Ecosyste.ms: Papers

10.3389/fmicb.2018.03259

Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing
Cited by: 10
Author(s): Feipeng Wang, Yuyuan Xie, Wenxue Wu, Ping Sun, Lei Wang, Bangqin Huang
Software Mentions: 4
Published: almost 6 years ago

10.1128/mSphere.00562-20

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota
Cited by: 4
Author(s): L. Patrick Schenck, Joshua J.C. McGrath, Daphnée Lamarche, Martin R. Stämpfli, Dawn M. E. Bowdish, Michael G. Surette
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmed.2021.607255

Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds
Cited by: 9
Author(s): Aleksander Mahnič, Vesna Breznik, Maja Bombek Ihan, Maja Rupnik
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.647921

Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs
Cited by: 11
Author(s): Gabrielle Maria Fonseca Pierangeli, Mércia Regina Domingues, Tatiane Araújo de Jesus, Lúcia Helena Gomes Coelho, Werner Siegfried Hanisch, Marcelo Luiz Martins Pompêo, Flávia Talarico Saia, Gustavo Bueno Gregoracci, Roseli Frederigi Benassi
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0085097

Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity
Cited by: 7
Author(s): Leah C. Blasiak, Alex W. Schmidt, Honoré Andriamiarinoro, Temesgen Belayneh Mulaw, Rado Rasolomampianina, Wendy L. Applequist, Chris Birkinshaw, Félicitée Rejo-Fienena, Porter P. Lowry, Thomas M. Schmidt, Russell T. Hill
Software Mentions: 4
Published: almost 11 years ago

10.3389/fcell.2020.570484

Fine Particulate Matter Exposure Alters Pulmonary Microbiota Composition and Aggravates Pneumococcus-Induced Lung Pathogenesis
Cited by: 18
Author(s): Yu Wen Chen, Shiao Wen Li, Chia Der Lin, Mei Huang, Hwai Jeng Lin, Chia Yin Chin, Yi Ru Lai, Cheng Hsun Chiu, Chia Yu Yang, Chih Ho Lai
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-61092-1

Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning
Cited by: 35
Author(s): Miguel de Celis, Ignacio Belda, Rüdiger Ortiz‐Álvarez, Lucía Arregui, Domingo Marquina, Susana Serrano, Andrés de la Oliva Santos
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-60304-y

Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling
Cited by: 15
Author(s): Gábor Fidler, Emese Tolnai, Anikó Stágel, Judit Remenyik, László Stündl, Ferenc Gál, Sándor Bíró, Melinda Paholcsek
Software Mentions: 4
Published: over 4 years ago

10.3390/microorganisms9040822

Rootstocks Shape Their Microbiome—Bacterial Communities in the Rhizosphere of Different Grapevine Rootstocks
Cited by: 16
Author(s): Leonie Dries, Simone Bussotti, Carlo Pozzi, Robert Kunz, Sylvia Schnell, Otmar Löhnertz, Anne Vortkamp
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-017-1690-0

Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities
Cited by: 48
Author(s): Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman, David N. Fredricks
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0111228

Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs
Cited by: 135
Author(s): Marc A. Sze, Masashi Tsuruta, Shun Wei Julia Yang, Yeni Oh, S. F. Paul Man, James C. Hogg, Don D. Sin
Software Mentions: 4
Published: about 10 years ago

10.1186/s40104-020-00459-w

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens
Cited by: 33
Author(s): Joel J. Maki, Elizabeth Bobeck, Matthew J. Sylte, Torey Looft
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0166104

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
Cited by: 249
Author(s): Shoko Iwai, Thomas Weinmaier, Brian L. Schmidt, Donna G. Albertson, Neil J. Poloso, Karim Dabbagh, Todd Z. DeSantis
Software Mentions: 4
Published: about 8 years ago

10.3389/fimmu.2020.598152

Gut Microbiome of Children and Adolescents With Primary Sclerosing Cholangitis in Association With Ulcerative Colitis
Cited by: 16
Author(s): Ramon V. Cortez, Luana Moreira, Marina Padilha, Mariana D Bibas, Ricardo Katsuya Toma, Gilda Porta, Carla Romano Taddei
Software Mentions: 4
Published: almost 4 years ago

10.1111/1462-2920.13706

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir
Cited by: 21
Author(s): A. J. Freedman, BoonFei Tan, Janelle R. Thompson
Software Mentions: 4
Published: over 7 years ago

