cran: uclust | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0161050

Distinct Bacterial Microbiomes in Sexual and Asexual Potamopyrgus antipodarum, a New Zealand Freshwater Snail
Cited by: 23
Author(s): Cristina Takacs-Vesbach, Kayla C. King, David Van Horn, Katelyn Larkin, Maurine Neiman
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0192450

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens
Cited by: 100
Author(s): Sanjay Kumar, Chongxiao Chen, Nagaraju Indugu, Gabriela Orosco Werlang, Manpreet Singh, Woo Kyun Kim, Harshavardhan Thippareddi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0224950

Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus)
Cited by: 10
Author(s): Stephen C. Artim, Alexander Sheh, Monika Burns, James G. Fox
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-017-06687-x

Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach
Cited by: 43
Author(s): Vera G. Fonseca, Frédéric Sinniger, John Gaspar, Christopher Quince, Simon Creer, Deborah M. Power, Lloyd S. Peck
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0184717

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing
Cited by: 21
Author(s): Li Ou, Rong Xiao, Lihua Sun, Cheng-Lin Guan, Dedong Kong, Xiufang Hu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0147809

Allergic Patients with Long-Term Asthma Display Low Levels of Bifidobacterium adolescentis
Cited by: 77
Author(s): Arancha Hevia, Christian Milani, Patricia López, Carmen Díaz Donado, Adriana Cuervo, Sonia González, Ana Suárez, Francesca Turroni, Miguel Gueimonde, Marco Ventura, Borja Sánchez, Abelardo Margollés
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0141424

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity
Cited by: 62
Author(s): Richard R. Rodrigues, Rosana P. Pineda, Jacob N. Barney, Erik T. Nilsen, John E. Barrett, Mark A. Williams
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.00201

Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour
Cited by: 35
Author(s): Charlotte Urien, Judith Legrand, Pierre Montalent, Serge Casarégola, Delphine Sicard
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0194404

A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog
Cited by: 5
Author(s): Joshua D. Sackett, Desiree C. Huerta, Brittany R. Kruger, Scott D. Hamilton-Brehm, Duane P. Moser
Software Mentions: 2
Published: over 6 years ago

10.1186/2049-2618-1-20

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants
Cited by: 131
Author(s): Erika C. Claud, Kevin P. Keegan, Jennifer M. Brulc, Lei Lü, Daniela Bartels, Elizabeth M. Glass, Eugene B. Chang, Patrick Meyer, Dionysios A. Antonopoulos
Software Mentions: 2
Published: over 11 years ago

10.1186/s13075-014-0486-0

Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis
Cited by: 165
Author(s): Matthew L. Stoll, Ranjit Kumar, Casey D. Morrow, Elliot J. Lefkowitz, Xiangqin Cui, Anna Genin, Randy Q. Cron, Charles O. Elson
Software Mentions: 2
Published: almost 10 years ago

10.1186/2049-2618-2-35

Intestinal anastomotic injury alters spatially defined microbiome composition and function
Cited by: 118
Author(s): Benjamin D. Shogan, Daniel P. Smith, Scott Christley, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-017-05312-1

Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber
Cited by: 44
Author(s): Gang Yang, Mo Peng, Xiangli Tian, Shuanglin Dong
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0220463

The feline cutaneous and oral microbiota are influenced by breed and environment
Cited by: 31
Author(s): Caitlin E. Older, Alison Diesel, Sara D. Lawhon, Cintia R. R. Queiroz, Luan Cleber Henker, Aline Rodrigues Hoffmann
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-03706-9

Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing
Cited by: 76
Author(s): Yu Xu, Zhenrong Xie, Huawei Wang, Zongwen Shen, Youbing Guo, Yunhong Gao, Xin Chen, Wu Qiang, Xuejun Li, Kunhua Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-6334-5

Seed interior microbiome of rice genotypes indigenous to three agroecosystems of Indo-Burma biodiversity hotspot
Cited by: 30
Author(s): Garima Raj, Mohammad Umar. Shadab, Sujata Deka, Manashi Das, Jilmil Baruah, Rupjyoti Bharali, Narayan Chandra Talukdar
Software Mentions: 2
Published: almost 5 years ago

