger, Peter Steinbacher, Jens Amendt
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcimb.2018.00301

Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies
Cited by: 105
Author(s): Zheng Wang, Christine P. Zolnik, Yunping Qiu, Mykhaylo Usyk, Tao Wang, Howard D. Strickler, Carmen R. Isasi, Robert C. Kaplan, Irwin J. Kurland, Qibin Qi, Robert D. Burk
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2021.629449

Diversity of Weissella confusa in Pozol and Its Carbohydrate Metabolism
Cited by: 5
Author(s): Diana Hernández-Oaxaca, Rafael López-Sánchez, Luis Lozano, Carmen Wacher, Lorenzo Segovia, Agustín López Munguía
Software Mentions: 5
Published: over 5 years ago

10.1093/gigascience/giy054

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
Cited by: 82
Author(s): Alexandre Almeida, Alex L. Mitchell, Aleksandra Tarkowska, Alex Bateman
Software Mentions: 5
Published: over 8 years ago

10.3390/microorganisms8060905

First Detection of Paralytic Shellfish Toxins from Alexandrium pacificum above the Regulatory Limit in Blue Mussels (Mytilus galloprovincialis) in New South Wales, Australia
Cited by: 8
Author(s): Abanti Barua, Penelope Ajani, Rendy Ruvindy, H. Farrell, A. Zammit, Steve Brett, David R. Hill, Chowdhury Sarowar, Mona Hoppenrath, Shauna A. Murray
Software Mentions: 5
Published: over 6 years ago

10.1186/s13068-016-0652-5

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
Cited by: 56
Author(s): Jo De Vrieze, Leticia Regueiro, Ruben Props, Ramiro Vílchez-Vargas, Ruy Jáuregui, Dietmar H. Pieper, Juan M. Lema, Marta Carballa
Software Mentions: 5
Published: almost 10 years ago

10.1002/ece3.4518

Ecological patterns in the skin microbiota of frogs from tropical Australia
Cited by: 15
Author(s): Keith A. Christian, Chava L. Weitzman, Alea Rose, Mirjam Kaestli, Karen S. Gibb
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2019.01204

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria
Cited by: 22
Author(s): Laura Gómez‐Consarnau, David M. Needham, Peter K. Weber, Jed A. Fuhrman, Xavier Mayali
Software Mentions: 5
Published: over 7 years ago

10.1186/s40478-020-00988-5

Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimer’s disease
Cited by: 64
Author(s): Charlotte Mezö, Nikolaos Dokalis, Omar Mossad, Ori Staszewski, Jana Neuber, Bahtiyar Yılmaz, Daniel Schnepf, Mercedes Gomez de Agüero, Stephanie C. Ganal‐Vonarburg, Andrew J. Macpherson, Melanie Meyer‐Luehmann, Peter Staeheli, Thomas Blank, Marco Prinz, Daniel Erny
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2019.02118

Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)
Cited by: 20
Author(s): Elizabeth M. Reinhart, Benjamin J. Korry, Aislinn D. Rowan-Nash, Peter Belenky
Software Mentions: 5
Published: about 7 years ago

10.1128/AEM.02969-19

Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil
Cited by: 12
Author(s): Yuan Zhang, Xiuli Hao, Adriana M. García-Lemos, Inês Nunes, Mette Haubjerg Nicolaisen, Ole Nybroe
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1831-z

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity
Cited by: 83
Author(s): Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Álvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica Williams-Nguyen, Michael C. Wu, Kari E. North, Justin P. Shaffer, Christopher C. Sollecito, Qibin Qi, Carmen R. Isasi, Tao Wang, Rob Knight, Robert D. Burk
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-021-02401-3

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
Cited by: 18
Author(s): Enrique Zozaya‐Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah‐Jane Dawson
Software Mentions: 5
Published: over 5 years ago

Projects: bioconductor: phyloseq

Science Score: 75/100

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Papers Mentioning phyloseq 1,702