10.1038/srep26425

The microbiomes and metagenomes of forest biochars
Cited by: 42
Author(s): Genevieve L. Noyce, C. L. Winsborough, Roberta R. Fulthorpe, Nathan Basiliko
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-35578-y

Gene mutation associated with esl mediates shifts on fungal community composition in rhizosphere soil of rice at grain-filling stage
Cited by: 1
Author(s): Puleng Letuma, Yasir Arafat, Muhammad Mohsin Waqas, Feifan Lin, Wenxiong Lin, Yiyang Zhang, Mamello Masita, Kai Fan, Zhaowei Li
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pntd.0008230

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota
Cited by: 12
Author(s): Sivaranjani Namasivayam, Bassirou Diarra, Seydou Diabaté, Yeya dit Sadio Sarro, A. Koné, Bourahima Kone, Mohamed Tolofoudié, Bocar Baya, M L Diakité, Ousmane Kodio, Keira A. Cohen, Jane L. Holl, Chad Achenbach, S. Chatterjee, Robert L. Murphy, William R. Bishai, Souleymane Diallo, Alan Sher, Mamoudou Maiga
Software Mentions: 4
Published: over 4 years ago

10.1128/MRA.00968-20

16S rRNA Gene Diversity of Bacterial Endophytes in Parasitic Cuscuta campestris and Its Helianthus annuus Host
Cited by: 0
Author(s): Adam T. Avila, Tricia A. Van Laar, John V. H. Constable, Katherine Waselkov
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-016-0982-0

Modeling the integration of bacterial rRNA fragments into the human cancer genome
Cited by: 5
Author(s): Karsten B. Sieber, Pawel Gajer, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 8 years ago

10.3389/fvets.2020.00438

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats
Cited by: 2
Author(s): Andrea Balboni, Giovanni Franzo, Luca Bano, Stefano Arcangeli, Alessia Rizzardi, Lorenza Urbani, Sofia Segatore, Federica Serafini, Francesco Dondi, Mara Battilani
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.1758

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon
Cited by: 7
Author(s): Florent E. Angly, Olga Pantos, Thomas C. Morgan, V. I. Rich, Hemerson Tonin, David G. Bourne, Philip Mercurio, Andrew P. Negri, Gene W. Tyson
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2019.00169

Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients
Cited by: 43
Author(s): Luo Zhengming, Jinxian Liu, Pengyu Zhao, Tong Jia, Cui Li, Bo Chai
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcimb.2021.622550

Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
Cited by: 7
Author(s): Lorena Ruíz, Claudio Alba, Cristina García-Carral, Esther Jiménez, Kimberly A. Lackey, Michelle K. McGuire, Courtney L. Meehan, James A. Foster, Daniel Sellen, Elizabeth Kamau-Mbuthia, Egidioh W. Kamundia, Samwel Mbugua, Sophie E. Moore, Andrew M. Prentice, Debela Gindola K, Gloria E. Otoo, Rossina G. Pareja, Lars Bode, Mark A. McGuire, Janet E. Williams, Juan M. Rodríguez
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22157804

Skin Wound Healing Rate in Fish Depends on Species and Microbiota
Cited by: 9
Author(s): Tery Yun, Soeun Shin, Kyungwon Bang, Mugeun Lee, Jung-Ah Cho, Min Won Baek
Software Mentions: 4
Published: over 3 years ago

10.3390/nu13062032

Gut Microbiota Profile and Its Association with Clinical Variables and Dietary Intake in Overweight/Obese and Lean Subjects: A Cross-Sectional Study
Cited by: 60
Author(s): Judit Companys, María José Gosalbes, Laura Pla‐Pagà, Lorena Calderón-Pérez, Elisabet Llauradó, Anna Pedret, Rosa M. Valls, Nuria Jiménez‐Hernández, Berner Andrée Sandoval-Ramírez, Josep Maria del Bas, Antoni Caimari, Laura Rubió, Rosa Solà
Software Mentions: 4
Published: over 3 years ago

10.1016/j.wroa.2020.100056

Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households
Cited by: 5
Author(s): Erica R. Fuhrmeister, Ayşe Ercümen, Jessica A. Grembi, Mahfuza Islam, Amy J. Pickering, Kara L. Nelson
Software Mentions: 4
Published: almost 4 years ago