10.1242/dmm.031070

Environmental factors regulate Paneth cell phenotype and host susceptibility to intestinal inflammation in Irgm1-deficient mice
Cited by: 20
Author(s): Allison R. Rogala, Alexi A. Schoenborn, Brian E. Fee, Viviana Cantillana, Maria Joyce, Raad Z. Gharaibeh, Sanjeet Roy, Anthony A. Fodor, R. Balfour Sartor, Gregory A. Taylor, Ajay Gulati
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pntd.0007297

Genetic changes associated with the temporal shift in invasive non-typhoidal Salmonella serovars in Bamako Mali
Cited by: 4
Author(s): Kristin Bornstein, Sharon M. Tennant, Tracy H. Hazen, John D. Sorkin, Milagritos D. Tapia, Samba O. Sow, Uma Onwuchekwa, Myron M. Levine, David A. Rasko
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.01342

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions
Cited by: 81
Author(s): Cristina Riquelme, Jennifer J.M. Hathaway, Maria de Lurdes Enes Dapkevicius, Ana Z. Miller, Ara Kooser, Diana E. Northup, Valme Jurado, Octavio Fernández, Cesáreo Sáiz‐Jiménez, Naowarat Cheeptham
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pntd.0007383

Hindgut microbiota in laboratory-reared and wild Triatoma infestans
Cited by: 34
Author(s): Andreea Waltmann, Alexandra C Willcox, Sujata Balasubramanian, Katty Borrini Mayorí, Sandra Mendoza Guerrero, R Sánchez, Jeffrey Roach, Carlos Condori Pino, Robert H. Gilman, Caryn Bern, Jonathan J. Juliano, Michael Z. Levy, Steven R. Meshnick, Natalie M. Bowman
Software Mentions: 2
Published: over 5 years ago

10.1038/srep21871

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate
Cited by: 139
Author(s): Francesca De Filippis, Alessandro Genovese, Pasquale Ferranti, Jack A. Gilbert
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1004782

ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing
Cited by: 132
Author(s): Justin R. Pritchard, Michael C. Chao, Sören Abel, Brigid M. Davis, Catherine Baranowski, Yanjia J. Zhang, Eric J. Rubín, Matthew K. Waldor
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.8051

High-throughput sequence analysis reveals variation in the relative abundance of components of the bacterial and fungal microbiota in the rhizosphere ofGinkgo biloba
Cited by: 2
Author(s): Rujue Ruan, Zhifang Jiang, Yuhuan Wu, Meifeng Xu, Jun Ni
Software Mentions: 2
Published: almost 5 years ago

10.1111/j.1462-2920.2012.02799.x

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau
Cited by: 444
Author(s): Jinbo Xiong, Yongqin Liu, Xiangui Lin, Huayong Zhang, Jun Zeng, Juzhi Hou, Yongping Yang, Tandong Yao, Rob Knight, Haiyan Chu
Software Mentions: 2
Published: over 12 years ago

10.1038/srep18078

Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure
Cited by: 15
Author(s): Jean Nimusiima, Martina Köberl, John Baptist Tumuhairwe, Jerome Kubiriba, Charles Staver, Gabriele Berg
Software Mentions: 2
Published: almost 9 years ago

10.1111/1462-2920.14902

A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone
Cited by: 36
Author(s): Saara Suominen, Nina Dombrowski, Jaap S. Sinninghe Damsté, Laura Villanueva
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40793-020-00358-7

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences
Cited by: 261
Author(s): Franziska Wemheuer, Jessica Averitt Taylor, Rolf Daniel, Emma L. Johnston, Peter Meinicke, Torsten Thomas, Bernd Wemheuer
Software Mentions: 2
Published: over 4 years ago

10.1038/srep16498

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
Cited by: 118
Author(s): Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea L. Waters‐Rist, Menno L. P. Hoogland, Domingo C. Salazar‐García, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis, Corinne L. Hofman, Christina Warinner
Software Mentions: 2
Published: almost 9 years ago

10.1007/s10096-016-2805-7

Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method - the observation of DNAemia
Cited by: 113
Author(s): Tomasz Gosiewski, Agnieszka H. Ludwig-Gałęzowska, K. Huminska, Agnieszka Sroka-Oleksiak, Piotr Radkowski, Dominika Salamon, Jacek Wojciechowicz, Marta Kus-Slowinska, Małgorzata Bulanda, Paweł Wołkow
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.6392

Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations
Cited by: 8
Author(s): Jacob J. Grothjan, Erica B. Young
Software Mentions: 2
Published: over 5 years ago

10.1186/s12866-016-0877-2

High-throughput sequencing technology to reveal the composition and function of cecal microbiota in Dagu chicken
Cited by: 62
Author(s): Yan Xu, Huixin Yang, Lili Zhang, Yuhong Su, Donghui Shi, Haidi Xiao, Yuan Tian
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2016.02142

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children
Cited by: 5
Author(s): Elisabeth Santigli, Slave Trajanoski, Katharina Eberhard, Barbara Klug
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2015.00855

Response of leaf endophytic bacterial community to elevated CO2 at different growth stages of rice plant
Cited by: 23
Author(s): Guohao Ren, Huayong Zhang, Xiangui Lin, Jiang Zhu, Zhongjun Jia
Software Mentions: 2
Published: about 9 years ago

10.1038/srep10918

Opioid Exacerbation of Gram-positive sepsis, induced by Gut Microbial Modulation, is Rescued by IL-17A Neutralization
Cited by: 73
Author(s): Jingjing Meng, Santanu Banerjee, Dan Li, Gregory M. Sindberg, Fuyuan Wang, Jing Ma, Sabita Roy
Software Mentions: 2
Published: over 9 years ago

10.1098/rsos.160829

Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes
Cited by: 16
Author(s): Anni Djurhuus, Svein‐Ole Mikalsen, Helge-Ansgar Giebel, Alex D. Rogers
Software Mentions: 2
Published: over 7 years ago

10.3382/ps/pev381

Increased water contamination and grow-out Pekin duck mortality when raised with water troughs compared to pin-metered water lines using a United States management system
Cited by: 13
Author(s): A. Katrin Schenk, Amanda Porter, E. Alenciks, Kendall S. Frazier, Aaron A. Best, Susan M. Fraley, Gregory S. Fraley
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-016-0151-8

Composition and dynamics of the respiratory tract microbiome in intubated patients
Cited by: 129
Author(s): Brendan J Kelly, Ize Imai, Kyle Bittinger, Alice Laughlin, Barry D. Fuchs, Frederic D. Bushman, Ronald G. Collman
Software Mentions: 2
Published: over 8 years ago

10.1186/s40168-016-0169-y

Diet may influence the oral microbiome composition in cats
Cited by: 40
Author(s): Christina Adler, Richard Malík, Gina V. Browne, Jacqueline M. Norris
Software Mentions: 2
Published: over 8 years ago

10.3389/fnagi.2017.00195

16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain
Cited by: 199
Author(s): David C. Emery, Deborah K. Shoemark, Thomas E Batstone, Christy Waterfall, Jane A. Coghill, Tanya L. Cerajewska, Malcolm Davies, Nicola West, Shelley J Allen
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-019-0625-6

Genomic and metagenomic insights into the microbial community of a thermal spring
Cited by: 38
Author(s): Renato Pedron, Alfonso Esposito, Irene Bianconi, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Mario Cristofolini, Nicola Segata, Olivier Jousson
Software Mentions: 2
Published: almost 6 years ago

10.3390/plants9111501

Response of Horticultural Soil Microbiota to Different Fertilization Practices
Cited by: 12
Author(s): Iratxe Zarraonaindia, Xabier Simón Martínez‐Goñi, Olaia Liñero, Marta Muñoz-Colmenero, Mikel Aguirre, David Abad, Igor Baroja-Careaga, Alberto de Diego, Jack A. Gilbert, Andone Estonba
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2018.00062

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers
Cited by: 23
Author(s): H.M. Golder, Jennifer M. Thomson, Stuart E. Denman, Christopher S. McSweeney, I.J. Lean
Software Mentions: 2
Published: over 6 years ago

10.1098/rstb.2015.0328

Dissecting host-associated communities with DNA barcodes
Cited by: 23
Author(s): Christopher C. M. Baker, Leonora S. Bittleston, Jon G. Sanders, Naomi E. Pierce
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2015.01287

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA
Cited by: 36
Author(s): Matthew F. Kirk, Brien H. Wilson, Kyle A. Marquart, Lydia H. Zeglin, David S. Vinson, Theodore M. Flynn
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.340

The evolutionary history and diagnostic utility of the CRISPR-Cas system withinSalmonella entericassp.enterica
Cited by: 30
Author(s): James B. Pettengill, Ruth Timme, Rodolphe Barrangou, Mauricio Toro, Marc W. Allard, Errol Strain, Steven M. Musser, Eric W. Brown
Software Mentions: 2
Published: over 10 years ago