10.3390/nu13062069

Timing of Tributyrin Supplementation Differentially Modulates Gastrointestinal Inflammation and Gut Microbial Recolonization Following Murine Ileocecal Resection
Cited by: 1
Author(s): Valentin Mocanu, Heekuk Park, Jerry Dang, Naomi Hotte, Aducio Thiesen, Michael Laffin, Haili Wang, Daniel W. Birch, Karen Madsen
Software Mentions: 4
Published: over 3 years ago

10.3390/nu13093248

The Gut Microbiota during a Behavioral Weight Loss Intervention
Cited by: 17
Author(s): Maggie A. Stanislawski, Daniel N. Frank, Sarah J. Borengasser, Danielle M. Ostendorf, Diana Ir, Purevsuren Jambal, Kristen Bing, Liza Wayland, Janet Siebert, Daniel H. Bessesen, Paul S. MacLean, Edward L. Melanson, Victoria A. Catenacci
Software Mentions: 4
Published: about 3 years ago

10.1080/20002297.2019.1633194

Bacterial biofilm composition in healthy subjects with and without caries experience.
Cited by: 37
Author(s): Kyrill Schoilew, Helena Ueffing, Alexander H. Dalpke, Björn Wolff, Cornelia Frese, Diana Wolff, Sébastien Boutin
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2019.00170

Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater
Cited by: 18
Author(s): Florian Trigodet, Nicolas Larché, Hilary G. Morrison, Mohamed Jebbar, Dominique Thierry, Loïs Maignien
Software Mentions: 4
Published: almost 6 years ago

10.3390/nu12072147

A Comprehensive Evaluation of the Impact of Bovine Milk Containing Different Beta-Casein Profiles on Gut Health of Ageing Mice
Cited by: 22
Author(s): Barbara Guantario, Marzia Giribaldi, Chiara Devirgiliis, Alberto Finamore, Elena Colombino, Maria Teresa Capucchio, Rocchina Evangelista, Vincenzo Motta, Paola Zinno, Simona Cirrincione, Sara Antoniazzi, Laura Cavallarin, Marianna Roselli
Software Mentions: 4
Published: over 4 years ago

10.3390/nu13061937

Characterizing the Effects of Calcium and Prebiotic Fiber on Human Gut Microbiota Composition and Function Using a Randomized Crossover Design—A Feasibility Study
Cited by: 8
Author(s): Lara Yoon, Karin B. Michels
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.600516

Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai–Tibetan Plateau
Cited by: 21
Author(s): Jian Ma, Yixiao Zhu, Zhisheng Wang, Yan Xiong, Rui Hu, Xueying Wang, Guang Cao, Huawei Zou, Ali Mujtaba Shah, Quanhui Peng, Bai Xue, Lizhi Wang, Suonan Zhao, Xiangying Kong
Software Mentions: 3
Published: almost 4 years ago

10.1038/ismej.2016.35

Capturing the most wanted taxa through cross-sample correlations
Cited by: 9
Author(s): Mathieu Almeida, Mihai Pop, Edi Prifti, Nicolas Pons, Amine Ghozlane, S. Dusko Ehrlich
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2021.635772

Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles
Cited by: 5
Author(s): Eugeni Belda, Boubacar Coulibaly, Tullu Bukhari, Karin Eiglmeier, Raymond Kone, Mamadou B. Coulibaly, Soumanaba Zongo, Megan Barry, Awa Gnémé, Wamdaogo Moussa Guelbéogo, Abdoul Habib Béavogui, Sékou F. Traorè, N’Falé Sagnon, Kenneth D. Vernick, Michelle M. Riehle
Software Mentions: 3
Published: over 3 years ago

10.1038/s41396-018-0215-9

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome
Cited by: 28
Author(s): Zachary Armstrong, Keith Mewis, Feng Liu, Connor Morgan-Lang, Melanie Scofield, Evan W Durno, Hong Ming Chen, Kevin Mehr, Stephen G. Withers, Steven J. Hallam
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.03335

Microbial-Driven Butyrate Regulates Jejunal Homeostasis in Piglets During the Weaning Stage
Cited by: 33
Author(s): Xi Zhong, Zhongwei Zhang, Shujin Wang, Lili Cao, Lin Zhou, Aomin Sun, Zhendong Zhong, Miranda Nabben
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41396-020-0631-5

Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible
Cited by: 50
Author(s): Julian Mönnich, Jan Tebben, Jennifer Bergemann, Rebecca J. Case, Sylke Wohlrab, Tilmann Harder
Software Mentions: 3
Published: over 4 years ago

10.3390/jof6040335

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence
Cited by: 12
Author(s): Vladimir Gorshkov, Elena Osipova, М. Л. Пономарева, Sergey Ponomarev, Natalia Gogoleva, Olga Petrova, Olga Gogoleva, Azat Meshcherov, Alexander S. Balkin, Е. П. Ветчинкина, Kim O. Potapov, Alexander A. Kamnev, Viktor Korzun
Software Mentions: 3
Published: almost 4 years ago

10.1128/AEM.02189-20

Dichotomy between Regulation of Coral Bacterial Communities and Calcification Physiology under Ocean Acidification Conditions
Cited by: 8
Author(s): Amanda Shore, Rusty D. Day, Joseph Stewart, Colleen A. Burge
Software Mentions: 3
Published: over 3 years ago

10.3390/biomedicines8110469

Dietary Vitamin B6 Deficiency Impairs Gut Microbiota and Host and Microbial Metabolites in Rats
Cited by: 28
Author(s): Shyamchand Mayengbam, Faye Chleilat, Raylene A. Reimer
Software Mentions: 3
Published: about 4 years ago

10.1186/s42523-021-00073-9

Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats
Cited by: 25
Author(s): Juan Manuel Palma-Hidalgo, Elisabeth Jiménez, Milka Popova, Diego P. Morgavi, A. I. Martin-García, D. R. Yáñez-Ruíz, Alejandro Belanche
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2020.581219

Investigation of Physicochemical Indices and Microbial Communities in Termite Fungus-Combs
Cited by: 6
Author(s): Guiying Yang, Farhan Ahmad, Qihuan Zhou, Meixia Guo, Shiyou Liang, Hassan Ga’al, Jianchu Mo
Software Mentions: 3
Published: almost 4 years ago

10.1155/2018/6280484

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches
Cited by: 13
Author(s): Michele Pittol, Erin D. Scully, Daniel N. Miller, Lisa M. Durso, Lídia Mariana Fiuza, Victor Hugo Valiati
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2016.00337

Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones
Cited by: 7
Author(s): Daniel Aguirre de Cárcer, Carlos Pedrós-Alió, David A. Pearce, Antonio Alcamı́
Software Mentions: 3
Published: over 8 years ago

10.3390/microorganisms7060160

The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica
Cited by: 17
Author(s): Stefanie Lutz, Lori A. Ziolkowski, Liane G. Benning
Software Mentions: 3
Published: over 5 years ago

10.1128/AEM.02574-17

Temporal and Regional Variability in the Skin Microbiome of Humpback Whales along the Western Antarctic Peninsula
Cited by: 37
Author(s): K. C. Bierlich, Colin Miller, Emelia DeForce, Ari S. Friedlaender, David W. Johnston, Amy Apprill
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2014.00031

Shotgun metagenomic data reveals significant abundance but low diversity of “Candidatus Scalindua” marine anammox bacteria in the Arabian Sea oxygen minimum zone
Cited by: 28
Author(s): Laura Villanueva, Daan R. Speth, Theo van Alen, Alexander Hoischen, Mike S. M. Jetten
Software Mentions: 3
Published: almost 11 years ago

10.3390/bioengineering7010003

Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste
Cited by: 26
Author(s): Jan Moestedt, Maria Westerholm, Simon Isaksson, Anna Schnürer
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0099517

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity
Cited by: 69
Author(s): Frederiek‐Maarten Kerckhof, Emilie Courtens, Annelies Geirnaert, Sven Hoefman, Adrian Ho, Ramiro Vílchez-Vargas, Dietmar H. Pieper, Ruy Jáuregui, Siegfried E. Vlaeminck, Tom Van de Wiele, Peter Vandamme, Kim Heylen, Nico Boon
Software Mentions: 3
Published: over 10 years ago

10.1128/mSphere.00950-19

Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread
Cited by: 44
Author(s): Aspen T. Reese, Anne A. Madden, Marie Joossens, Lacaze Guylaine, Robert R. Dunn
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2017.00232

Response of Deep Subsurface Microbial Community to Different Carbon Sources and Electron Acceptors during ∼2 months Incubation in Microcosms
Cited by: 30
Author(s): Lotta Purkamo, Malin Bomberg, Mari Nyyssönen, Lasse Ahonen, Ilmo Kukkonen, Merja Itävaara
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2018.02045