10.3390/insects11020134

First Insight into Microbiome Profiles of Myrmecophilous Beetles and Their Host, Red Wood Ant Formica polyctena (Hymenoptera: Formicidae)—A Case Study
Cited by: 9
Author(s): Agnieszka Kaczmarczyk‐Ziemba, Mirosław Zagaja, Grzegorz K. Wagner, Ewa Pietrykowska‐Tudruj, Bernard Staniec
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.7293

A highly diverse fungal community associated with leaves of the mangrove plant Acanthus ilicifolius var. xiamenensis revealed by isolation and metabarcoding analyses
Cited by: 27
Author(s): Wei-Chiung Chi, Weiling Chen, Chih-Chiao He, Sheng−Yu Guo, Hyojung Cha, Ling Ming Tsang, Tsz Wai Ho, Ka−Lai Pang
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2016.00875

DGV: Dengue Genographic Viewer
Cited by: 16
Author(s): Akifumi Yamashita, Tetsuya Sakamoto, Tsuyoshi Sekizuka, Kengo Kato, Tomohiko Takasaki, Makoto Kuroda
Software Mentions: 2
Published: over 8 years ago

10.3390/microorganisms8050665

Metagenomic- and Cultivation-Based Exploration of Anaerobic Chloroform Biotransformation in Hypersaline Sediments as Natural Source of Chloromethanes
Cited by: 6
Author(s): Peng Peng, Yue Lu, Tom N. P. Bosma, Ivonne Nijenhuis, Bart Nijsse, Sudarshan A. Shetty, Alexander Ruecker, Alexander Umanets, Javier Ramiro-García, Andreas Kappler, Detmer Sipkema, Hauke Smidt, Siavash Atashgahi
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2018.02430

Effects of a Commercial Microbial Agent on the Bacterial Communities in Shrimp Culture System
Cited by: 20
Author(s): Zidan Liu, Linglin Qiuqian, Zhiyuan Yao, Xin Wang, Lei Huang, Jialai Zheng, Kai Wang, Laiguo Li, Demin Zhang
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2015.00739

Microbial community changes along the active seepage site of one cold seep in the Red Sea
Cited by: 8
Author(s): Huiluo Cao, Weipeng Zhang, Yong Wang, Pei‐Yuan Qian
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2017.01929

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs
Cited by: 23
Author(s): Bo Zeng, Jiangchao Zhao, Wei Guo, Siyuan Zhang, Yutong Hua, Jingsi Tang, Fanli Kong, Xuewu Yang, Lizhi Fu, K. yen. Liao, Xianqiong Yu, Guohong Chen, Long Jin, Surong Shuai, Jiandong Yang, Xiaohui Si, Ruihong Ning, Saurabh Mishra, Ying Liu
Software Mentions: 2
Published: about 7 years ago

10.1186/s12866-020-01895-4

Characterization of the bacterial communities of psyllids associated with Rutaceae in Bhutan by high throughput sequencing
Cited by: 19
Author(s): Jennifer L. Morrow, Namgay Om, G. A. C. Beattie, Grant Chambers, N. J. Donovan, L. W. Liefting, Markus Riegler, Paul Holford
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2017.01749

How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers
Cited by: 70
Author(s): Chiara Ferrario, Rosario Statello, Luca Carnevali, Leonardo Mancabelli, Christian Milani, Marta Mangifesta, Sabrina Duranti, Gabriele Andrea Lugli, Beatriz Jiménez, Samantha Lodge, Alice Viappiani, Giulia Alessandri, Margerita Dall’Asta, Daniele Del Rio, Andrea Sgoifo, Douwe van Sinderen, Marco Ventura, Francesca Turroni
Software Mentions: 2
Published: about 7 years ago

10.1093/gbe/evv097

Evolution of the Translocation and Assembly Module (TAM)
Cited by: 58
Author(s): Eva Heinz, Joel Selkrig, Matthew J. Belousoff, Trevor Lithgow
Software Mentions: 2
Published: over 9 years ago

10.1186/s12866-018-1212-x

Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms
Cited by: 16
Author(s): Irina M. Velsko, Luciana M. Shaddox
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2015.00887

Microbiome interplay: plants alter microbial abundance and diversity within the built environment
Cited by: 53
Author(s): Alexander Mahnert, Christine Moissl-Eichinger, Gabriele Berg
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2019.01258

Presence, Diversity, and Enrichment of Respiratory Reductive Dehalogenase and Non-respiratory Hydrolytic and Oxidative Dehalogenase Genes in Terrestrial Environments
Cited by: 17
Author(s): Hanna R. Temme, Aaron Carlson, Paige J. Novak
Software Mentions: 2
Published: over 5 years ago

10.1093/molbev/msv261

No Accumulation of Transposable Elements in Asexual Arthropods
Cited by: 56
Author(s): Jens Bast, Ina Schaefer, Tanja Schwander, Mark Maraun, Stefan Scheu, Ken Kraaijeveld
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-019-1765-5

Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters
Cited by: 41
Author(s): Cristian Crisan, Aroon T. Chande, Kenneth C. Williams, Vishnu Raghuram, Lavanya Rishishwar, Gabi Steinbach, Samit S. Watve, Peter Yunker, I. King Jordan, Brian K. Hammer
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2016.01122

Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle
Cited by: 89
Author(s): Gonzalo Martínez Fernández, Stuart E. Denman, Chunlei Yang, Jane Cheung, Makoto Mitsumori, Christopher S. McSweeney
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2017.01200

Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils
Cited by: 1
Author(s): Fuyan Li, Fengfeng Zheng, Yongli Wang, Weiguo Liu, Chuanlun L. Zhang
Software Mentions: 2
Published: over 7 years ago

10.3390/biom11020303

A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats
Cited by: 3
Author(s): Julia Hernandez-Baixauli, Pere Puigbò, Helena Torrell, Hector H. Palacios, Vicent J. Ribas Ripoll, Antoni Caimari, Josep Maria del Bas, Laura Baselga-Escudero, Miquel Mulero
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-018-1450-0

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies
Cited by: 28
Author(s): Qi Zheng, Casey Bartow‐McKenney, Jacquelyn S. Meisel, Elizabeth A. Grice
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11103

The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis
Cited by: 10
Author(s): Qingmin Kong, Peijun Tian, Jianxin Zhao, Hao Zhang, Gang Wang
Software Mentions: 2
Published: over 3 years ago

10.1155/2016/5916067

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau
Cited by: 28
Author(s): Xiaowu Huang, Gonzalo Martínez Fernández, Jagadish Padmanabha, Ruijun Long, Stuart E. Denman, Christopher S. McSweeney
Software Mentions: 2
Published: almost 9 years ago

10.3390/genes9020102

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis
Cited by: 139
Author(s): Faraz Bishehsari, Phillip A. Engen, Nailliw Z. Preite, Yunus E. Tunçil, Ankur Naqib, Maliha Shaikh, Marco Rossi, Sherry Wilber, Stefan J. Green, Bruce R. Hamaker, Khashayarsha Khazaie, Robin M. Voigt, Christopher B. Forsyth, Ali Keshavarzian
Software Mentions: 2
Published: over 6 years ago

10.1186/s13068-016-0532-z

Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system
Cited by: 19
Author(s): Margreet J. Oosterkamp, Celia Méndez–García, Chang H. Kim, Štefan Bauer, Ana B. Ibáñez, Sabrina Zimmerman, Pei‐Ying Hong, Isaac Cann, Roderick I. Mackie
Software Mentions: 2
Published: over 8 years ago

10.1155/2018/4832912

16S rRNA Long-Read Sequencing of the Granulation Tissue from Nonsmokers and Smokers-Severe Chronic Periodontitis Patients
Cited by: 4
Author(s): Rebecca Chowdhry, Neetu Singh, Dinesh Kumar Sahu, Ratnesh Kumar Tripathi, Archana Mishra, Anjana Singh, Hari Shyam, Pratap Shankar, Nand Lal, Madan Lal Brahma Bhatt, Ravi Kant
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2016.02062

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection
Cited by: 40
Author(s): Caroline De Tender, Annelies Haegeman, Bart Vandecasteele, Lieven Clement, Pieter Cremelie, Peter Dawyndt, Martine Maes, Jane Debode
Software Mentions: 2
Published: almost 8 years ago

10.1155/2019/8163591

Dysbiosis and Variation in Predicted Functions of the Granulation Tissue Microbiome in HPV Positive and Negative Severe Chronic Periodontitis
Cited by: 10
Author(s): Rebecca Chowdhry, Neetu Singh, Dinesh Kumar Sahu, Ratnesh Kumar Tripathi, Archana Mishra, Anjana Singh, Indrashis Mukerjee, Nand Lal, Madan Lal Brahma Bhatt, Ravi Kant
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0168152