Design of Primers for Evaluation of Lactic Acid Bacteria Populations in Complex Biological Samples
Cited by: 37
Author(s): Qiangchuan Hou, Xiaoye Bai, Weicheng Li, Xu Gao, Faming Zhang, Zhihong Sun, Heping Zhang
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2015.00674

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes
Cited by: 45
Author(s): Jatta Saarenheimo, Marja Tiirola, Antti J. Rissanen
Software Mentions: 3
Published: over 9 years ago

10.1128/mSystems.00358-21

Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments
Cited by: 16
Author(s): Sean Ting-Shyang Wei, Yi Lung Chen, Yu Wei Wu, Tien Yu Wu, Yi Li Lai, Po Hsiang Wang, Wael Ismail, Tzong‐Huei Lee, Yin-Ru Chiang
Software Mentions: 3
Published: over 3 years ago

10.1186/s40168-018-0427-2

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs
Cited by: 50
Author(s): Maelle Sevellec, Nicolas Derôme, Louis Bernatchez
Software Mentions: 3
Published: over 6 years ago

10.1186/1752-0509-7-S4-S13

Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems
Cited by: 9
Author(s): Lei Shang, David P. Gardner, Wei Xu, Jamie J. Cannone, Daniel P. Miranker, Stuart Ozer, Robin R. Gutell
Software Mentions: 3
Published: about 11 years ago

10.3389/fcimb.2021.615770

Differences in the Genital Microbiota in Women Who Naturally Clear Chlamydia trachomatis Infection Compared to Women Who Do Not Clear; A Pilot Study
Cited by: 9
Author(s): Patricia Dehon Mott, Christopher M. Taylor, Rebecca A. Lillis, Caleb M. Ardizzone, Hannah L. Albritton, Meng Luo, Kaitlyn G. Calabresi, David H. Martín, Leann Myers, Alison J. Quayle
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-61446-9

Bubble-mediated transport of benthic microorganisms into the water column: Identification of methanotrophs and implication of seepage intensity on transport efficiency
Cited by: 9
Author(s): Sebastian Jordan, Tina Treude, Ira Leifer, René Janßen, Johannes Werner, Heide N. Schulz-Vogt, Oliver Schmale
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0142603

Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities
Cited by: 33
Author(s): Jamie A. FitzGerald, Eoin Allen, David Wall, Stephen A. Jackson, Jerry D. Murphy, Alan D. W. Dobson
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-020-57464-2

Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach
Cited by: 38
Author(s): Mario Moreno-Pino, Antonia Cristi, James F. Gillooly, Nicole Trefault
Software Mentions: 3
Published: almost 5 years ago

10.1093/femsec/fiz033

Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes
Cited by: 44
Author(s): Dean J. Horton, Kevin R. Theis, Donald G Uzarski, Deric R. Learman
Software Mentions: 3
Published: over 5 years ago

10.12688/f1000research.10443.1

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
Cited by: 7
Author(s): Espen Mikal Robertsen, Hubert Denise, Alex L. Mitchell, Alex Bateman, Lars Ailo Bongo, Nils Peder Willassen
Software Mentions: 3
Published: almost 8 years ago

10.3389/fendo.2020.569085

Six-Week Exercise Training With Dietary Restriction Improves Central Hemodynamics Associated With Altered Gut Microbiota in Adolescents With Obesity
Cited by: 20
Author(s): Junhao Huang, Jingwen Liao, Yang Fang, Hailin Deng, Honggang Yin, Bing Shen, Min Hu
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-17445-4

Bacterial community structure and novel species of magnetotactic bacteria in sediments from a seamount in the Mariana volcanic arc
Cited by: 29
Author(s): Jia Liu, Wenyan Zhang, Xue-Gong Li, Xuegang Li, Xumiao Chen, Jin Hua Li, Zhao-Jie Teng, Cong Xu, Claire‐Lise Santini, Li Zhao, Yuan Zhao, Heng Zhang, Wei Jia Zhang, Kuidong Xu, Chaolun Li, Yongxin Pan, Tian Xiao, Hongmiao Pan, Long-Fei Wu
Software Mentions: 3
Published: almost 7 years ago