Response of Bacteria Community to Long-Term Inorganic Nitrogen Application in Mulberry Field Soil
Cited by: 11
Author(s): Chengqun Yu, Xingming Hu, Ding Wen, Yong Li, Guangming Han, Chao Xiong
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13068-019-1468-x

Continuous n-valerate formation from propionate and methanol in an anaerobic chain elongation open-culture bioreactor
Cited by: 37
Author(s): Sanne M. de Smit, Kasper D. de Leeuw, Cees J.N. Buisman, D.P.B.T.B. Strik
Software Mentions: 2
Published: over 5 years ago

10.5713/ajas.19.0221

Effects of the dietary digestible fiber-to-starch ratio on pellet quality, growth and cecal microbiota of Angora rabbits
Cited by: 3
Author(s): Yang Gao, Fei Zhao, Ting He, Jiantao Li, Dan Guo
Software Mentions: 2
Published: over 4 years ago

10.1007/s00335-014-9540-0

Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics
Cited by: 60
Author(s): Annalouise O’Connor, Pamela M. Quizon, Jody Albright, Fred T. Lin, Brian J. Bennett
Software Mentions: 2
Published: about 10 years ago

10.1111/1755-0998.12236

Next‐generation<scp>DNA</scp>barcoding: using next‐generation sequencing to enhance and accelerate<scp>DNA</scp>barcode capture from single specimens
Cited by: 178
Author(s): Shadi Shokralla, Joel F. Gibson, Hamid Nikbakht, Daniel H. Janzen, Winnie Hallwachs, Mehrdad Hajibabaei
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.08973

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Cited by: 74
Author(s): Xue Liang, Kyle Bittinger, Xuanwen Li, Darrell R. Abernethy, Frederic D. Bushman, Garret A. FitzGerald
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-020-76204-0

An unusual microbiome characterises a spatially-aggressive crustose alga rapidly overgrowing shallow Caribbean reefs
Cited by: 7
Author(s): Bryan Wilson, Chen‐Ming Fan, Peter J. Edmunds
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0107460

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells
Cited by: 16
Author(s): Husen Zhang, Xi Chen, Daniel T. Braithwaite, Zhen He
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2019.01520

Raw Material Regulates Flavor Formation via Driving Microbiota in Chinese Liquor Fermentation
Cited by: 34
Author(s): Chongchong Liu, Shengbao Feng, Qun Wu, Heqiang Huang, Zhanxiu Chen, Shanwen Li, Yan Xu
Software Mentions: 2
Published: over 5 years ago

10.1093/jn/nxz006

The Combination of 2′-Fucosyllactose with Short-Chain Galacto-Oligosaccharides and Long-Chain Fructo-Oligosaccharides that Enhance Influenza Vaccine Responses Is Associated with Mucosal Immune Regulation in Mice
Cited by: 19
Author(s): Xiao Ling, Phillip A. Engen, Thea Leusink-Muis, Ingrid van Ark, Bernd Stahl, Saskia A. Overbeek, Johan Garssen, Ankur Naqib, Stefan J. Green, Ali Keshavarzian, Gert Folkerts, Belinda van’t Land
Software Mentions: 2
Published: over 5 years ago

10.1080/20002297.2018.1487741

Defining the gut microbiota in individuals with periodontal diseases: an exploratory study
Cited by: 78
Author(s): Talita Gomes Baeta Lourenςo, Sarah J. Spencer, Eric J. Alm, Ana Paula Vieira Colombo
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.116.029207

Patching Holes in the Chlamydomonas Genome
Cited by: 7
Author(s): Frej Tulin, Frederick R. Cross
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0161211

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study
Cited by: 54
Author(s): Paula Smith‐Brown, Mark Morrison, Lutz Krause, Peter S. W. Davies
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0123216

Sinonasal Microbiome Sampling: A Comparison of Techniques
Cited by: 47
Author(s): Ahmed Bassiouni, Edward John Cleland, Alkis J. Psaltis, Sarah Vreugde, Peter‐John Wormald
Software Mentions: 2
Published: over 9 years ago

10.3390/nu11081853

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice
Cited by: 12
Author(s): Daniela Gräf, Jennifer M. Monk, Dion Lepp, Wenqing Wu, Laurel McGillis, Kyle Roberton, Yolanda Brummer, Susan M. Tosh, Krista A. Power
Software Mentions: 2
Published: about 5 years ago

10.1111/1751-7915.12164

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil
Cited by: 46
Author(s): Sharon Huws, Eun Joong Kim, Simon Cameron, Susan Elizabeth Girdwood, Lynfa Davies, John K. S. Tweed, Hannah Vallin, Nigel D. Scollan
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-019-42257-z

Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota
Cited by: 21
Author(s): Giulia Alessandri, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Thibaut Ranjanoro, Salvatore Modica, Luca Carnevali, Rosario Statello, Francesca Bottacini, Francesca Turroni, Maria Cristina Ossiprandi, Andrea Sgoifo, Douwe van Sinderen, Marco Ventura
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-32747-x

First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages: molecular evidence of Wolbachia endosymbiosis
Cited by: 18
Author(s): Agnieszka Kaczmarczyk, Halina Kucharczyk, Marek Kucharczyk, Przemysław Kapusta, Jerzy Sell, Sylwia Zielińska
Software Mentions: 2
Published: about 6 years ago

10.3390/nu11112596

Maternal Human Milk Oligosaccharide Profile Modulates the Impact of an Intervention with Iron and Galacto-Oligosaccharides in Kenyan Infants
Cited by: 32
Author(s): Daniela Paganini, Mary A Uyoga, Guus A. M. Kortman, Jos Boekhorst, Sacha Schneeberger, Simon Karanja, Thierry Hennet, Michael Zimmermann
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2018.00914

Variation in Bat Guano Bacterial Community Composition With Depth
Cited by: 17
Author(s): Molli M. Newman, Laura N. Kloepper, Makenzie B. Duncan, John A. McInroy, Joseph W. Kloepper
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0146566

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest
Cited by: 17
Author(s): Julia Elidia Lima-Perim, Emiliana Manesco Romagnoli, Francisco Dini‐Andreote, Ademir Durrer, Armando Cavalcante Franco Dias, Fernando Dini Andreote
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-016-1270-8

SAMSA: a comprehensive metatranscriptome analysis pipeline
Cited by: 51
Author(s): Samuel T. Westreich, Ian F Korf, David A. Mills, Danielle G. Lemay
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0080702

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease
Cited by: 142
Author(s): Man‐Li Tong, Xiaoxiao Li, Laura Wegener Parfrey, Bennett E. Roth, Andrew Ippoliti, Bo Wei, James Borneman, Dermot P. McGovern, Daniel N. Frank, Ellen Li, Steve Horvath, Rob Knight, Jonathan Braun
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-018-30901-z

Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype
Cited by: 16
Author(s): Dawn B. Goldsmith, Christina A. Kellogg, Cheryl L. Morrison, Michael A. Gray, Robert P. Stone, Rhian G. Waller, Sandra Brooke, Steve W. Ross
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0217609

Exploring the effects of COLOSTRONONI on the mammalian gut microbiota composition
Cited by: 6
Author(s): Sabrina Duranti, Leonardo Mancabelli, Walter Mancino, Rosaria Anzalone, Giulia Longhi, Rosario Statello, Luca Carnevali, Andrea Sgoifo, Sergio Bernasconi, Francesca Turroni, Marco Ventura
Software Mentions: 2
Published: over 5 years ago

10.1111/1751-7915.12733

Simultaneous fermentation of cellulose and current production with an enriched mixed culture of thermophilic bacteria in a microbial electrolysis cell
Cited by: 21
Author(s): Bradley G. Lusk, Alexandra Colin, Prathap Parameswaran, Bruce E. Rittmann, César I. Torres
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.02882

Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India
Cited by: 67
Author(s): Abhishek Gupta, Avishek Dutta, Jayeeta Sarkar, M. K. Panigrahi, Pinaki Sar
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00248-016-0846-1

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait
Cited by: 49
Author(s): Kevin Panke-Buisse, Stacey Lee, Jenny Kao‐Kniffin
Software Mentions: 2
Published: about 8 years ago

10.3390/nu10091154

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model
Cited by: 130
Author(s): Ariel Bier, Tzipi Braun, Rawan Khasbab, Ayelet Di Segni, Ehud Grossman, Yael Haberman, Avshalom Leibowitz
Software Mentions: 1
Published: about 6 years ago

Projects: cran: uclust

Papers Mentioning uclust 454