10.1186/s40168-020-00900-2

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
Cited by: 115
Author(s): Jennifer Lu, Steven L. Salzberg
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-05243-x

Effects of sediment smothering on the sponge holobiont with implications for dredging management
Cited by: 21
Author(s): Mari Carmen Pineda, Brian Strehlow, Miriam Sternel, Alan Duckworth, Joost den Haan, Ross Jones, Nicole S. Webster
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-28905-w

Unique subgingival microbiota associated with periodontitis in cirrhosis patients
Cited by: 24
Author(s): A. S. Jensen, Lea Ladegaard Grønkjær, Palle Holmstrup, Hendrik Vilstrup, Mogens Kilian
Software Mentions: 3
Published: over 6 years ago

10.1098/rsos.160296

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica
Cited by: 9
Author(s): Paul Czechowski, Duanne White, Laurence J. Clarke, Alan McKay, Alan Cooper, Mark I. Stevens
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41597-021-01015-5

Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement
Cited by: 20
Author(s): Daniel Roush, Ana Giraldo-Silva, Ferrán García-Pichel
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0091092

Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges
Cited by: 55
Author(s): Jonathan Kennedy, Burkhardt Flemer, Stephen A. Jackson, John P. Morrissey, Fergal O’Gara, Alan D. W. Dobson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12866-021-02320-0

Oral iron supplementation after antibiotic exposure induces a deleterious recovery of the gut microbiota
Cited by: 13
Author(s): Thibault Cuisiniere, Annie Calvé, Gabriela Fragoso, Manon Oliero, Roy Hajjar, Emmanuel Gonzalez, Manuela M. Santos
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-021-98119-0

The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability
Cited by: 4
Author(s): Lucy Rebecca Davies, Volker Loeschcke, Mads Fristrup Schou, Andreas Schramm, Torsten Nygård Kristensen
Software Mentions: 3
Published: about 3 years ago

10.1186/s13028-018-0415-3

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging
Cited by: 33
Author(s): Marie Lisandra Zepeda Mendoza, Michael Roggenbuck, Karla Manzano Vargas, Lars Hestbjerg Hansen, Søren Brunak, M. Thomas P. Gilbert, Thomas Sicheritz-Pontén
Software Mentions: 3
Published: about 6 years ago

10.1186/s12866-020-01859-8

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies
Cited by: 11
Author(s): Barbora Bendová, Jaroslav Piálek, Ľudovít Ďureje, Lucie Schmiedová, Dagmar Čížková, Jean‐François Martin, Jakub Kreisinger
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-45490-8

Seasonal development of a coastal microbial mat
Cited by: 22
Author(s): Daniela Clara Cardoso, Mariana Silvia Cretoiu, Lucas J. Stal, Henk Bolhuis
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-50730-y

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability
Cited by: 22
Author(s): Océane Nicolitch, Maureen Feucherolles, Jean-Louis Churin, Laure Fauchery, M.-P. Turpault, Stéphane Uroz
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.5676

Evidence for host effect on the intestinal microbiota of whitefish (<i>Coregonus</i> sp.) species pairs and their hybrids
Cited by: 22
Author(s): Maelle Sevellec, Martin Laporte, Alex Bernatchez, Nicolas Derôme, Louis Bernatchez
Software Mentions: 3
Published: about 5 years ago

10.1186/gb-2011-12-5-r44

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Cited by: 309
Author(s): Christopher S. Miller, Brett J. Baker, Brian C. Thomas, Steven W. Singer, Jillian F. Banfield
Software Mentions: 3
Published: over 13 years ago

10.3389/fvets.2020.599337

Characterization of the Intestinal Microbiota of Broiler Breeders With Different Egg Laying Rate
Cited by: 6
Author(s): Zengqiao Yang, Chunhua Zhang, Jianping Wang, Pietro Celi, Xuemei Ding, Shiping Bai, Qiufeng Zeng, Xiangbing Mao, Yong Zhuo, Shengyu Xu, Hui Yan, Keying Zhang, Zhiguo Shan
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12866-020-01861-0

Bacterial diversity associated with the abdomens of naturally Plasmodium-infected and non-infected Nyssorhynchus darlingi
Cited by: 7
Author(s): Tatiane Marques Porangaba de Oliveira, Sabri Saeed Sanabani, Maria Anice Mureb Sallum
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0157966

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA
Cited by: 54
Author(s): Lee F. Stanish, Natalie M. Hull, Charles E. Robertson, J. Kirk Harris, Mark J. Stevens, John R. Spear, Norman R. Pace
Software Mentions: 3
Published: over 8 years ago

10.1186/s12866-015-0497-2

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing
Cited by: 49
Author(s): Karen G. Jarvis, James R. White, Christopher J. Grim, Laura Ewing, Andrea Ottesen, Junia Jean Gilles Beaubrun, James B. Pettengill, Eric W. Brown, Darcy E. Hanes
Software Mentions: 3
Published: over 9 years ago

10.3390/diagnostics10110879

The Dwindling Microbiota of Aerobic Vaginitis, an Inflammatory State Enriched in Pathobionts with Limited TLR Stimulation
Cited by: 18
Author(s): Eline Oerlemans, Sander Wuyts, Gert Bellen, Stijn Wittouck, Ilke De Boeck, Kateryna Ruban, Camille Nina Allonsius, Marianne F.L. van den Broek, Gilbert Donders, Sarah Lebeer
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.9538

A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition
Cited by: 5
Author(s): Laura Leonard, Kristin M. Mikkelson, Zhao Hao, Eoin L. Brodie, Kenneth H. Williams, Jonathan O. Sharp
Software Mentions: 3
Published: over 4 years ago

10.1186/s12934-019-1265-z

Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)
Cited by: 31
Author(s): Chaoqun Li, Beili Zhang, Xin Wang, Xionge Pi, X Wang, Huihui Zhou, Kangsen Mai, Gang He
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-018-5325-2

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.
Cited by: 12
Author(s): Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 3
Published: over 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

10.1371/journal.pone.0174765

A comparison of sampling methods for examining the laryngeal microbiome
Cited by: 7
Author(s): Alissa S. Hanshew, Marie E. Jetté, Stephanie N. Tadayon, Susan L. Thibeault
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0069973

Tracking Fungal Community Responses to Maize Plants by DNA- and RNA-Based Pyrosequencing
Cited by: 25
Author(s): Eiko E. Kuramae, Erik Verbruggen, Remy Hillekens, Mattias de Hollander, Wilfred F. M. Röling, Marcel G. A. van der Heijden, George A. Kowalchuk
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0177488

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)
Cited by: 38
Author(s): J. Morrison, Kristina Baker, Richard M. Zamor, Steve Nikolai, Mostafa S. Elshahed
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.10194

Diversity of the gut microbiome in three grasshopper species using 16S rRNA and determination of cellulose digestibility
Cited by: 11
Author(s): Jianmei Wang, Jing Bai, Fang-Yuan Zheng, Lei Yao, Xiang Li, Jing Wang, Yong-Chao Zhi, Xin-Jiang Li
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2018.02794

Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments
Cited by: 35
Author(s): María Isabel Arce, Daniel von Schiller, Mia M. Bengtsson, Christian Hinze, Hoseung Jung, Ricardo J. Eloy Alves, Tim Urich, Gabriel Singer
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0202858

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing
Cited by: 14
Author(s): Kara D. McGaughey, Tulay Yilmaz-Swenson, Nourhan M. Elsayed, Dianne A. Cruz, Ramona Rodriguez, Michael D. Kritzer, Angel V. Peterchev, Megan Gray, Samantha R. Lewis, Jeffrey Roach, William C. Wetsel, Douglas E. Williamson
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.02619

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats
Cited by: 10
Author(s): Mercedes Berlanga, Montserrat Palau, Ricardo Guerrero
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2021.631882

Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community
Cited by: 18
Author(s): Xiaoya Gong, Jie Shi, Xingang Zhou, Tao Yuan, Danmei Gao, Fengzhi Wu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0222394

Gut microbiome diversity is associated with sleep physiology in humans
Cited by: 136
Author(s): Robert P. Smith, Cole G. Easson, Sarah M. Lyle, Ritishka Kapoor, Chase P. Donnelly, Eileen J. Davidson, Esha Parikh, Jose V. Lopez, Jaime L. Tartar
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2018.01192

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources
Cited by: 24
Author(s): Paula B. Matheus Carnevali, Craig W. Herbold, K. P. Hand, John C. Priscu, Alison E. Murray
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-021-04316-z

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Cited by: 2
Author(s): Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch‐Mizrachi, Eric P. Nawrocki
Software Mentions: 3
Published: over 3 years ago